bluuebunny/crossref_metadata_2025 huggingface dataset:
Introducing Pep McConst—A user‐friendly peptide modeler for biophysical applications
Authors: Schuhmann Fabian , Korol Vasili , Solov'yov Ilia A.
Published: January 2021

We are introducing Pep McConst—a software that employs a Monte‐Carlo algorithm to construct 3D structures of polypeptide chains which could subsequently be studied as stand‐alone macromolecules or complement the structure of known proteins. Using an approach to avoid steric clashes, Pep McConst allows to create multiple structures for a predefined primary sequence of amino acids. These structures could then effectively be used for further structural analysis and investigations. The article introduces the algorithm and describes its user‐friendly approach that was made possible through the VIKING online platform. Finally, the manuscript provides several highlight examples where Pep McConst was used to predict the structure of the C‐terminal of a known protein, generate a missing bit of already crystallized protein structures and simply generate short polypeptide chains.
Two‐step solvothermal synthesis of high capacity LiNi0.8Co0.15Al0.05O2 cathode for Li‐ion batteries
Authors: Cheng Xiang , Wang Yingying , Wang Xinlu , Yu Wensheng , Liu Guixia , Dong Xiangting , Wang Jinxian
Published: January 2021

Lithium‐ion batteries are attracting increasing interest for a new type of green energy battery. Among many electrode materials, layered ternary LiNi1‐x‐yCoxMyO2 (M = Mn or Al) is considered a promising commercial prospect because of its low cost, excellent electrical conductivity, high discharge specific capacity, and environmentally friendly. In this paper, a ternary cathode material LiNi0.8Co0.15Al0.05O2 with high specific capacity was prepared by a two‐step solvothermal method. The effects of solvothermal time and temperature on the morphology and electrochemical properties for the electrode materials were studied. It was found that the electrochemical performance of the LiNi0.8Co0.15Al0.05O2 cathode material synthesized at 180°C for 12 hr was better.
Evaluation of the detection ability of uropathogen morphology and vaginal contamination by the Atellica UAS800 automated urine microscopy analyzer and its effectiveness
Authors: Nakamura Akihiro , Shinke Tetsuya , Noguchi Nobuyoshi , Komatsu Masaru , Yamanishi Hachiro
Published: January 2021

Background

To help combat the worldwide spread of multidrug‐resistant Enterobacterales, which are responsible for many causes of urinary tract infection (UTI), we evaluated the ability of the Atellica UAS800 automated microscopy system, the only one offering the capability of bacterial morphological differentiation, to determine its effectiveness.

Methods

We examined 118 outpatient spot urine samples in which pyuria and bacteriuria were observed using flow cytometry (training set: 81; cross‐validation set: 37). The ability of the Atellica UAS800 to differentiate between bacilli and cocci was verified. To improve its ability, multiple logistic regression analysis was used to construct a prediction formula.

Results

This instrument's detection sensitivity was 106 CFU/ml, and reproducibility in that range was good, but data reliability for the number of cocci was low. Multiple logistic regression analysis with each explanatory variable (14 items from the Atellica UAS800, age and sex) showed the best prediction formula for discrimination of uropathogen morphology was a model with 5 explanatory variables: number of bacilli (p < 0.001), squamous epithelial cells (p = 0.004), age (p = 0.039), number of cocci (p = 0.107), and erythrocytes (p = 0.111). For a predicted cutoff value of 0.449, sensitivity was 0.879 and specificity was 0.854. In the cross‐validation set, sensitivity was 0.813 and specificity was 0.857.

Conclusions

The Atellica UAS800 could detect squamous epithelial cells, an indicator of vaginal contamination, with high sensitivity, which further improved performance. Simultaneous use of this probability prediction formula with urinalysis results may facilitate real‐time prediction of uropathogens and vaginal contamination, thus providing helpful information for empiric therapy.
Endocrine Adverse Events Caused by Different Types and Different Doses of Immune Checkpoint Inhibitors in the Treatment of Solid Tumors: A Meta‐Analysis and Systematic Review
Authors: Yang Yaxian , Liu Jingfang , Yang Kaili , Ma Yanqi , Fu Songbo , Tang Xulei , Wang Yan , Zhou Liyuan
Published: January 2021

The aim of this meta‐analysis was to assess the risks of endocrine adverse events in patients with malignancies treated with different types and different doses of immune checkpoint inhibitors (ICIs). PubMed and Embase were searched for randomized controlled trials on ICIs and endocrine adverse events since 2000, and meta‐analysis was carried out. Twenty‐six randomized controlled trials comprising 13 824 patients with malignancies were included. Compared with the other tumor therapies (used as a control group), patients treated with programmed death‐1 inhibitors appeared to be at higher risks of hypothyroidism, hyperthyroidism, thyroiditis, hypophysitis or hypopituitarism, and type 1 diabetes mellitus, while there was no difference in the risk of primary adrenal insufficiency. It was also found that patients treated with cytotoxic T‐lymphocyte–associated protein‐4 inhibitors were at higher risk of hypophysitis or hypopituitarism, primary adrenal insufficiency, and hypothyroidism. In comparison, patients treated with programmed death‐ligand 1 inhibitors were at higher risk of hyperthyroidism and hypothyroidism. Compared with the control group, both low‐dose and high‐dose ICI groups were at higher risk of hypothyroidism and hyperthyroidism, and the low‐dose group had increased risk of thyroiditis and primary adrenal insufficiency. There was no significant difference in the risk of type 1 diabetes between the low‐dose group and the high‐dose group. The risk of hypophysitis or hypopituitarism in the high‐dose group (relative risk, 20.12; 95% confidence interval, 8.02‐50.46) was significantly higher than that in the low‐dose group (relative risk, 4.92; 95% confidence interval, 2.11‐11.47). The risk of endocrine adverse events was increased in patients treated with ICIs. Different types and doses of ICIs have varying characteristics of endocrine adverse events.
Brain MR patterns in inherited disorders of monoamine neurotransmitters: An analysis of 70 patients
Authors: Kuseyri Hübschmann Oya , Mohr Alexander , Friedman Jennifer , Manti Filippo , Horvath Gabriella , Cortès‐Saladelafont Elisenda , Mercimek‐Andrews Saadet , Yildiz Yilmaz , Pons Roser , Kulhánek Jan , Oppebøen Mari , Koht Jeanette Aimee , Podzamczer‐Valls Inés , Domingo‐Jimenez Rosario , Ibáñez Salvador , Alcoverro‐Fortuny Oscar , Gómez‐Alemany Teresa , de Castro Pedro , Alfonsi Chiara , Zafeiriou Dimitrios I. , López‐Laso Eduardo , Guder Philipp , Santer René , Honzík Tomáš , Hoffmann Georg F. , Garbade Sven F. , Sivri H. Serap , Leuzzi Vincenzo , Jeltsch Kathrin , García‐Cazorla Angeles , Opladen Thomas ,   International Working Group on Neurotransmitter Related Disorders (iNTD), Harting Inga
Published: January 2021

