bluuebunny/crossref_metadata_2025_split huggingface dataset:
PABPN1L assemble into “ring-like” aggregates in the cytoplasm of MII oocytes and is associated with female infertility†
Authors: Wang Ying , Feng Tianhao , Zhu Mingcong , Shi Xiaodan , Wang Zerui , Liu Siyu , Zhang Xin , Zhang Jintao , Zhao Shuqin , Zhang Junqiang , Ling Xiufeng , Liu Mingxi 
Published: November 2021

Abstract
Infertility affects 10–15% of families worldwide. However, the pathogenesis of female infertility caused by abnormal early embryonic development is not clear. A recent study showed that poly(A)binding protein nuclear 1-like (PABPN1L) recruited BTG anti-proliferation factor 4 (BTG4) to mRNA 3′-poly(A) tails and was essential for maternal mRNA degradation. Here, we generated a PABPN1L-antibody and found “ring-like” PABPN1L aggregates in the cytoplasm of MII oocytes. PABPN1L–EGFP proteins spontaneously formed “ring-like” aggregates in vitro. This phenomenon is similar with CCR4–NOT catalytic subunit, CCR4-NOT transcription complex subunit 7 (CNOT7), when it starts deadenylation process in vitro. We constructed two mouse model (Pabpn1l−/− and Pabpn1l tm1a/tm1a) simulating the intron 1–exon 2 abnormality of human PABPN1L and found that the female was sterile and the male was fertile. Using RNA-Seq, we observed a large-scale up-regulation of RNA in zygotes derived from Pabpn1l−/− MII oocytes. We found that 9222 genes were up-regulated instead of being degraded in the Pabpn1l−♀/+♂zygote. Both the Btg4 and CCR4-NOT transcription complex subunit 6 like (Cnot6l) genes are necessary for the deadenylation process and Pabpn1l−/− resembled both the Btg4 and Cnot6l knockouts, where 71.2% genes stabilized in the Btg4−♀/+♂ zygote and 84.2% genes stabilized in the Cnot6l−♀/+♂zygote were also stabilized in Pabpn1l−♀/+♂ zygote. BTG4/CNOT7/CNOT6L was partially co-located with PABPN1L in MII oocytes. The above results suggest that PABPN1L is widely associated with CCR4–NOT-mediated maternal mRNA degradation and PABPN1L variants on intron 1–exon 2 could be a genetic marker of female infertility.
Effect of additive, dominant and epistatic variances on breeding and deployment strategy in Norway spruce
Authors: Nguyen Hong T H , Chen Zhi-Qiang , Fries Anders , Berlin Mats , Hallingbäck Henrik R , Wu Harry X 
Published: November 2021

Abstract
Genetic variances are important parameters and have a great impact on the determination of optimal breeding strategies of tree species. A large clonal testing program was conducted to estimate additive, dominant and epistatic variances for the development of breeding and deployment strategies in Norway spruce (Picea abies (L.) Karst.). The analysis results of genetic variation for growth and wood properties in two clonal trials in central Sweden indicated that the important sources of total genetic variation were both additive and non-additive genetic variances. Additive genetic variation accounted for the majority of total genetic variation for diameter at breast height (DBH) and wood quality traits, whereas non-additive genetic variation was significant only for tree height at an early age. Predicted genetic gain was the highest for clonal deployment based on best tested (replicated) clones (4.7–65.3 per cent), followed by clonal deployment of the best individual trees from a full-sib family trial (3.5–57.7 per cent), and the deployment of seedlings generated by open-pollination (1.9–48.3 per cent).
Elevated DLL3 in stomach cancer by tumor-associated macrophages enhances cancer-cell proliferation and cytokine secretion of macrophages
Authors: Ye Jian-Bin , Wen Jun-Jie , Wu Dan-Lin , Hu Bing-Xin , Luo Mei-Qun , Lin Yan-Qing , Ning Yun-Shan , Li Yan 
Published: November 2021

Abstract

Background
The notch signal pathway is important in the development of both tumor-associated macrophages (TAMs) and stomach cancer, but how Notch signaling affects TAMs in stomach cancer is barely understood.

