bluuebunny/crossref_metadata_2025 huggingface dataset:
Astral hydrogels mimic tissue mechanics by aster-aster interpenetration
Authors: Xie Qingqiao , Zhuang Yuandi , Ye Gaojun , Wang Tiankuo , Cao Yi , Jiang Lingxiang
Published: July 2021

Many soft tissues are compression-stiffening and extension-softening in response to axial strains, but common hydrogels are either inert (for ideal chains) or tissue-opposite (for semiflexible polymers). Herein, we report a class of astral hydrogels that are structurally distinct from tissues but mechanically tissue-like. Specifically, hierarchical self-assembly of amphiphilic gemini molecules produces radial asters with a common core and divergently growing, semiflexible ribbons; adjacent asters moderately interpenetrate each other via interlacement of their peripheral ribbons to form a gel network. Resembling tissues, the astral gels stiffen in compression and soften in extension with all the experimental data across different gel compositions collapsing onto a single master curve. We put forward a minimal model to reproduce the master curve quantitatively, underlying the determinant role of aster-aster interpenetration. Compression significantly expands the interpenetration region, during which the number of effective crosslinks is increased and the network strengthened, while extension does the opposite. Looking forward, we expect this unique mechanism of interpenetration to provide a fresh perspective for designing and constructing mechanically tissue-like materials.
Topographic correlates of driver mutations and endogenous gene expression in pediatric diffuse midline gliomas and hemispheric high-grade gliomas
Authors: Kazarian Eve , Marks Asher , Cui Jin , Darbinyan Armine , Tong Elizabeth , Mueller Sabine , Cha Soonmee , Aboian Mariam S.
Published: July 2021

We evaluate the topographic distribution of diffuse midline gliomas and hemispheric high-grade gliomas in children with respect to their normal gene expression patterns and pathologic driver mutation patterns. We identified 19 pediatric patients with diffuse midline or high-grade glioma with preoperative MRI from tumor board review. 7 of these had 500 gene panel mutation testing, 11 patients had 50 gene panel mutation testing and one 343 gene panel testing from a separate institution were included as validation set. Tumor imaging features and gene expression patterns were analyzed using Allen Brain Atlas. Twelve patients had diffuse midline gliomas and seven had hemispheric high-grade gliomas. Three diffuse midline gliomas had the K27M mutation in the tail of histone H3 protein. All patients undergoing 500 gene panel testing had additional mutations, the most common being in ACVR1, PPM1D, and p53. Hemispheric high-grade gliomas had either TP53 or IDH1 mutation and diffuse midline gliomas had H3 K27M-mutation. Gene expression analysis in normal brains demonstrated that genes mutated in diffuse midline gliomas had higher expression along midline structures as compared to the cerebral hemispheres. Our study suggests that topographic location of pediatric diffuse midline gliomas and hemispheric high-grade gliomas correlates with driver mutations of tumor to the endogenous gene expression in that location. This correlation suggests that cellular state that is required for increased gene expression predisposes that location to mutations and defines the driver mutations within tumors that arise from that region.
Finite element analysis predicts Ca2+ microdomains within tubular-sarcoplasmic reticular junctions of amphibian skeletal muscle
Authors: Bardsley Oliver J. , Matthews Hugh R. , Huang Christopher L.-H.
Published: July 2021

A finite element analysis modelled diffusional generation of steady-state Ca2+ microdomains within skeletal muscle transverse (T)-tubular-sarcoplasmic reticular (SR) junctions, sites of ryanodine receptor (RyR)-mediated SR Ca2+ release. It used established quantifications of sarcomere and T-SR anatomy (radial diameter $$d=220 \, \mathrm{n}\mathrm{m}$$

d
=
220

n
m

; axial distance $$w=12 \, \mathrm{n}\mathrm{m}$$

w
=
12

n
m

). Its boundary SR Ca2+ influx densities,$${J}_{\mathrm{influx}}$$

J
influx

, reflected step impositions of influxes, $$\it {\Phi }_{\mathrm{influx}}={J}_{\mathrm{influx}}\left(\frac{\pi {d}^{2}}{4}\right),$$

Φ
influx

=

J
influx

π

d

2

4

,

deduced from previously measured Ca2+ signals following muscle fibre depolarization. Predicted steady-state T-SR junctional edge [Ca2+], [Ca2+]edge, matched reported corresponding experimental cytosolic [Ca2+] elevations given diffusional boundary efflux$$\it \it {\Phi }_{\mathrm{efflux}}=\frac{D [ {{{\mathrm{Ca}}^{2+}}}]_{\mathrm{edge}}}{\lambda } (\pi dw),$$

Φ
efflux

=

D

[

Ca

2
+

]

edge

λ

(
π
dw
)

,

established cytosolic Ca2+ diffusion coefficients $$(D = 4 \times {10}^{7} \mathrm{nm}^{2}/\mathrm{s})$$

(
D
=
4
×

10

7

nm

2

/
s
)

and exit length $$\lambda = 9.2 \, \mathrm{n}\mathrm{m}$$

λ
=
9.2

n
m

. Dependences of predicted [Ca2+]edge upon $${J}_{\mathrm{influx}}$$

J
influx

then matched those of experimental [Ca2+] upon Ca2+ release through their entire test voltage range. The resulting model consistently predicted elevated steady-state T-SR junctional ~ µM-[Ca2+] elevations radially declining from maxima at the T-SR junction centre along the entire axial T-SR distance. These [Ca2+] heterogeneities persisted through 104- and fivefold, variations in D and w around, and fivefold reductions in d below, control values, and through reported resting muscle cytosolic [Ca2+] values, whilst preserving the flux conservation ($$\it \it {\Phi }_{\mathrm{influx}}={\Phi }_{\mathrm{efflux}})$$