Inherited monoamine neurotransmitter disorders (iMNDs) are rare disorders with clinical manifestations ranging from mild infantile hypotonia, movement disorders to early infantile severe encephalopathy. Neuroimaging has been reported as non‐specific. We systematically analyzed brain MRIs in order to characterize and better understand neuroimaging changes and to re‐evaluate the diagnostic role of brain MRI in iMNDs. 81 MRIs of 70 patients (0.1‐52.9 years, 39 patients with tetrahydrobiopterin deficiencies, 31 with primary disorders of monoamine metabolism) were retrospectively analyzed and clinical records reviewed. 33/70 patients had MRI changes, most commonly atrophy (n = 24). Eight patients, six with dihydropteridine reductase deficiency (DHPR), had a common pattern of bilateral parieto‐occipital and to a lesser extent frontal and/or cerebellar changes in arterial watershed zones. Two patients imaged after acute severe encephalopathy had signs of profound hypoxic‐ischemic injury and a combination of deep gray matter and watershed injury (aromatic l‐amino acid decarboxylase (AADCD), tyrosine hydroxylase deficiency (THD)). Four patients had myelination delay (AADCD; THD); two had changes characteristic of post‐infantile onset neuronal disease (AADCD, monoamine oxidase A deficiency), and nine T2‐hyperintensity of central tegmental tracts. iMNDs are associated with MRI patterns consistent with chronic effects of a neuronal disorder and signs of repetitive injury to cerebral and cerebellar watershed areas, in particular in DHPRD. These will be helpful in the (neuroradiological) differential diagnosis of children with unknown disorders and monitoring of iMNDs. We hypothesize that deficiency of catecholamines and/or tetrahydrobiopterin increase the incidence of and the CNS susceptibility to vascular dysfunction.
SNB‐PSSM: A spatial neighbor‐based PSSM used for protein–RNA binding site prediction
Authors: Liu Yang , Gong Weikang , Yang Zhen , Li Chunhua
Published: January 2021

Protein–RNA interactions play essential roles in a wide variety of biological processes. Recognition of RNA‐binding residues on proteins has been a challenging problem. Most of methods utilize the position‐specific scoring matrix (PSSM). It has been found that considering the evolutionary information of sequence neighboring residues can improve the prediction. In this work, we introduce a novel method SNB‐PSSM (spatial neighbor–based PSSM) combined with the structure window scheme where the evolutionary information of spatially neighboring residues is considered. The results show our method consistently outperforms the standard and smoothed PSSM methods. Tested on multiple datasets, this approach shows an encouraging performance compared with RNABindRPlus, BindN+, PPRInt, xypan, Predict_RBP, SpaPF, PRNA, and KYG, although is inferior to RNAProSite, RBscore, and aaRNA. In addition, since our method is not sensitive to protein structure changes, it can be applied well on binding site predictions of modeled structures. Thus, the result also suggests the evolution of binding sites is spatially cooperative. The proposed method as an effective tool of considering evolutionary information can be widely used for the nucleic acid–/protein‐binding site prediction and functional motif finding.
Rapid screening and quantitation of PAHs in water and complex sample matrices by solid‐phase microextraction coupled to capillary atmospheric pressure photoionization‐mass spectrometry
Authors: Mirabelli Mario F. , Zenobi Renato
Published: January 2021

A capillary atmospheric pressure photoionization (cAPPI) source was used to analyze polycyclic aromatic hydrocarbons (PAHs) in complex matrices like grilled meat extract and urban dust reference material, as well as screening for PAHs in aqueous samples such as tap and lake water. A high‐throughput workflow was developed that allowed rapid screening of unknown samples by direct solid‐phase microextraction (SPME) coupled with cAPPI‐MS, with confirmatory gas chromatography performed only for samples containing trace amounts of PAHs. Extraction times were as low as 15 s, with a total analysis time of 2 min per sample for screening. Limits of detections were in the low pg/ml range and in the subpg/ml range for the direct and chromatographic approach, respectively, with a linear dynamic range between two and three orders of magnitude, as determined for 15 model PAHs. This rapid approach represents an attractive way to screen samples containing nonpolar compounds using an ambient ionization source.
Multiple reaction monitoring profiling as an analytical strategy to investigate lipids in extracellular vesicles
Authors: Edwards Madison E. , De Luca Thomas , Ferreira Christina R. , Collins Kimberly S. , Eadon Michael T. , Benson Eric A. , Sobreira Tiago J.P. , Cooks Robert Graham
Published: January 2021