Methods
The expressions of Notch1, Notch2, Notch3, Notch4, hes family bHLH transcription factor 1 (Hes1), and delta-like canonical Notch ligand 3 (DLL3) were detected by Western blot and the expressions of interleukin (IL)-10, IL-12, and IL1-β were detected using enzyme-linked immunosorbent assay after the co-culture of macrophages and stomach-cancer cells. The proliferation and migration of cancer cells were detected using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and scratch assay, respectively, and the cell cycle was detected using Annexin V/propidium iodide assay. The protein interactions with DLL3 were detected using co-immunoprecipitation and mass spectrometry.

Results
The co-culture of macrophages and stomach-cancer cells MKN45 and BGC823 could enhance cell proliferation accompanied by the activation of Notch1/Notch2 signaling and upregulation of DLL3. Notch signaling gamma-secretase inhibitor (DAPT) blocked this process. The overexpression of DLL3 in stomach-cancer cells could promote the proliferation of cancer cells, enhance the activation of Notch1/Notch2 signaling, induce the expression of IL-33, lead to the degradation of galectin-3–binding protein (LG3BP) and heat shock cognate 71 kDa protein (HSPA8), and result in elevated IL-1β, IL-12, and IL-10 secretion by macrophages. Higher expression of DLL3 or IL-33 could lead to a lower survival rate based on University of California, Santa Cruz Xena Functional Genomics Explorer and The Cancer Genome Atlas data set.

Conclusions
This is evidence that DLL3 regulates macrophages in stomach cancer, suggesting that DLL3 may be a novel and potential target for stomach-cancer therapy.
Neuronal KGB-1 JNK MAPK signaling regulates the dauer developmental decision in response to environmental stress in Caenorhabditis elegans
Authors: Dogra Deepshikha , Kulalert Warakorn , Schroeder Frank C , Kim Dennis H 
Published: November 2021

Abstract
In response to stressful growth conditions of high population density, food scarcity, and elevated temperature, young larvae of nematode Caenorhabditis elegans can enter a developmentally arrested stage called dauer that is characterized by dramatic anatomic and metabolic remodeling. Genetic analysis of dauer formation of C. elegans has served as an experimental paradigm for the identification and characterization of conserved neuroendocrine signaling pathways. Here, we report the identification and characterization of a conserved c-Jun N-terminal Kinase-like mitogen-activated protein kinase (MAPK) pathway that is required for dauer formation in response to environmental stressors. We observed that loss-of-function mutations in the MLK-1-MEK-1-KGB-1 MAPK pathway suppress dauer entry. A loss-of-function mutation in the VHP-1 MAPK phosphatase, a negative regulator of KGB-1 signaling, results in constitutive dauer formation, which is dependent on the presence of dauer pheromone but independent of diminished food levels or elevated temperatures. Our data suggest that the KGB-1 pathway acts in the sensory neurons, in parallel to established insulin and TGF-β signaling pathways, to transduce the dauer-inducing environmental cues of diminished food levels and elevated temperature.
IL-4i1 Regulation of Immune Protection During Mycobacterium tuberculosis Infection
Authors: Hlaka Lerato , Ozturk Mumin , Chia Julius E , Jones Shelby-Sara , Pillay Shandre , Poswayo Sibongiseni K L , Mpotje Thabo , Nono Justin K , Simelane Simphiwe R N , Parihar Suraj P , Roy Sugata , Suzuki Harukazu , Brombacher Frank , Guler Reto 
Published: November 2021

Abstract

Background
Interleukin 4 (IL-4i1)–induced gene 1 encodes L-phenylalanine oxidase that catabolizes phenylalanine into phenylpyruvate. IL-4i1 is mainly expressed by antigen-presenting cells (APCs), inhibits T-cell proliferation, regulates B-cell activation, modulates T cell responses, and drives macrophage polarization, but its role in bacterial infections is understudied.

Methods
We evaluated IL-4i1 deletion in macrophages and mice on infection with virulent H37Rv and W-Beijing lineage hypervirulent HN878 Mycobacterium tuberculosis (Mtb) strains. The bacterial growth and proinflammatory responses were measured in vitro and in vivo. Histopathological analysis, lung immune cell recruitment, and macrophage activation were assessed at the early and chronic stages of Mtb infection.

Results
IL-4i1–deficient (IL-4i1−/−) mice displayed increased protection against acute H37Rv, HN878 and chronic HN878 Mt infections, with reduced lung bacterial burdens and altered APC responses compared with wild-type mice. Moreover, “M1-like” interstitial macrophage numbers, and nitrite and Interferon-γ production were significantly increased in IL-4i1−/− mice compared with wild-type mice during acute Mtb HN878 infection.