Φ
influx

=

Φ
efflux

)

condition, $${\left[\mathrm{C}{\mathrm{a}}^{2+}\right]}_{\mathrm{edge}}=\frac{\lambda {dJ}_{\mathrm{influx}}}{4Dw}$$

C

a

2
+

edge

=

λ

dJ

influx

4
D
w

. Skeletal muscle thus potentially forms physiologically significant ~ µM-[Ca2+] T-SR microdomains that could regulate cytosolic and membrane signalling molecules including calmodulin and RyR, These findings directly fulfil recent experimental predictions invoking such Ca2+ microdomains in observed regulatory effects upon Na+ channel function, in a mechanism potentially occurring in similar restricted intracellular spaces in other cell types.
Exogenous misfolded protein oligomers can cross the intestinal barrier and cause a disease phenotype in C. elegans
Authors: Perni Michele , Mannini Benedetta , Xu Catherine K. , Kumita Janet R. , Dobson Christopher M. , Chiti Fabrizio , Vendruscolo Michele
Published: July 2021

Misfolded protein oligomers are increasingly recognized as highly cytotoxic agents in a wide range of human disorders associated with protein aggregation.In this study, we assessed the possible uptake and resulting toxic effects of model protein oligomers administered toC. elegansthrough the culture medium.We used an automated machine-vision, high-throughput screening procedure to monitor the phenotypic changes in the worms, in combination with confocal microscopy to monitor the diffusion of the oligomers, and oxidative stress assays to detect their toxic effects. Our results suggest that the oligomers can diffuse from the intestinal lumen to other tissues, resulting in a disease phenotype. We also observed that pre-incubation of the oligomers with a molecular chaperone (αB-crystallin) or a small molecule inhibitor of protein aggregation (squalamine), reduced the oligomer absorption. These results indicate that exogenous misfolded protein oligomers can be taken up by the worms from their environment and spread across tissues, giving rise to pathological effects in regions distant from their place of absorbance.
The impact of a closed-loop thalamocortical model on the spatiotemporal dynamics of cortical and thalamic traveling waves
Authors: Bhattacharya Sayak , Cauchois Matthieu B. L. , Iglesias Pablo A. , Chen Zhe Sage
Published: July 2021

Propagation of activity in spatially structured neuronal networks has been observed in awake, anesthetized, and sleeping brains. How these wave patterns emerge and organize across brain structures, and how network connectivity affects spatiotemporal neural activity remains unclear. Here, we develop a computational model of a two-dimensional thalamocortical network, which gives rise to emergent traveling waves similar to those observed experimentally. We illustrate how spontaneous and evoked oscillatory activity in space and time emerge using a closed-loop thalamocortical architecture, sustaining smooth waves in the cortex and staggered waves in the thalamus. We further show that intracortical and thalamocortical network connectivity, cortical excitation/inhibition balance, and thalamocortical or corticothalamic delay can independently or jointly change the spatiotemporal patterns (radial, planar and rotating waves) and characteristics (speed, direction, and frequency) of cortical and thalamic traveling waves. Computer simulations predict that increased thalamic inhibition induces slower cortical frequencies and that enhanced cortical excitation increases traveling wave speed and frequency. Overall, our results provide insight into the genesis and sustainability of thalamocortical spatiotemporal patterns, showing how simple synaptic alterations cause varied spontaneous and evoked wave patterns. Our model and simulations highlight the need for spatially spread neural recordings to uncover critical circuit mechanisms for brain functions.
Mn-induced Fermi-surface reconstruction in the SmFeAsO parent compound
Authors: Meinero M. , Bonfà P. , Onuorah I. J. , Sanna S. , De Renzi R. , Eremin I. , Müller M. A. , Orain J.-C. , Martinelli A. , Provino A. , Manfrinetti P. , Putti M. , Shiroka T. , Lamura G.
Published: July 2021

The electronic ground state of iron-based materials is unusually sensitive to electronic correlations. Among others, its delicate balance is profoundly affected by the insertion of magnetic impurities in the FeAs layers. Here, we address the effects of Fe-to-Mn substitution in the non-superconducting Sm-1111 pnictide parent compound via a comparative study of SmFe$$_{1-x}$$

1
-
x

Mn$$_{x}$$

x

AsO samples with $$x(\text{Mn})=$$

x
(
Mn
)
=

0.05 and 0.10. Magnetization, Hall effect, and muon-spin spectroscopy data provide a coherent picture, indicating a weakening of the commensurate Fe spin-density-wave (SDW) order, as shown by the lowering of the SDW transition temperature $$T_\text{SDW}$$

T
SDW

with increasing Mn content, and the unexpected appearance of another magnetic order, occurring at $$T^{*} \approx 10$$

T

∗

≈
10

and 20 K for $$x=0.05$$

x
=
0.05

and 0.10, respectively. We attribute the new magnetic transition at $$T^{*}$$

T

∗

, occurring well inside the SDW phase, to a reorganization of the Fermi surface due to Fe-to-Mn substitutions. These give rise to enhanced magnetic fluctuations along the incommensurate wavevector $$\varvec{Q}_2 =(\pi \pm \delta ,\pi \pm \delta )$$

Q

2

=

(
π
±
δ
,
π
±
δ
)