Extracellular vesicles (EVs) convey information used in cell‐to‐cell interactions. Lipid analysis of EVs remains challenging because of small sample amounts available. Lipid discovery using traditional mass spectrometry platforms based on liquid chromatography and high mass resolution typically employs milligram sample amounts. We report a simple workflow for lipid profiling of EVs based on multiple reaction monitoring (MRM) profiling that uses microgram amounts of sample. After liquid–liquid extraction, individual EV samples were injected directly into the electrospray ionization (ESI) ion source at low flow rates (10 μl/min) and screened for 197 MRM transitions chosen to be a characteristic of several classes of lipids. This choice was based on a discovery experiment, which applied 1,419 MRMs associated with multiple lipid classes to a representative pooled sample. EVs isolated from 12 samples of human lymphocytes and 16 replicates from six different rat cells lines contained an estimated amount of total lipids of 326 to 805 μg. Samples showed profiles that included phosphatidylcholine (PC), sphingomyelin (SM), cholesteryl ester (CE), and ceramide (Cer) lipids, as well as acylcarnitines. The lipid profiles of human lymphocyte EVs were distinguishable using principal component and cluster analysis in terms of prior antibody and drug exposure. Lipid profiles of rat cell lines EV's were distinguishable by their tissue of origin.
Long‐term changes in layered soil temperature based on ground measurements in Jiangsu Province, China
Authors: Shi Xiao , Wang Guojie , Chen Tiexi , Li Shijie , Lu Jiao , Hagan Daniel Fiifi T.
Published: January 2021

While air temperature has been widely investigated to better understand the recent climate changes, the importance of soil temperature has been underestimated and rarely studied. Here, the long‐term soil temperature changes and the occurrence of extreme heats have been studied based on daily measurements in Jiangsu Province for 1970–2017. A general warming trend in soil temperature is observed at most stations, and these trends are more pronounced in the cold seasons than the warm seasons. Due to the asymmetric warming of maximum and minimum soil temperatures over the past 48 years, the diurnal range shows a long‐term decreasing trend with a rate of −0.34°C/10a. The occurrences of extreme soil temperatures have been analysed based on the probability density functions. It is found that the hot soil days have increased and cold soil days have decreased significantly, and these changes are particularly significant in the most recent decades.
Simulation of management strategies to mitigate nitrogen losses from crop rotations in Southland, New Zealand
Authors: Khaembah Edith N , Cichota Rogerio , Vogeler Iris
Published: January 2021

BACKGROUND

Nitrogen (N) fertiliser used on crops is among the main sources of water pollution. Reliable measurement of N losses from land uses in catchments is key to designing effective management strategies that minimise those losses at the same time as keeping farms profitable. In the present study, we used a management simulation tool within the Agricultural Production Systems sIMulator (APSIM) to assess the effect of fertiliser management on N leaching from croplands in the Aparima catchment in Southland, New Zealand. The assessment was based on two N‐fertiliser regimes: (i) Scheduled (conventional) where, N‐fertiliser rates and timing of application followed a prescribed programme, and (ii) Soil‐test where, N‐fertiliser rates and timing depended on daily analysis of simulated soil N levels. Four rotations (continuous wheat, pasture‐wheat‐grain oats, wheat‐fodder beet‐peas and wheat‐green oats‐fodder beet‐peas) were used in the evaluation.

RESULTS

APSIM simulated crop productivity with reasonable accuracy. Yields were 2% greater, fertiliser N input was 11% lower and leaching was 20% lower under the Soil‐test compared to the Scheduled fertiliser management. These results show the potential of a Soil‐test based fertiliser application to increase fertiliser‐N use efficiency and reduce the risk of N loss to the Southland catchment water systems.

CONCLUSION

The present study demonstrates a dynamic farm systems model can be a viable tool to generate valuable data for assessing the productivity and environmental effects of cropping systems at a catchment scale. © 2021 Society of Chemical Industry
Ultrasensitive monitoring strategy of PCR‐like levels for zearalenone contamination based DNA barcode
Authors: Li Ming , Hong Xia , Qiu Xuchun , Yang Chuqin , Mao Yuhao , Li Yan , Liu Zhenjiang , Du Daolin
Published: January 2021

BACKGROUND

The ultrasensitive monitoring strategy of zearalenone (ZEN) is essential and desirable for food safety and human health. In the present study, a coupling of gold nanoparticles‐DNA barcode and direct competitive immunoassay‐based real‐time polymerase chain reaction signal amplification (RT‐IPCR) for ZEN close to the sensitivity of PCR‐like levels is described and evaluated.

RESULTS

The RT‐IPCR benefited from the use of a DNA barcode and RT‐PCR detection strategy, thus resulting in ultrasensitive and simple detection for ZEN. Under the optimal RT‐IPCR, the linear range of detection was from 0.5 to 1000 pg mL−1 and the limit of detection was 0.5 pg mL−1, which was 400‐fold lower than the enzyme‐linked immunosorbent assay. The detection procedure was simplified and the detection time was shortened. The specificity, accuracy and precision of the RT‐IPCR confirmed a high performance. ZEN‐positive contamination levels were from 0.056 to 152.12 ng g−1 by the RT‐IPCR, which was demonstrated to be highly reliable by liquid chromatography‐tandem mass spectrometry.

