bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans
Authors: Tan Shengjun , Ma Huijing , Wang Jinbo , Wang Man , Wang Mengxia , Yin Haodong , Zhang Yaqiong , Zhang Xinying , Shen Jieyu , Wang Danyang , Banes Graham L. , Zhang Zhihua , Wu Jianmin , Huang Xun , Chen Hua , Ge Siqin , Chen Chun-Long , Zhang Yong E. 
Published: July 2021

AbstractDespite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example isMutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find thatSsk-FB4srepresent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.
Geminiviruses encode additional small proteins with specific subcellular localizations and virulence function
Authors: Gong Pan , Tan Huang , Zhao Siwen , Li Hao , Liu Hui , Ma Yu , Zhang Xi , Rong Junjie , Fu Xing , Lozano-Durán Rosa , Li Fangfang , Zhou Xueping 
Published: July 2021

AbstractGeminiviruses are plant viruses with limited coding capacity. Geminivirus-encoded proteins are traditionally identified by applying a 10-kDa arbitrary threshold; however, it is increasingly clear that small proteins play relevant roles in biological systems, which calls for the reconsideration of this criterion. Here, we show that geminiviral genomes contain additional ORFs. Using tomato yellow leaf curl virus, we demonstrate that some of these small ORFs are expressed during the infection, and that the encoded proteins display specific subcellular localizations. We prove that the largest of these additional ORFs, which we name V3, is required for full viral infection, and that the V3 protein localizes in the Golgi apparatus and functions as an RNA silencing suppressor. These results imply that the repertoire of geminiviral proteins can be expanded, and that getting a comprehensive overview of the molecular plant-geminivirus interactions will require the detailed study of small ORFs so far neglected.
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

AbstractMany 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

AbstractWe 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

AbstractA 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

AbstractMisfolded 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

AbstractPropagation 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

AbstractThe 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

AbstractMatrix 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

AbstractRecent 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

AbstractFreshwater 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

AbstractLung 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

AbstractEmotional 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

AbstractAirway 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.