Conclusions
Together, these data suggest that IL-4i1 regulates APC-mediated inflammatory responses during acute and chronic Mtb infection. Hence, IL-4i1 targeting has potential as an immunomodulatory target for host-directed therapy.
Forum: Conflict Delegation in Civil Wars
Authors: Karlén Niklas , Rauta Vladimir , Salehyan Idean , Mumford Andrew , San-Akca Belgin , Stark Alexandra , Wyss Michel , Moghadam Assaf , Duursma Allard , Tamm Henning , Jenne Erin K , Popovic Milos , Siroky David S , Meier Vanessa , Chinchilla Alexandra , Rickard Kit , Spatafora Giuseppe 
Published: November 2021

AbstractThis forum provides an outlet for an assessment of research on the delegation of war to non-state armed groups in civil wars. Given the significant growth of studies concerned with this phenomenon over the last decade, this forum critically engages with the present state of the field. First, we canvass some of the most important theoretical developments to demonstrate the heterogeneity of the debate. Second, we expand on the theme of complexity and investigate its multiple facets as a window into pushing the debate forward. Third, we draw the contours of a future research agenda by highlighting some contemporary problems, puzzles, and challenges to empirical data collection. In essence, we seek to connect two main literatures that have been talking past each other: external support in civil wars and proxy warfare. The forum bridges this gap at a critical juncture in this new and emerging scholarship by offering space for scholarly dialogue across conceptual labels.
Axillary Imaging Following a New Invasive Breast Cancer Diagnosis—A Radiologist’s Dilemma
Authors: Dialani Vandana , Dogan Basak , Dodelzon Katerina , Dontchos Brian N , Modi Neha , Grimm Lars 
Published: November 2021

AbstractTraditionally, patients with newly diagnosed invasive breast cancer underwent axillary US to assess for suspicious axillary lymph nodes (LNs), which were then targeted for image-guided needle biopsy to determine the presence of metastasis. Over the past decade, there has been a shift towards axillary preservation. For patients with palpable lymphadenopathy, the decision to perform axillary imaging with documentation of the number and location of abnormal LNs in preparation for image-guided LN sampling is straightforward. Since LN involvement correlates with cancer size, it is reasonable to image the axilla in patients with tumors larger than 5 cm; however, for tumors smaller than 5 cm, axillary imaging is often deferred until after the tumor molecular subtype and treatment plan are established. Over the last decade, neoadjuvant chemotherapy (NACT) is increasingly used for smaller cancers with more aggressive molecular subtypes. In most cases, detecting axillary metastasis is critical when deciding whether the patient would benefit from NACT. There is increasing evidence that abnormal axillary US findings correlates with LN metastases and reliably establishes a baseline to monitor response to NACT. Depending on hormone receptor status, practices may choose to image the axilla in the setting of clinical stage T1 and T2 cancers to evaluate nodal status and help determine further steps in care. Radiologists should understand the nuances of axillary management and the scope and challenges of LN marking techniques that significantly increase the precision of limited axillary surgery.
Deep carbonate reservoir characterisation using multi-seismic attributes via machine learning with physical constraints
Authors: Chen Yuanyuan , Zhao Luanxiao , Pan Jianguo , Li Chuang , Xu Minghui , Li Kejian , Zhang Fengshou , Geng Jianhua 
Published: November 2021

AbstractSeismic characterisation of deep carbonate reservoirs is of considerable interest for reservoir distribution prediction, reservoir quality evaluation and reservoir structure delineation. However, it is challenging to use the traditional methodology to predict a deep-buried carbonate reservoir because of the highly nonlinear mapping relationship between heterogeneous reservoir features and seismic responses. We propose a machine-learning-based method (random forest) with physical constraints to enhance deep carbonate reservoir prediction performance from multi-seismic attributes. We demonstrate the effectiveness of this method on a real data application in the deep carbonate reservoir of Tarim Basin, Western China. We first perform feature selection on multi-seismic attributes, then four kinds of physical constraint (continuity, boundary, spatial and category constraint) transferred from domain knowledge are imposed on the process of model building. Using the physical constraints, the F1 score of reservoir quality and reservoir type can be significantly improved and the combination of the effective physical constraints gives the best prediction of performance. We also apply the proposed strategy on 2D seismic data to predict the spatial distribution of reservoir quality and type. The seismic prediction results provide a reasonable description of the strong heterogeneity of the reservoir, offering insights into sweet spot detection and reservoir development.
Acoustic wave propagation with new spatial implicit and temporal high-order staggered-grid finite-difference schemes
Authors: Wang Jing , Liu Yang , Zhou Hongyu 
Published: November 2021