CONCLUSION

The proposed RT‐IPCR could be used as an alternative for detecting ZEN with satisfactory ultrasensitivity, simplicity, low cost and high‐throughput. The present study could provide a strategy for the ultrasensitive detection of the small molecule with a simple and practical approach, which has significant appeal and application prospects.
Tumor characteristics and clinical outcome of peritoneal metastasis of gastric origin treated with a hyperthermic intraperitoneal chemotherapy procedure in the PERISCOPE I trial
Authors: Koemans Willem J. , van der Kaaij Rosa T. , Wassenaar Emma C. E. , Boerma Djamila , Boot Henk , Sikorska Karolina , Los Maartje , Grootscholten Cecile , Hartemink Koen J. , Veenhof Alexander A. F. A. , Kodach Liudmila , Snaebjornsson Petur , van Sandick Johanna W.
Published: January 2021

Introduction

The PERISCOPE I (Treatment of PERItoneal dissemination in Stomach Cancer patients with cytOreductive surgery and hyPErthermic intraperitoneal chemotherapy) study was conducted to investigate the safety and feasibility of hyperthermic intraperitoneal chemotherapy (HIPEC) in gastric cancer patients with limited peritoneal dissemination. In this study, tumor characteristics and clinical outcome of the patients treated in the PERISCOPE I trial were investigated.

Methods

Patients who had undergone the full study protocol were selected; that is, preoperative systemic chemotherapy, followed by a surgical procedure consisting of a (sub)total gastrectomy, cytoreductive surgery, and HIPEC with oxaliplatin (460 mg/m2) and docetaxel (in escalating doses).

Results

Twenty‐five PERISCOPE I patients underwent the full study protocol. Most patients had an ypT3‐4 tumor (96%) and the diffuse‐type histology was predominant (64%). Seven patients (28%) had a microscopically irradical (R1) resection. In all patients, a complete cytoreduction was achieved. Median follow‐up was 37 (95% confidence interval [CI]: 34–39) months. Disease recurrence was detected in 17 patients (68%). Median disease‐free and overall survival were 12 and 15 months, respectively.

Conclusion

In this series of gastric cancer patients with limited peritoneal dissemination who underwent HIPEC surgery, unfavorable tumor characteristics were common. Survival might be encouraging but disease recurrence was frequent. The efficacy of an HIPEC procedure in improving prognosis is currently being investigated in the PERISCOPE II trial.
Neuroprotectin D1 Attenuates Blast Overpressure Induced Reactive Microglial Cells in the Cochlea
Authors: Ríos José David , Hughes Charlotte K. , Lally John , Wienandt Nathan , Esquivel Carlos , Serhan Charles N. , Weitzel Erik K.
Published: January 2021

Objective/Hypothesis

We examined a neuroinflammatory response associated with glial activation in the cochlea exposed to blast overpressure and evaluated the potential therapeutic efficacy of specialized pro‐resolving mediators such as neuroprotectin D1, NPD1; (10R, 17S‐dihydroxy‐4Z, 7Z, 11E, 13E, 15Z, 19Z‐docosahexaenoic acid) in a rodent blast‐induced auditory injury model.

Study Design

Animal Research.

Methods

A compressed‐air driven shock tube was used to expose anesthetized adult male Long‐Evan rats to shock waves simulating an open‐field blast exposure. Approximately 30 minutes after blast exposure, rats were treated with NPD1 (100 ng/kg body wt.) or vehicle delivered intravenously via tail vein injection. Rats were then euthanized 48 hours after blast exposure. Unexposed rats were included as controls. Tissue sections containing both middle and inner ear were prepared with hematoxylin–eosin staining to elucidate histopathological changes associated with blast exposure. Cochlear tissues were evaluated for relative expression of ionized calcium‐binding adaptor 1 (Iba1), as an indicator of microglial activation by immunohistochemistry and western blot analyses.

Results

Our animal model resulted in an acute injury mechanism manifested by damage to the tympanic membrane, hemorrhage, infiltration of inflammatory cells, and increased expression of Iba1 protein. Moreover, therapeutic intervention with NPD1 significantly reduced Iba1 expression in the cochlea, suggesting a reduction of a neuroinflammatory response caused by blast overpressure.

Conclusions

Blast overpressure resulted in an increased expression of proteins involved in gliosis within the auditory system, which were reduced by NPD1. Treatment of NPD1 suggests an effective strategy to reduce or halt auditory microglial cell activation due to primary blast exposure.

Level of Evidence

NA Laryngoscope, 131:E2018–E2025, 2021
Predominant Vertical Location of Benign Vocal Fold Lesions by Sex and Music Genre: Implication for Pathogenesis
Authors: Hirosaki Mayu , Kanazawa Takeharu , Komazawa Daigo , Konomi Ujimoto , Sakaguchi Yu , Katori Yukio , Watanabe Yusuke
Published: January 2021

Objectives/Hypothesis

Vertical locations of vocal fold mucosal lesions (VFMLs) vary along the free edge. As the vertical contact area of vocal folds (VFs) depends on the vocal register, lesions may occur in the contact area of more frequently used vocal registers. This study investigated the cause of location variations by comparing the vertical sites of VFMLs in singers of both sexes with different music genres.

Study Design

Retrospective review.

Methods

Sixty professional classical and rock singers (11 male classical [M‐classical], 22 male rock [M‐rock], 13 female classical [F‐classical], and 14 female rock [F‐rock] singers) who underwent microlaryngeal surgery for VF polyps and nodules and their 108 lesions were enrolled. The VF free edge was vertically divided into three equal parts and classified into the following four lesion sites: upper, middle, lower, and multiple sites.

Results

Upper lesions were most common among F‐classical singers (73.9%), whereas lower lesions were most common among M‐classical (90.0%) and M‐rock (60.6%) singers. Among lesions localized to a single site, lower lesions were most common among F‐rock singers (37.0%). F‐classical singers had significantly more upper lesions than the other groups (P < .001). M‐classical singers had significantly more lower lesions than female singers of any genre (P < .001).