, further increased by the RKKY interactions among Mn impurities.
An in vitro investigation to understand the synergistic role of MMPs-1 and 9 on articular cartilage biomechanical properties
Authors: Mixon Allison , Savage Andrew , Bahar-Moni Ahmed Suparno , Adouni Malek , Faisal Tanvir
Published: July 2021

Matrix metalloproteinases (MMPs) play a crucial role in enzymatically digesting cartilage extracellular matrix (ECM) components, resulting in degraded cartilage with altered mechanical loading capacity. Overexpression of MMPs is often caused by trauma, physiologic conditions and by disease. To understand the synergistic impact MMPs have on cartilage biomechanical properties, MMPs from two subfamilies: collagenase (MMP-1) and gelatinase (MMP-9) were investigated in this study. Three different ratios of MMP-1 (c) and MMP-9 (g), c1:g1, c3:g1 and c1:g3 were considered to develop a degradation model. Thirty samples, harvested from bovine femoral condyles, were treated in groups of 10 with one concentration of enzyme mixture. Each sample was tested in a healthy state prior to introducing degradative enzymes to establish a baseline. Samples were subjected to indentation loading up to 20% bulk strain. Both control and treated samples were mechanically and histologically assessed to determine the impact of degradation. Young’s modulus and peak load of the tissue under indentation were compared between the control and degraded cartilage explants. Cartilage degraded with the c3:g1 enzyme concentration resulted in maximum 33% reduction in stiffness and peak load compared to the other two concentrations. The abundance of collagenase is more responsible for cartilage degradation and reduced mechanical integrity.
A VigiBase descriptive study of fluoroquinolone induced disabling and potentially permanent musculoskeletal and connective tissue disorders
Authors: Huruba Madalina , Farcas Andreea , Leucuta Daniel Corneliu , Bucsa Camelia , Sipos Mariana , Mogosan Cristina
Published: July 2021

Recent drug safety concerns described fluoroquinolone (FQ)-induced serious musculoskeletal reactions. The objective of this study was to characterize reports with FQ-associated disabling musculoskeletal disorders, from VigiBase. The analysis included all FQ-induced musculoskeletal and connective tissue disorders adverse drug reaction (ADR) reports (up to July-2019), (disabling/incapacitating, or recovered/resolved with sequelae or fatal). We described aspects like reporter, suspected FQs, ADRs, associated corticosteroid therapy. We also looked into the disproportionality data in terms of proportional reporting ratio (PRR) and information component (IC) values. A total of 5355 reports with 13,563 ADRs and 5558 FQs were reported. The majority of reports were for patients aged 18–64 (62.67%), and the female gender prevailed (61.76%). Consumers reported almost half (45.99%), with a peak in reporting rates in 2017. Top reported ADRs were arthralgia (16.34%), tendonitis (11.04%), pain in extremity (9.98%), tendon pain (7.63%), and myalgia (7.17%). Top suspected FQs were levofloxacin (50.04%), ciprofloxacin (38.41%), moxifloxacin (5.16%), ofloxacin (3.17%) and norfloxacin (1.01%). For these, FQs-ADR association was supported by the disproportionality analysis. Corticosteroids were associated with about 7% of tendon related reports. The results augment the existing data on FQs safety concerns, specifically their potential effect on the musculoskeletal system.
Performance characterization and application of composite adsorbent LiCl@ACFF for moisture harvesting
Authors: Liu X. Y. , Wang W. W. , Xie S. T. , Pan Q. W.
Published: July 2021

Freshwater scarcity is a global threat to modern era of human society. Sorption-based atmospheric water harvesting (AWH) is prospective to provide fresh water for remote water-stressed areas lacking in water and electricity. Adsorbent material plays a vital role in such AWH systems. Here, we report a solid adsorbent synthesized by impregnating hygroscopic salt lithium chloride (LiCl) into solidified activated carbon fiber felt (ACFF modified by silica sol). Composite samples immersed with different mass concentrations of silica sol are prepared and characterized for dynamic water uptake, equilibrium water uptake, textural and thermal properties. AS5Li30 (ACFF + 5 wt% silica gel + 30 wt% LiCl) exhibits an efficient water uptake of 2.1 g/g at 25 °C and 70% relative humidity (RH). The material further demonstrates a heat storage capacity of 5456 kJ/kg. Its low regeneration temperature (< 80 °C) and good cycle stability make it feasible to be used in practical water production applications, driven by solar energy and other low-grade energy. Estimation results show that water harvesting unit can produce 1.41 gH2O/gAS5Li30 under 25 °C and 75% RH.
HLA-DR cancer cells expression correlates with T cell infiltration and is enriched in lung adenocarcinoma with indolent behavior
Authors: Senosain Maria-Fernanda , Zou Yong , Novitskaya Tatiana , Vasiukov Georgii , Balar Aneri B. , Rowe Dianna J. , Doxie Deon B. , Lehman Jonathan M. , Eisenberg Rosana , Maldonado Fabien , Zijlstra Andries , Novitskiy Sergey V. , Irish Jonathan M. , Massion Pierre P.
Published: July 2021