AbstractThe implicit staggered-grid (SG) finite-difference (FD) method can obtain significant improvement in spatial accuracy for performing numerical simulations of wave equations. Normally, the second-order central grid FD formulas are used to approximate the temporal derivatives, and a relatively fine time step has to be used to reduce the temporal dispersion. To obtain high accuracy both in space and time, we propose a new spatial implicit and temporal high-order SG FD stencil in the time–space domain by incorporating some additional grid points to the conventional implicit FD one. Instead of attaining the implicit FD coefficients by approximating spatial derivatives only, we calculate the coefficients by approximating the temporal and spatial derivatives simultaneously through matching the dispersion formula of the seismic wave equation and compute the FD coefficients of our new stencil by two schemes. The first one is adopting a variable substitution-based Taylor-series expansion (TE) to derive the FD coefficients, which can attain (2M + 2)th-order spatial accuracy and (2N)th-order temporal accuracy. Note that the dispersion formula of our new stencil is non-linear with respect to the axial and off-axial FD coefficients, it is complicated to obtain the optimal spatial and temporal FD coefficients simultaneously. To tackle the issue, we further develop a linear optimisation strategy by minimising the L2-norm errors of the dispersion formula to further improve the accuracy. Dispersion analysis, stability analysis and modelling examples demonstrate the accuracy, stability and efficiency advantages of our two new schemes.
Observational measures of halo properties beyond mass
Authors: Behroozi Peter , Hearin Andrew , Moster Benjamin P 
Published: November 2021

ABSTRACT
Different properties of dark matter haloes, including growth rate, concentration, interaction history, and spin, correlate with environment in unique, scale-dependent ways. While these halo properties are not directly observable, galaxies will inherit their host haloes’ correlations with environment. In this paper, we show how these characteristic environmental signatures allow using measurements of galaxy environment to constrain which dark matter halo properties are most tightly connected to observable galaxy properties. We show that different halo properties beyond mass imprint distinct scale-dependent signatures in both the galaxy two-point correlation function and the distribution of distances to galaxies’ kth nearest neighbours, with features strong enough to be accessible even with low-resolution (e.g. grism) spectroscopy at higher redshifts. As an application, we compute observed two-point correlation functions for galaxies binned by half-mass radius at $z$ = 0 from the Sloan Digital Sky Survey, showing that classic galaxy size models (i.e. galaxy size being proportional to halo spin) as well as other recent proposals show significant tensions with observational data. We show that the agreement with observed clustering can be improved with a simple empirical model in which galaxy size correlates with halo growth.
Heart function in juvenile idiopathic arthritis patients: A biventricular two-dimensional speckle-tracking echocardiography study
Authors: Lianza Alessandro C , Leal Gabriela N , Aikawa Nádia E , Kozu Katia T , Diniz Maria De Fátima R , Sawamura Karen S S , Menezes Carolina R B , Martins Camila Lino , Campos Lucia M , Elias Adriana M , Silva Clovis A 
Published: November 2021

ABSTRACT

Objectives
We evaluated cardiac function in juvenile idiopathic arthritis (JIA) patients by 2D speckle-tracking echocardiography (2DSTE) and to assess possible associations with clinical, laboratorial, and treatment data.

Methods
A group of 42 JIA patients and 42 healthy controls were evaluated using both conventional echocardiography and 2DSTE. JIA patients underwent clinical and laboratory assessment.

Results
Conventional echocardiography data demonstrated normal left ventricular (LV) ejection fraction in both groups (71 vs. 71%; p = .69). 2DSTE analysis demonstrated that JIA patients presented significantly lower LV global systolic longitudinal strain (LVGLS) (−18.76 vs. −22%; p &lt; .0001), LV systolic strain rate (LVSSR) (1.06 vs. 1.32 s−1; p &lt; .0001), LV diastolic strain rate (LVDSR) (1.58 vs. 1.8 s−1; p &lt; .0137), right ventricular global systolic strain (RVGLS) (−24.1% vs. −27.7%; p = .0002), and right ventricular systolic strain rate (RVSSR) (1.4 vs. 1.8 s−1; p = .0035). JIA patients under biological agents presented higher LVGLS (p = .02) and RVLS (p = .01). We also detected an association between LVGLS and C-reactive protein [CRP; −20% in normal CRP (10/42) vs. −18% in elevated CRP patients (32/42), p = .03].