Conclusion

Upper lesions were most common among F‐classical singers who mostly used the head voice. Lower lesions were most common among singers who mainly used the modal voice. This study suggests that sex, the dominant vocal register used for singing, and mechanical stress on VFs influence the vertical site of VFMLs.

Level of Evidence

4 Laryngoscope, 131:E2284–E2291, 2021
Glutamine Inhibition Reduces Iatrogenic Laryngotracheal Stenosis
Authors: Tsai Hsiu‐Wen , Lina Ioan , Motz Kevin M , Chung Liam , Ding Dacheng , Murphy Michael K. , Feeley Michael , Elisseeff Jennifer H. , Hillel Alexander T.
Published: January 2021

Objective/Hypothesis

Glutamine inhibition has been demonstrated an antifibrotic effect in iatrogenic laryngotracheal stenosis (iLTS) scar fibroblasts in vitro. We hypothesize that broadly active glutamine antagonist, DON will reduce collagen formation and fibrosis‐associated gene expression in iLTS mice.

Study Design

Prospective controlled animal study.

Methods

iLTS in mice were induced by chemomechanical injury of the trachea using a bleomycin‐coated wire brush. PBS or DON (1.3 mg/kg) were administered by intraperitoneal injection (i.p.) every other day. Laryngotracheal complexes were harvested at days 7 and 14 after the initiation of DON treatment for the measurement of lamina propria thickness, trichrome stain, immunofluorescence staining of collagen 1, and fibrosis‐associated gene expression.

Results

The study demonstrated that DON treatment reduced lamina propria thickness (P = .025) and collagen formation in trichrome stain and immunofluorescence staining of collagen 1. In addition, DON decreased fibrosis‐associated gene expression in iLTS mice. At day 7, DON inhibited Col1a1 (P < .0001), Col3a1 (P = .0046), Col5a1 (P < .0001), and Tgfβ (P = .023) expression. At day 14, DON reduced Co1a1 (P = .0076) and Tgfβ (P = .023) expression.

Conclusions

Broadly active glutamine antagonist, DON, significantly reduces fibrosis in iLTS mice. These results suggest that the concept of glutamine inhibition may be a therapeutic option to reduce fibrosis in the laryngotracheal stenosis.

Level of Evidence

N/A Laryngoscope, 131:E2125–E2130, 2021
Quantifying seasonal succession of phytoplankton trait‐environment associations in human‐altered landscapes
Authors: Loewen Charlie J. G. , Vinebrooke Rolf D. , Zurawell Ron W.
Published: January 2021

Integration of species traits in direct gradient analysis generates insights into how communities are assembled and may respond to environmental changes. We investigated phytoplankton trait‐environment relationships for over 300 taxa during the open‐water season across 75 north‐temperate lakes and reservoirs in Alberta, Canada. An innovative, data‐driven approach was applied using iterative model selection for RLQ optimization to reveal key monthly associations. Fourth‐corner analysis then tested the significance of relationships using spatially and phylogenetically constrained null models derived by Moran spectral randomization. Both local‐ and regional‐scale drivers of succession were found with evidence of deterministic filtering by traits increasing in mid‐summer. Trait associations to land‐use and water quality highlighted potential anthropogenic cross‐scale interactions, such as logging and pasture development affecting phytoplankton via allochthonous nutrient inputs. Biogeographic factors (e.g., elevation and habitat size) and associated temperature and chemical gradients (e.g., pH and bicarbonate) were also linked to multiple morphological, physiological, and behavioral traits, including potential toxin production. Several correlated traits emphasized importance of trait syndromes corresponding to distinct taxonomic groups (e.g., cyanobacteria and green algae). However, rather than clustering species with shared ecological preferences or roles, our study builds on past trait‐based approaches to phytoplankton by testing for explicit trait associations with a range of environmental factors. Thus, we provide a novel, quantitative means of revealing environmental constraints on communities and translating their compositional changes under climate and other human influences into functional impacts on freshwater ecosystems.
Nonionic UCST–LCST Diblock Copolymers with Tunable Thermoresponsiveness Synthesized via PhotoRAFT Polymerization
Authors: Xu Jingcong , Abetz Volker
Published: January 2021

Nonionic double thermoresponsive diblock copolymers with both upper critical solution temperature (UCST) and lower critical solution temperature (LCST) phase transitions are synthesized via eco‐friendly photoiniferter reversible addition–fragmentation chain transfer polymerization. While the biocompatible random copolymer of di(ethylene glycol) methyl ether methacrylate and oligo(ethylene glycol) methacrylate accounts for the LCST transition, the block of polymethacrylamide from an easily accessible monomer with low health hazard is responsible for the UCST transition. Temperature‐dependent dynamic light scattering measurements confirm the formation of micellar aggregates in water at the temperatures below UCST‐ and above LCST‐type cloud points. Additionally, the temperature interval between UCST and LCST, where both blocks are dissolved, can be tailored by varying the comonomer ratio in the random copolymer block. With these unique advantages, the presented work introduces a new polymer system for the design of schizophrenic polymers.
Identification of a conserved N‐terminal domain in the first module of ACV synthetases
Authors: Iacovelli Riccardo , Mózsik László , Bovenberg Roel A.L. , Driessen Arnold J.M.
Published: January 2021