Lung adenocarcinoma (ADC) is a heterogeneous group of tumors associated with different survival rates, even when detected at an early stage. Here, we aim to investigate whether CyTOF identifies cellular and molecular predictors of tumor behavior. We developed and validated a CyTOF panel of 34 antibodies in four ADC cell lines and PBMC. We tested our panel in a set of 10 ADCs, classified into long- (LPS) (n = 4) and short-predicted survival (SPS) (n = 6) based on radiomics features. We identified cellular subpopulations of epithelial cancer cells (ECC) and their microenvironment and validated our results by multiplex immunofluorescence (mIF) applied to a tissue microarray (TMA) of LPS and SPS ADCs. The antibody panel captured the phenotypical differences in ADC cell lines and PBMC. LPS ADCs had a higher proportion of immune cells. ECC clusters (ECCc) were identified and uncovered two ADC groups. ECCc with high HLA-DR expression were correlated with CD4+ and CD8+ T cells, with LPS samples being enriched for those clusters. We confirmed a positive correlation between HLA-DR expression on ECC and T cell number by mIF staining on TMA slides. Spatial analysis demonstrated shorter distances from T cells to the nearest ECC in LPS. Our results demonstrate a distinctive cellular profile of ECC and their microenvironment in ADC. We showed that HLA-DR expression in ECC is correlated with T cell infiltration, and that a set of ADCs with high abundance of HLA-DR+ ECCc and T cells is enriched in LPS samples. This suggests new insights into the role of antigen presenting tumor cells in tumorigenesis.
Decreased intersubject synchrony in dynamic valence ratings of sad movie contents in dysphoric individuals
Authors: Li Xueqiao , Zhu Yongjie , Vuoriainen Elisa , Ye Chaoxiong , Astikainen Piia
Published: July 2021

Emotional reactions to movies are typically similar between people. However, depressive symptoms decrease synchrony in brain responses. Less is known about the effect of depressive symptoms on intersubject synchrony in conscious stimulus-related processing. In this study, we presented amusing, sad and fearful movie clips to dysphoric individuals (those with elevated depressive symptoms) and control participants to dynamically rate the clips’ valences (positive vs. negative). We analysed both the valence ratings’ mean values and intersubject correlation (ISC). We used electrodermal activity (EDA) to complement the measurement in a separate session. There were no group differences in either the EDA or mean valence rating values for each movie type. As expected, the valence ratings’ ISC was lower in the dysphoric than the control group, specifically for the sad movie clips. In addition, there was a negative relationship between the valence ratings’ ISC and depressive symptoms for sad movie clips in the full sample. The results are discussed in the context of the negative attentional bias in depression. The findings extend previous brain activity results of ISC by showing that depressive symptoms also increase variance in conscious ratings of valence of stimuli in a mood-congruent manner.
Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
Authors: Banerjee Priyanka , Balraj Premanand , Ambhore Nilesh Sudhakar , Wicher Sarah A. , Britt Rodney D. , Pabelick Christina M. , Prakash Y. S. , Sathish Venkatachalem
Published: July 2021

Airway smooth muscle (ASM) is known for its role in asthma exacerbations characterized by acute bronchoconstriction and remodeling. The molecular mechanisms underlying multiple gene interactions regulating gene expression in asthma remain elusive. Herein, we explored the regulatory relationship between ASM genes to uncover the putative mechanism underlying asthma in humans. To this end, the gene expression from human ASM was measured with RNA-Seq in non-asthmatic and asthmatic groups. The gene network for the asthmatic and non-asthmatic group was constructed by prioritizing differentially expressed genes (DEGs) (121) and transcription factors (TFs) (116). Furthermore, we identified differentially connected or co-expressed genes in each group. The asthmatic group showed a loss of gene connectivity due to the rewiring of major regulators. Notably, TFs such as ZNF792, SMAD1, and SMAD7 were differentially correlated in the asthmatic ASM. Additionally, the DEGs, TFs, and differentially connected genes over-represented in the pathways involved with herpes simplex virus infection, Hippo and TGF-β signaling, adherens junctions, gap junctions, and ferroptosis. The rewiring of major regulators unveiled in this study likely modulates the expression of gene-targets as an adaptive response to asthma. These multiple gene interactions pointed out novel targets and pathways for asthma exacerbations.
Regularized machine learning on molecular graph model explains systematic error in DFT enthalpies
Authors: Bhattacharjee Himaghna , Anesiadis Nikolaos , Vlachos Dionisios G.
Published: July 2021

A major goal of materials research is the discovery of novel and efficient heterogeneous catalysts for various chemical processes. In such studies, the candidate catalyst material is modeled using tens to thousands of chemical species and elementary reactions. Density Functional Theory (DFT) is widely used to calculate the thermochemistry of these species which might be surface species or gas-phase molecules. The use of an approximate exchange correlation functional in the DFT framework introduces an important source of error in such models. This is especially true in the calculation of gas phase molecules whose thermochemistry is calculated using the same planewave basis set as the rest of the surface mechanism. Unfortunately, the nature and magnitude of these errors is unknown for most practical molecules. Here, we investigate the error in the enthalpy of formation for 1676 gaseous species using two different DFT levels of theory and the ‘ground truth values’ obtained from the NIST database. We featurize molecules using graph theory. We use a regularized algorithm to discover a sparse model of the error and identify important molecular fragments that drive this error. The model is robust to rigorous statistical tests and is used to correct DFT thermochemistry, achieving more than an order of magnitude improvement.
Risk factors for urosepsis in chronic kidney disease patients with urinary tract infections
Authors: Dimitrijevic Zorica , Paunovic Goran , Tasic Danijela , Mitic Branka , Basic Dragoslav
Published: July 2021