Conclusions
JIA patients present different echocardiographic status from healthy patients. Moreover, our data suggest that JIA patients under biological agents present association with better cardiac function as shown by strain analysis.
Wound-inducible WUSCHEL-RELATED HOMEOBOX 13 is required for callus growth and organ reconnection
Authors: Ikeuchi Momoko , Iwase Akira , Ito Tasuku , Tanaka Hayato , Favero David S , Kawamura Ayako , Sakamoto Shingo , Wakazaki Mayumi , Tameshige Toshiaki , Fujii Haruki , Hashimoto Naoki , Suzuki Takamasa , Hotta Kazuhiro , Toyooka Kiminori , Mitsuda Nobutaka , Sugimoto Keiko 
Published: November 2021

Abstract
Highly efficient tissue repair is pivotal for surviving damage-associated stress. Plants generate callus upon injury to heal wound sites, yet regulatory mechanisms of tissue repair remain elusive. Here, we identified WUSCHEL-RELATED HOMEOBOX 13 (WOX13) as a key regulator of callus formation and organ adhesion in Arabidopsis (Arabidopsis thaliana). WOX13 belongs to an ancient subclade of the WOX family, and a previous study shows that WOX13 orthologs in the moss Physcomitrium patens (PpWOX13L) are involved in cellular reprogramming at wound sites. We found that the Arabidopsis wox13 mutant is totally defective in establishing organ reconnection upon grafting, suggesting that WOX13 is crucial for tissue repair in seed plants. WOX13 expression rapidly induced upon wounding, which was partly dependent on the activity of an AP2/ERF transcription factor, WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1). WOX13 in turn directly upregulated WIND2 and WIND3 to further promote cellular reprogramming and organ regeneration. We also found that WOX13 orchestrates the transcriptional induction of cell wall-modifying enzyme genes, such as GLYCOSYL HYDROLASE 9Bs, PECTATE LYASE LIKEs and EXPANSINs. Furthermore, the chemical composition of cell wall monosaccharides was markedly different in the wox13 mutant. These data together suggest that WOX13 modifies cell wall properties, which may facilitate efficient callus formation and organ reconnection. Furthermore, we found that PpWOX13L complements the Arabidopsis wox13 mutant, suggesting that the molecular function of WOX13 is partly conserved between mosses and seed plants. This study provides key insights into the conservation and functional diversification of the WOX gene family during land plant evolution.
Mechanical characterization of rose bengal and green light crosslinked collagen scaffolds for regenerative medicine
Authors: Braun Joy , Eckes Stefanie , Kilb Michelle Fiona , Fischer Dirk , Eßbach Claudia , Rommens Pol Maria , Drees Philipp , Schmitz Katja , Nickel Daniela , Ritz Ulrike 
Published: November 2021

Abstract
Collagen is one of the most important biomaterials for tissue engineering approaches. Despite its excellent biocompatibility, it shows the non-negligible disadvantage of poor mechanical stability. Photochemical crosslinking with rose bengal and green light (RGX) is an appropriate method to improve this property. The development of collagen laminates is helpful for further adjustment of the mechanical properties as well as the controlled release of incorporated substances. In this study, we investigate the impact of crosslinking and layering of two different collagen scaffolds on the swelling behavior and mechanical behavior in micro tensile tests to obtain information on its wearing comfort (stiffness, strength and ductility). The mechanical stability of the collagen material after degradation due to cell contact is examined using thickness measurements. There is no linear increase or decrease due to layering homologous laminates. Unexpectedly, a decrease in elongation at break, Young’s modulus and ultimate tensile strength are measured when the untreated monolayer is compared to the crosslinked one. Furthermore, we can detect a connection between stability and cell proliferation. The results show that with variation in number and type of layers, collagen scaffolds with tailored mechanical properties can be produced. Such a multi-layered structure enables the release of biomolecules into inner or outer layers for biomedical applications.