The l‐δ‐(α‐aminoadipoyl)‐l‐cysteinyl‐d‐valine synthetase (ACVS) is a trimodular nonribosomal peptide synthetase (NRPS) that provides the peptide precursor for the synthesis of β‐lactams. The enzyme has been extensively characterized in terms of tripeptide formation and substrate specificity. The first module is highly specific and is the only NRPS unit known to recruit and activate the substrate l‐α‐aminoadipic acid, which is coupled to the α‐amino group of l‐cysteine through an unusual peptide bond, involving its δ‐carboxyl group. Here we carried out an in‐depth investigation on the architecture of the first module of the ACVS enzymes from the fungus Penicillium rubens and the bacterium Nocardia lactamdurans. Bioinformatic analyses revealed the presence of a previously unidentified domain at the N‐terminus which is structurally related to condensation domains, but smaller in size. Deletion variants of both enzymes were generated to investigate the potential impact on penicillin biosynthesis in vivo and in vitro. The data indicate that the N‐terminal domain is important for catalysis.
Identification of a novel TNRC18‐RARA fusion in acute promyelocytic leukemia lacking t(15;17)(q24;q12)/PML‐RARA
Authors: Wang Zheng , Wen Lijun , Zhang Ling , Xu Xiaoyu , Chen Xiaoqian , Yao Li , Wang Man , Shen Zhen , Mo Guangquan , Wang Yao , Zhao Dewan , Cai Wei , Shen Jingzhi , Chi Xiaomeng , Xu Yi , Zeng Zhao , Pan Jinlan , Ruan Changgeng , Wu Depei , Jia Zhilin , Chen Suning
Published: January 2021

Acute promyelocytic leukemia (APL) is a unique disease entity in acute myeloid leukemia, characterized by PML‐RARA fusion gene, which is generated by chromosomal translocation t(15;17)(q24;q21). We identified TNRC18‐RARA as novel RARA fusion in resembling APL. Our study highlights the importance of combining multiple molecular techniques to characterize and optimally manage APL lacking classic t(15;17)(q24;q12)/PML‐RARA fusion.
Exact analytical solution of a mechanical oscillator for phase transition involving spatially inhomogeneous distribution of the order parameter
Authors: Big‐Alabo Akuro , Ossia Chinwuba Victor , Ekpruke Emmanuel Ogheneochuko
Published: January 2021

In this paper, we derive the exact analytical solution for the periodic oscillations of a nonlinear mechanical oscillator that is capable of describing phase transition phenomenon with spatially inhomogeneous distribution of the order parameter. The exact analytical solution was derived in terms of the elliptic integral of the third kind and covers the cases where the physical variable influencing the order parameter is negative or positive. The conditions for obtaining periodic oscillations for the two cases were discussed, and results were simulated for small‐ and large‐amplitude nonlinear oscillations. The results also cover periodic responses with bistable oscillations, which indicate the existence of bifurcation in phase transition. Furthermore, the error of the numerical solution and other published approximate analytical solutions were analyzed and discussed. The present study can be viewed as a benchmark solution for the mechanical oscillator for phase transition and can be used to verify the accuracy of existing and future approximate solutions.
New regularity criteria for the 3D magneto‐micropolar fluid equations in Lorentz spaces
Authors: Li Zhouyu , Niu Pengcheng
Published: January 2021

In this paper, we consider the regularity of weak solutions to the 3D magneto‐micropolar fluid equations. It is shown that if the velocity field or pressure belongs to some Lorentz spaces in both time and spatial directions, then the weak solutions are regular on[0, T]. In particular, we also obtain regularity criteria for the micropolar fluid equations and the MHD equations, respectively. Our results extend and generalize previous results.
Stability of stationary solutions for the glioma growth equations with radial or axial symmetries
Authors: Polovinkina Marina V. , Debbouche Amar , Polovinkin Igor P. , David Sergio A.
Published: January 2021

We investigate a class of nonlinear time‐partial differential equations describing the growth of glioma cells. The main results show sufficient conditions for the stability of stationary solutions for these kind of equations. More precisely, we study different spatial variables involving radial or axial symmetries. In addition, we also numerically simulate the system based on three distinct scenarios by considering symmetry across all spatial variables. The numerical results confirm the presence of possible stable states.
Diet and Inflammatory Bowel Disease: What Quality Standards Should Be Applied in Clinical and Laboratory Studies?
Authors: Rogler Gerhard , Scharl Michael , Spalinger Marianne , Yilmaz Bahtiyar , Zaugg Michael , Hersberger Martin , Schreiner Philipp , Biedermann Luc , Herfarth Hans
Published: January 2021

Many patients suffering from inflammatory bowel disease (IBD) follow restrictive diets, as many respective recommendations circulate. Efforts are made to evaluate and summarize the published information, for example, in a recent consensus manuscript by the International Organization for the Study of IBD (IOIBD). However, the standards that should be applied to make claims about dietary effects are poorly defined. In this manuscript, the scientific basis of recommendations for nutritional interventions in IBD is analyzed. Epidemiological evidence on diet in IBD is always biased by numerous factors, and the number of robust dietary intervention studies is limited due to methodological difficulties. Therefore, animal models are used to test hypotheses with respect to dietary factors and intestinal inflammation. Naturally, animal models have limitations, and knowledge of key characteristics of colitis animal models is crucial to understand their advantages and disadvantages. In recent years the important role of the microbiota for IBD and dietary factors has been discovered. Microbiota data are added to many publications on IBD and nutrition. The quality of those data varies largely. Subsequently, quality standards for microbiota analyses also are discussed. Finally, quality requirements to be applied on recommendations for dietary changes in patients with IBD are suggested.
Technical Note: First report on an in vivo range probing quality control procedure for scanned proton beam therapy in head and neck cancer patients
Authors: Meijers Arturs , Seller Oria Carmen , Free Jeffrey , Langendijk Johannes A , Knopf Antje C , Both Stefan
Published: January 2021

Purpose

The capability of proton therapy to provide highly conformal dose distributions is impaired by range uncertainties. The aim of this work is to apply range probing (RP), a form of a proton radiography‐based quality control (QC) procedure for range accuracy assessment in head and neck cancer (HNC) patients in a clinical setting.