Occurrence of urosepsis is not uncommon following urinary tract infections (UTI). However, there is a lack of evidence explaining the risk factors predisposing to urosepsis in patients with chronic kidney disease (CKD). This retrospective study was undertaken to evaluate the incidence and possible risk factors for urosepsis among patients hospitalized with UTI in a cohort of CKD patients. Patients were divided into the urosepsis group and the non-urosepsis group. Of 489 hospitalized patients with UTI, 70 (14.3%) acquired urosepsis. Stepwise multivariate logistic regression demonstrated that diabetes, urinary catheter and length of hospital stay (p < 0.001 for all) were significant independent predictive risk factors for urosepsis in CKD patients with UTI in addition to age, glomerular filtration rate, hydronephrosis, acute kidney injury andE. coliinfection (p < 0.05 for all). Finally,Klebsiella spp. cases were associated with significantly higher odds for urosepsis thanE. colicases (OR: 3.5, 95% CI: 2.86–7.23,p < 0.001 vs. OR: 1.38, 95% CI: 1.19–3.69,p = 0.038). Diabetes, presence of an indwelling urinary catheter, length of hospitalization, and infection withKlebsiellaspp were independent risk factors for urosepsis in CKD patients with UTI.
Association between statin medication and hearing impairment in a national health screening cohort
Authors: Kim So Young , Lee Chang Ho , Min Chanyang , Yoo Dae Myoung , Choi Hyo Geun
Published: July 2021

This study aimed to investigate the association of previous stain use with hearing impairment in an adult population. Data from the ≥ 40-year-old population in the Korean National Health Insurance Service Health Screening Cohort were used. The hearing impairment group was classified based on the national registry of hearing-impaired persons. Control participants were randomly selected and matched for age, sex, income, and region of residence. The number of days of statin prescription during the 2 years before the diagnosis of hearing impairment was compared between the hearing impairment group and the control group using conditional logistic regression analysis. Additional analyses were conducted according to age and sex. The number of days of previous statin use was not different between the hearing impairment group and the control group (adjusted odds ratio [aOR] = 0.94, 95% confidence interval (CI) = 0.86–1.02, P = 0.118). According to age, in the ≥ 70-year-old group, those with hearing impairment had 11% lower rates of previous statin use than those in the control group (aOR = 0.89, 95% CI = 0.80–0.99, P = 0.039). According to sex, in the male group, 12% lower rates of previous statin use were observed among those with hearing impairment than among those in the control group (aOR = 0.88, 95% CI = 0.79–0.99, P = 0.037). Previous statin use might have an effect on reducing the prevalence of hearing impairment in elderly individuals and men.
Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning
Authors: Nieboer Marleen M. , Nguyen Luan , de Ridder Jeroen
Published: July 2021

Over the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in these data. Here, we introduce svMIL2, an improved version of our Multiple Instance Learning-based method to study the effect of somatic non-coding SVs disrupting boundaries of TADs and CTCF loops in 1646 cancer genomes. We demonstrate that svMIL2 predicts pathogenic non-coding SVs with an average AUC of 0.86 across 12 cancer types, and identifies non-coding SVs affecting well-known driver genes. The disruption of active (super) enhancers in open chromatin regions appears to be a common mechanism by which non-coding SVs exert their pathogenicity. Finally, our results reveal that the contribution of pathogenic non-coding SVs as opposed to driver SNVs may highly vary between cancers, with notably high numbers of genes being disrupted by pathogenic non-coding SVs in ovarian and pancreatic cancer. Taken together, our machine learning method offers a potent way to prioritize putatively pathogenic non-coding SVs and leverage non-coding SVs to identify driver genes. Moreover, our analysis of 1646 cancer genomes demonstrates the importance of including non-coding SVs in cancer diagnostics.
Prognostic stratification for IDH-wild-type lower-grade astrocytoma by Sanger sequencing and copy-number alteration analysis with MLPA
Authors: Makino Yasuhide , Arakawa Yoshiki , Yoshioka Ema , Shofuda Tomoko , Kawauchi Takeshi , Terada Yukinori , Tanji Masahiro , Kanematsu Daisuke , Mineharu Yohei , Miyamoto Susumu , Kanemura Yonehiro
Published: July 2021

The characteristics of IDH-wild-type lower-grade astrocytoma remain unclear. According to cIMPACT-NOW update 3, IDH-wild-type astrocytomas with any of the following factors show poor prognosis: combination of chromosome 7 gain and 10 loss (+ 7/− 10), and/or EGFR amplification, and/or TERT promoter (TERTp) mutation. Multiplex ligation-dependent probe amplification (MLPA) can detect copy number alterations at reasonable cost. The purpose of this study was to identify a precise, cost-effective method for stratifying the prognosis of IDH-wild-type astrocytoma. Sanger sequencing, MLPA, and quantitative methylation-specific PCR were performed for 42 IDH-wild-type lower-grade astrocytomas surgically treated at Kyoto University Hospital, and overall survival was analysed for 40 patients who underwent first surgery. Of the 42 IDH-wild-type astrocytomas, 21 were classified as grade 4 using cIMPACT-NOW update 3 criteria and all had either TERTp mutation or EGFR amplification. Kaplan–Meier analysis confirmed the prognostic significance of cIMPACT-NOW criteria, and World Health Organization grade was also prognostic. Cox regression hazard model identified independent significant prognostic indicators of PTEN loss (risk ratio, 9.75; p < 0.001) and PDGFRA amplification (risk ratio, 13.9; p = 0.002). The classification recommended by cIMPACT-NOW update 3 could be completed using Sanger sequencing and MLPA. Survival analysis revealed PTEN and PDGFRA were significant prognostic factors for IDH-wild-type lower-grade astrocytoma.
The impact of large-scale afforestation on ecological environment in the Gobi region
Authors: Yao Zhengyi , Xiao Jianhua , Ma Xixi
Published: July 2021

In recent year, there has been large-scale afforestation in the gobi region of western Inner Mongolia, China. However, this area has low annual precipitation of 35–55 mm, and a high annual evaporation capacity of 3842 mm. Further, water resources in this region are scarce and cannot support the sustainable growth of shrubs. Thus, without effective irrigation, the shrubs cannot survive and ultimately, large-scale afforestation in the gobi region will destroy “black vegetation”. The surface of this area is covered by dense gravel (65.43–82.08%; average of 77.14%) as a result of long-term erosion caused by strong winds. The sediments underlying the gravel layer are rich in sand (60.34–87.51%) and silt (11.26–35.18%). Once the surface gravel layer is destroyed, the underlying sand and silt expose and increase dust supply, and result in increased intensity and frequency of dust storms. Thus, large-scale afforestation in the gobi region is an ecological disaster for these very dry lands.
The role of coherent epitaxy in forming a two-dimensional electron gas at LaIn1-xGaxO3/BaSnO3 interfaces
Authors: Kim Young Mo , Kim Youjung , Char Kookrin
Published: July 2021

Some oxide interfaces are known to exhibit unique properties such as a 2D electron gas, controlled by epitaxial strain and coherency between the two layers. Here, we study variation in the 2D electron density in the polar LaIn1-xGaxO3/Ba0.997La0.003SnO3 interface with changing x and LaIn1-xGaxO3 layer thickness. We find that the 2D electron density decreases as the gallium alloying ratio increases and the interface conductance eventually disappears, which shows that an interface with polar discontinuity is not a sufficient condition for 2D electron gas formation. The interface conductance reaches its maximum value when the LaIn1-xGaxO3 layer thickness is approximately 20 Å, beyond which conductance decreased to a constant value. Atomistic imaging reveals that dislocations start to form as the gallium ratio increases, forming away from the interface and then moving closer with increasing gallium alloying. The dislocations eventually destroy coherency in the case of LaGaO3 and suppress the formation of a 2D electron gas.
Periodic island-layer-island growth during deposition of ultrastable metallic glasses
Authors: Yang Fan , Wang Chao , Bai Haiyang , Wang Weihua , Liu Yanhui
Published: July 2021

The fast exploration of low energy configuration by surface atoms is believed to favor the formation of ultrastable metallic glasses, prepared by physical vapor deposition. Here, we find that the rearrangement of surface atoms is collective, rather than being dominated by individual atoms. Specifically, we experimentally observe the growth process of ultrastable metallic glasses at monolayer resolution, which follows a periodic island-layer-island pattern with morphology variation between islands and flat surfaces. The estimated surface diffusion coefficient is orders of magnitude higher than that for bulk diffusion. The fast surface dynamics allow the newly deposited clusters on the flat surface to form local islands with spherical shape, which substantially reduces the surface free energy in each island-layer-island growth cycle. Our findings are helpful for understanding the growth mechanisms of ultrastable metallic glasses and potentially for tailoring their properties.
Hydrophilic Interaction Chromatography–Mass Spectrometry (HILIC–MS) Approaches for Probing the Polar Metabolome
Authors: Gallart-Ayala H. , Teav T. , Ivanisevic J.
Published: July 2021

Hydrophilic interaction chromatography (HILIC) coupled to electrospray ionization (ESI) mass spectrometry (MS) has become one of the leading analytical technologies for polar metabolome analysis. With remarkable improvement of stationary phases, HILIC has reached the separation efficiency and reproducibility equivalent to RPLC-based methods with complementary selectivity and significantly higher sensitivity for the analysis of highly hydrophilic metabolites implicated in energy producing (glycolysis, pentose phosphate pathway, TCA cycle) and biosynthetic pathways (amino acids, nucleotides, vitamins and their precursors). For polar metabolome analysis, the HILIC applications range from the targeted quantification (with a focus on one specific pathway or class of metabolites) to broad-spectrum targeted screening (of hundreds of metabolites) and untargeted discovery profiling, including stable isotope-assisted tracing experiments. These HILIC-based approaches can be applied in many areas from model systems (i.e. cell and tissue lysate analysis) to large-scale human population studies (i.e. biofluid profiling). In this review we provide numerous examples of proof-of-principle studies which unambiguously demonstrate HILIC selectivity and reproducibility. Among different stationary phases, the polymer-based zwitterionic and amide columns show the best performance in achieving the broadest metabolite coverage. Recent developments are marked by the bloom of broad-coverage, multiple pathway targeted analysis (of the well-known cellular metabolome) to take advantage of the unprecedented scan speed, sensitivity and dynamic range of tandem MS spectrometers.
Advances in Solid Phase Microextraction (SPME) for Metabolomics
Authors: Boyaci E. , Gionfriddo E. , Roszkowska A. , Bojko B.
Published: July 2021

Solid phase microextraction (SPME) is an equilibrium-based technique that enables extraction of free-fraction metabolites of exogenous and endogenous origins. SPME combines sampling, extraction, and preconcentration into a single step, significantly simplifying analytical protocols and enabling on-site use. Other unique features of this method, such as low invasiveness and negligible depletion of extracted analytes from the sample, make it an ideal tool for characterization of living systems. During in vivo sampling, extraction into SPME devices enables metabolite quenching, resulting in the capture of the labile portion of the metabolome, thus providing a true chemical snapshot of the system under study. In this chapter, an overview of the technology is presented with emphasis on the characteristic features of SPME that most benefit metabolomics in comparison to other sample preparation techniques. Different aspects of the analysis of volatile, semi-, and non-volatile metabolites are discussed, and various sampling modes and phenomena associated with coating saturation, analyte replacement, and balanced coverage are explained. Commercial and lab-made extraction phases available for polar metabolome analysis are described. Also, several exemplary applications of SPME in foodomics, exposomics, and biomedical and clinical metabolomics are reviewed. Finally, future perspectives on the use of this technology in metabolomics are presented.
Ion Mobility–Time-of-flight Mass Spectrometry and Applications for Metabolomics
Authors: Feuerstein Max L. , Hann Stephan , Causon Tim
Published: July 2021