Methods and Materials

This study included seven HNC patients. RP acquisition was performed using a multi‐layer ionization chamber (MLIC). Per patient, two RP frames were acquired within the first two weeks of treatment, on days when a repeated CT scan was obtained. Per RP frame, integral depth dose (IDD) curves of 81 spots around the treatment isocenter were acquired. Range errors are determined as a discrepancy between calculated IDDs in the treatment planning system and measured residual ranges by the MLIC. Range errors are presented relative to the water equivalent path length of individual proton spots. In addition to reporting results for complete measurement frames, an analysis, excluding range error contributions due to anatomical changes, is presented.

Results

Discrepancies between measured and calculated ranges are smaller when performing RP calculations on the day‐specific patient anatomy rather than the planning CT. The patient‐specific range evaluation shows an agreement between calculated and measured ranges for spots in anatomically consistent areas within 3% (1.5 standard deviation).

Conclusions

The results of an RP‐based QC procedure implemented in the clinical practice for HNC patients have been demonstrated. The agreement of measured and simulated proton ranges confirms the 3% uncertainty margin for robust optimization. Anatomical variations show a predominant effect on range accuracy, motivating efforts towards the implementation of adaptive radiotherapy.
Free‐breathing mapping of hepatic iron overload in children using 3D multi‐echo UTE cones MRI
Authors: Kee Youngwook , Sandino Christopher M. , Syed Ali B. , Cheng Joseph Y. , Shimakawa Ann , Colgan Timothy J. , Hernando Diego , Vasanawala Shreyas S.
Published: January 2021

Purpose

To enable motion‐robust, ungated, free‐breathing mapping of hepatic iron overload in children with 3D multi‐echo UTE cones MRI.

Methods

A golden‐ratio re‐ordered 3D multi‐echo UTE cones acquisition was developed with chemical‐shift encoding (CSE). Multi‐echo complex‐valued source images were reconstructed via gridding and coil combination, followed by confounder‐corrected (=1/) mapping. A phantom containing 15 different concentrations of gadolinium solution (0–300 mM) was imaged at 3T. 3D multi‐echo UTE cones with an initial TE of 0.036 ms and Cartesian CSE‐MRI (IDEAL‐IQ) sequences were performed. With institutional review board approval, 85 subjects (81 pediatric patients with iron overload + 4 healthy volunteers) were imaged at 3T using 3D multi‐echo UTE cones with free breathing (FB cones), IDEAL‐IQ with breath holding (BH Cartesian), and free breathing (FB Cartesian). Overall image quality of maps was scored by 2 blinded experts and compared by a Wilcoxon rank‐sum test. For each pediatric subject, the paired maps were assessed to determine if a corresponding artifact‐free 15 mm region‐of‐interest (ROI) could be identified at a mid‐liver level on both images. Agreement between resulting quantification from FB cones and BH/FB Cartesian was assessed with Bland‐Altman and linear correlation analyses.

Results

ROI‐based regression analysis showed a linear relationship between gadolinium concentration and in IDEAL‐IQ (y = 8.83x − 52.10, R2 = 0.995) as well as in cones (y = 9.19x − 64.16, R2 = 0.992). ROI‐based Bland‐Altman analysis showed that the mean difference (MD) was 0.15% and the SD was 5.78%. However, IDEAL‐IQ measurements beyond 200 mM substantially deviated from a linear relationship for IDEAL‐IQ (y = 5.85x + 127.61, R2 = 0.827), as opposed to cones (y = 10.87x − 166.96, R2 = 0.984). In vivo, FB cones had similar image quality with BH and FB Cartesian in 15 and 42 cases, respectively. FB cones had better image quality scores than BH and FB Cartesian in 3 and 21 cases, respectively, where BH/FB Cartesian exhibited severe ghosting artifacts. ROI‐based Bland‐Altman analyses were 2.23% (MD) and 6.59% (SD) between FB cones and BH Cartesian and were 0.21% (MD) and 7.02% (SD) between FB cones and FB Cartesian, suggesting a good agreement between FB cones and BH (FB) Cartesian . Strong linear relationships were observed between BH Cartesian and FB cones (y = 1.00x + 1.07, R2 = 0.996) and FB Cartesian and FB cones (y = 0.98x + 1.68, R2 = 0.999).

Conclusion

Golden‐ratio re‐ordered 3D multi‐echo UTE Cones MRI enabled motion‐robust, ungated, and free‐breathing mapping of hepatic iron overload, with comparable measurements and image quality to BH Cartesian, and better image quality than FB Cartesian.
Immune profiling beyond antibodies in double seronegative and acetylcholine receptor antibody positive myasthenia gravis: What do we learn?
Authors: Kushlaf Hani
Published: January 2021

See article on pages 578–585 in this issue.
Bifurcation analysis of shear band in sand under true triaxial conditions with hypoplasticity
Authors: Zhang Wei , Wang Shun , Wu Yang , Wu Wei
Published: January 2021

Predicting the onset of shear band is of significance in understanding the failure of geomaterials. The prediction accuracy is dictated by the constitutive model used for the description of the pre‐bifurcation behaviour. In this study, we first modify a recently proposed hypoplastic constitutive model by incorporating a general strength criterion and a stiffness function. We proceed to consider the onset of shear band in sand under true triaxial conditions. We demonstrate that our analyses capture the pre‐bifurcation stress–strain relationship at different values of intermediate principal stress and predict fairly well the onset of shear band. The acoustic tensor criterion generally adopted in elastoplastic approaches is inadequate for hypoplastic approaches. No special non‐coaxial treatment is required for the present approach to yield a reasonable variation trend of bifurcation strain with intermediate principal stress ratio .
Efficient ternary polymer solar cell using wide bandgap conjugated polymer donor with two non‐fullerene small molecule acceptors enabled power conversion efficiency of 16% with low energy loss of 0.47 eV
Authors: Keshtov Mukhamed L. , Kuklin Sergei. A. , Khokhlov Alexei R. , Peregudov Aleksander S. , Chen Fang C. , Xie Zhiyuan , Sharma Ganesh D.
Published: January 2021