Applications of ion mobility (IM) coupled to high-resolution mass spectrometry, i.e., quadrupole time-of-flight (QTOF) instruments, have experienced a significant growth in recent years, especially in the ‘omics fields including metabolomics. Several types of instrumental platforms are now commercially available and exploit different operation principles for the IM separation. In this contribution, we discuss the current state of commercial IM–QTOFMS technology and data acquisition strategies relevant to metabolomics studies. Particular focus is placed on the strengths and weaknesses of the application of this technology both for data generation and emerging strategies and opportunities within data processing workflows that take full advantage of the added IM dimension.
Chiral Metabolomics
Authors: Calderón Carlos , Lämmerhofer Michael
Published: July 2021

In this chapter the state-of-the-art in enantioselective metabolomics focusing on polar metabolites analyzed by liquid chromatography is summarized. The different methodologies commonly employed are outlined and critically discussed. Nowadays, direct enantioselective metabolomics can make use of several modern chiral HPLC as well as, recently, UHPLC columns containing chiral stationary phases based on various selectors, such as polysaccharide derivatives, macrocyclic antibiotics, chiral crown ethers, chiral ion exchangers, donor–acceptor phases and others. Where metabolites are concerned, many of them show class specific application profiles (e.g. for amino acids), such as chiral crown ether CSP, zwitterionic chiral ion-exchangers and teicoplanin CSP, or even wider scopes of applicability, such as amylose and cellulose tris (3,5-dimethylphenylcarbamate) CSPs. Since mass spectrometry is the detection principle of first choice in metabolomics applications, research concentrates on analytical separation systems that are compatible with MS detection. Since enantioselective UHPLC columns have only become available recently and often require tagging of the polar metabolites, indirect approaches have been utilized frequently up to now in particular for untargeted enantioselective metabolomics. A significant number of chiral derivatizing agents have been described for this purpose. Some caveats have to be considered to obtain accurate enantioselective assays by the indirect approach and are discussed in this chapter. The integration of these concepts in targeted and untargeted workflows is described, and some illustrative examples are given for targeted and untargeted enantioselective metabolomics applications.
Influence of hemolysis on serum procalcitonin measured by electrochemiluminescence in an emergency room
Authors: Liu Chong , Peng Ziyuan , Cui Liyan , Wang Tiancheng , Wu Yonghua
Published: July 2021

To investigate the effect of hemolysis on serum procalcitonin (PCT) detected by electrochemiluminescence (ECL) and to explore the possibility of establishment of a correction equation.
Electrochemical sandwich-type immunosensor for the detection of PSA based on a trimetallic AgAuPt nanocomposite synthesized using the galvanic replacement reaction
Authors: Khanmohammadi Akbar , Afkhami Abbas , Hajian Ali , Khoshsafar Hosein , Bagheri Hasan
Published: July 2021

An electrochemical immunoassay is prepared for the determination of PSA using a composite of AgAuPt, synthesized by galvanic replacement between the Ag framework and Pt and Au ions. The AgPt labeled-antibody is applied as the detection layer.
The role and mechanism of polydopamine and cuttlefish ink melanin carrying copper ion nanoparticles in antibacterial properties and promoting wound healing
Authors: Lin Zhenjie , Liu Lizhu , Wang Wei , Jia Li , Shen Yuqing , Zhang Xiuming , Ge Dongtao , Shi Wei , Sun Yanan
Published: July 2021

Cu(ii) Loaded PDA NPs have synergistic antibacterial effects by bacterial membrane rupture with ROS generation of copper ions and potential to accelerate wound healing by slowly releasing copper ion to promote cell migration and re-epithelization.
Carbazate-modified cross-linked dextran microparticles suppress the progression of osteoarthritis by ROS scavenging
Authors: Ding Yanfeng , Li Zhimin , Hu Wenwen , Feng Xianjing , Chen Ying , Yan Guohua , Wang Yonglin , Zhu Bo , Yao Wei , Zheng Li , He Maolin , Gao Ming , Zhao Jinmin
Published: July 2021

Reacting with reactive oxygen species (ROS) by C–H hydrogen abstraction, carbazate modified sephadex served as potent ROS scavengers, with excellent antioxidant and anti-inflammatory abilities, finally suppressing the progress of osteoarthritis.
Conversion-type NiCoMn triple perovskite fluorides for advanced aqueous supercapacitors, batteries and supercapatteries
Authors: Jia Ziyang , Shi Wei , Ding Rui , Yu Wujiang , Li Yi , Tan Caini , Sun Xiujuan , Liu Enhui
Published: July 2021

Conversion-type NiCoMn triple perovskite fluorides show promising applications in aqueous supercapacitors, batteries and supercapatteries.
Integrated, one-pot carbon capture and utilisation using porous ionic liquids
Authors: Zhou Yujiao , Avila Jocasta , Berthet Nicolas , Legrand Solène , Santini Catherine C. , Costa Gomes Margarida , Dufaud Véronique
Published: July 2021

Porous ionic liquids simultaneously absorb carbon dioxide and catalyse its reaction with epoxides to form cyclic carbonates under mild conditions.
Theoretical study of spodium bonding in the active site of three Zn-proteins and several model systems
Authors: Llull Rosa , Montalbán Gaizca , Vidal Ivan , Gomila Rosa M. , Bauzá Antonio , Frontera Antonio
Published: July 2021

This article evidences the existence and importance of spodium bonds (SpB) in Zn(ii) dependent enzymes. The energetic features of a series of complexes using Zn(ii) receptors have been analysed using DFT calculations.
Cost and low-carbon competitiveness of electrolytic hydrogen in China
Authors: Pan Guangsheng , Gu Wei , Hu Qinran , Wang Jianxiao , Teng Fei , Strbac Goran
Published: July 2021

To quantify the cost and low-carbon competitiveness of electrolytic hydrogen in China, this paper presents a detailed assessment of the levelized cost of electrolytic hydrogen produced by a photovoltaic and grid-based hydrogen system (PGHS).
A linear scaling law for predicting phase transition temperature via averaged effective electronegativity derived from A2M3O12-based compounds
Authors: Yuan Huanli , Wang Chunyan , Gao Qilong , Zeng Gaojie , Guo Juan , Chao Mingju , Kawaguchi Shogo , Jia Yu , Liang Erjun
Published: July 2021

A2M3O12-based compounds exhibit NTE properties only after phase transition from the monoclinic to the orthorhombic. The linear scaling law of averaged effective electronegativity (AEE) can be used to predict phase transition temperature (Tt).
Fluorinated nanotubes: synthesis and self-assembly of cyclic peptide–poly(vinylidene fluoride) conjugates
Authors: Folgado Enrique , Song Qiao , Perrier Sebastien , Ladmiral Vincent , Semsarilar Mona
Published: July 2021

Fluorinated hollow nanotubes were prepared from pre-assembled cyclic peptides bearing xanthate moieties by RAFT/MADIX of VDF.
N-Nosyl-O-bromoethyl hydroxylamine acts as a multifunctional formaldehyde, formaldimine, and 1,2-oxazetidine surrogate for C–C and C–O bond-forming reactions
Authors: Wu Binyu , Wen Xiaolu , Chen Hongbing , Hu Lin
Published: July 2021

Hydroxylamine could chemo- and stereoselectively produce α-hydroxymethyl and α-aminomethyl ketones and chiral α-alkoxyl and α-aminomethyl carboxylates in good yields.
Quinol-containing ligands enable high superoxide dismutase activity by modulating coordination number, charge, oxidation states and stability of manganese complexes throughout redox cycling
Authors: Senft Laura , Moore Jamonica L. , Franke Alicja , Fisher Katherine R. , Scheitler Andreas , Zahl Achim , Puchta Ralph , Fehn Dominik , Ison Sidney , Sader Safaa , Ivanović-Burmazović Ivana , Goldsmith Christian R.
Published: July 2021

Manganese complexes with polydentate quinol-containing ligands are found to catalyze the degradation of superoxide through inner-sphere mechanisms. The redox activity of the ligand stabilizes higher-valent manganese species.
A general, versatile and divergent synthesis of selectively deuterated amines
Authors: Lecomte Morgan , Lahboubi Mounsef , Thilmany Pierre , El Bouzakhi Adil , Evano Gwilherm
Published: July 2021

A general, versatile, divergent and metal-free synthesis of amines selectively deuterated at their α and/or β positions and relying on a simple treatment of ynamides with triflic acid and triethylsilane, either deuterated or not, is reported.
Numerical analysis and design of a light-driven liquid crystal polymer-based motorless miniature cart
Authors: Ramgopal Adithya , Peeketi Akhil Reddy , Annabattula Ratna Kumar
Published: July 2021

The work describes the kinematics of the light-driven rolling motion of azobenzene-doped glassy liquid crystal network wheels. Further, a finite element model is used to demonstrate the movement of a motorless miniature cart.
In-depth understanding of the energy loss and efficiency limit of dye-sensitized solar cells under outdoor and indoor conditions
Authors: Aftabuzzaman M. , Sarker Subrata , Lu Chunyuan , Kim Hwan Kyu
Published: July 2021

This perspective thoroughly explores the energy loss factors in DSSCs and estimates the feasible efficiency of DSSCs under outdoor and indoor conditions, and compares it with the SQ limit of an ideal solar cell.
Lithium stripping: anisotropic evolution and faceting of pits revealed byoperando3-D microscopy
Authors: Sanchez Adrian J. , Kazyak Eric , Chen Yuxin , Lasso Jose , Dasgupta Neil P.
Published: July 2021

Operando3-D microscopy of individual pits during Li metal anode stripping demonstrates anisotropic expansion, edge faceting, and surface microstructure effects.
Strategies of structural and defect engineering for high-performance rechargeable aqueous zinc-ion batteries
Authors: Du Min , Miao Zhenyu , Li Houzhen , Sang Yuanhua , Liu Hong , Wang Shuhua
Published: July 2021

Recent progress regarding the structural and defect engineering of aqueous ZIBs is summarized. Furthermore, advanced techniques, the existing challenges and future perspectives on the structural and defect engineering of ZIBs are discussed.
Two-step assembly induced Fe0-anchored graphitic N-rich graphene with biactive centers for enhanced heterogeneous peroxymonosulfate activation
Authors: Zhang Junjie , Gao Wenran , Yue Yamei , Wang Wei , Tan Fatang , Wang Xinyun , Qiao Xueliang , Wong Po Keung
Published: July 2021

Biactive centers of Fe0-anchored graphitic N-rich graphene (Fe-GNG) were constructed via coordination and hydrogen bonding assemblies followed by calcination, and induced excellent radical and nonradical oxidization processes.