The ternary polymer solar cells (PSCs) were fabricated using a wide bandgap conjugated polymer P and two non‐fullerene small molecule acceptors, i.e. Y6 and BThIND‐Cl, in which the BThIND‐Cl was introduced as the third component. The open‐circuit voltage (Voc) of ternary PSCs increased with the increase of BThIND‐Cl content in the acceptors, signifying the formation of an alloy between BThIND‐Cl and Y6. We have observed that the energy loss of the ternary PSCs is decreased as compared to the binary counterparts, contributing to the improvement in Voc of ternary PSCs. The short circuit current as well as fill factor (FF) of the ternary PSCs were also enhanced with 0.4 weight ratio of BThIND‐Cl in the acceptors i.e.P:BThIND‐Cl:Y6 (1:0.4:1.1), resulting in overall power conversion efficiency (PCE) up to 16.08% of the optimized ternary PSCs. The improvement in the short circuit current and FF of the ternary PSCs is originated from the more molecular packing and molecular crystallinity, efficient light harvesting, excess exciton generation dissociation, and balanced charge transport. Moreover, the low value of the energy loss (0.47 eV) which may be lowest for the ternary based PSCs with PCE exceeding 16% which may be originated from the suppressed non‐radiative recombination loss. The might be due to the small highest occupied molecular orbital offsets between the combined alloyed acceptor and donor, resulting to the improvement in Voc for ternary PSC as compared to P:Y6 based PSCs.
Heart up! RCT protocol to increase physical activity in cardiac patients who report hopelessness: Amended for the COVID‐19 pandemic
Authors: Dunn Susan L. , Robbins Lorraine B. , Tintle Nathan L. , Collins Eileen G. , Bronas Ulf G. , Goodyke Madison P. , Luong Anna , Gutierrez‐Kapheim Melissa , DeVon Holli A.
Published: January 2021

Hopelessness is associated with decreased physical activity (PA) and increased adverse events and death in patients with ischemic heart disease (IHD). Rates of PA in patients with IHD continue to be low in both hospital‐based cardiac rehabilitation and home settings. While researchers have investigated strategies to increase PA among patients with IHD, interventions to promote PA specifically in IHD patients who report hopelessness are lacking. We describe the protocol for a NIH‐funded randomized controlled trial designed to establish the effectiveness of a 6‐week intervention (Heart Up!) to promote increased PA in IHD patients who report hopelessness. Participants (n = 225) are randomized to one of three groups: (1) motivational social support (MSS) from a nurse, (2) MSS from a nurse plus significant other support (SOS), or (3) attention control. Aims are to: (1) test the effectiveness of 6 weeks of MSS and MSS with SOS on increasing mean minutes per day of moderate to vigorous PA; (2) determine the effects of change in moderate to vigorous PA on hopelessness; and (3) determine if perceived social support and motivation (exercise self‐regulation) mediate the effects of the intervention on PA. A total of 69 participants have been enrolled to date. The protocol has been consistently and accurately used by research personnel. We address the protocol challenges presented by the COVID‐19 pandemic and steps taken to maintain fidelity to the intervention. Findings from this study could transform care for IHD patients who report hopelessness by promoting self‐management of important PA goals that can contribute to better health outcomes.
Impact of Home Parenteral Nutrition on Quality of Life in Cancer Patients: Don't Throw the Baby Out With the Bath Water
Authors: Cotogni Paolo
Published: January 2021

This letter to the editor remarks on the recent article by Bouleuc et al. and considers the controversial question of whether home parenteral nutrition may have an impact on quality of life in patients with advanced cancer.
Preparation and mechanical properties characterization: plasma‐modified expanded vermiculite/fabric‐reinforced foam composite materials
Authors: Li Ting‐Ting , Yang Yandong , Dai Wenna , Wang Hongyang , Wang Jie , Lou Ching‐Wen , Lin Jia‐Horng
Published: January 2021

Expanded vermiculite (EV) powder was treated with a plasma, and the organic material polyurethane (PU) was combined with the inorganic material EV powder and fabric by means of particle reinforcement and surface reinforcement to prepare a PU cushioning composite material. EV was processed with plasma treatment beforehand. The resulting PU foam cushioning composites were evaluated for static compression performance and dynamic buffering performance, thereby examining the influences of plasma treatment time and fabric type. According to the correlation between the structure and compression performance, the presence of EV provides more nucleation sites during the foaming, which in turn increases the cell density and the compression performance of the PU cushioning composites. In particular, after plasma treatment of 800‐mesh EV for 20 and 30 min, the resulting composite foam had reduced cell diameter and increased density, and enhanced mechanical properties. Besides, in terms of surface reinforcement, covering the surface with fabric will make the foam enter the densification stage in advance, and its compression performance will be enhanced. As for the dynamic cushioning test, the surface‐covering fabric can increase the impact performance, and the foam cushioning material covered with double‐sided fabric is better. Specifically, PU foam covered with warp‐knitted spacer fabric on both sides exhibits a maximal dynamic compression performance as the impact load is attenuated to 5941 N, suggesting an energy absorption of 96.20%. © 2021 Society of Chemical Industry