bluuebunny/crossref_metadata_2025_split huggingface dataset:
Size doesn’t matter shape does: A morphological study of pitcher plant in distinct forest canopy structures
Authors: Harapan T S , Ikhwan A , Amolia R R , Zulaspita W , Ferbriamansyah T A , Bibas E , Sakdiah H T , Diniyati F , Mutashim M , Chairul C , Taufiq A , Nurainas N 
Published: February 2022

Abstract
Light exposure from the sun is the most crucial variable for producing optimal pitcher size and colour variation in Nepenthes. This study aimed to observe the effect of forest canopy structure on morphological character of Nepenthes ampullaria’s pitcher parts (longitudinal, front, and peristome) both on size and shape using Geometric morphometric (GM) approach and its prey diversity. We classified the forest canopy structure into two categories: inside the canopy and open space area (gap). We used Unmanned Aerial Vehicle (UAV) images to build Canopy Height Model (CHM). Then, ForestGapR R package used to analyse and generated the forest gaps area. The prey specimens and photograph samples comprised from 9 individuals with three lower pitchers in open space area with high light exposure as well as shaded area inside the canopy. Total of 54 images were marked by point and curve to generated a landmark analysis using GeoMorph R package. Based on GM analysis, we observed that the forest canopy structure could affect Nepenthes pitcher shape but not in pitcher size. Our field result revealed Nepenthes ampullaria likely dominated by darker colour with a red spot in the shaded area and bright green colour in the open. However, based on our study the pitcher in shaded area inside the canopy have a larger number of prey species than the open area.
Analysis of the mechanical properties and microstructure of titanium surfaces designed by electromagnetic induction nitriding
Authors: Guan Jing , Xiang Qing , Zhang Xiuhua , Liu Jing , Yang Feng 
Published: February 2022

Abstract
Nitride has high hardness and excellent wear resistance. It is frequently prepared on a material surface to improve material performance. The nitriding layer can be prepared in different ways, so the bonding strength and microstructure between the nitriding layer and the matrix differ, which will directly affect the surface mechanical properties of the material. In this study, pure titanium (TA1) was nitrided using electromagnetic induction nitriding, and the microstructure of nitriding layer was analysed using x-ray photoelectron spectroscopy (XPS), scanning electron microscopy-electron backscatter diffraction (SEM-EBSD) and scanning electron microscopy-energy-dispersive x-ray spectroscopy (SEM-EDS). In addition, the mechanical properties of the nitriding layer were studied using a nanoindentation and scratch tester. The experimental result shows a 20 μm induction nitriding layer composed of TiN, Ti2N and α(N)-Ti. The compound layer (Ti2N and TiN) was approximately 3 μm. The surface was contaminated with C and O elements, and evident segregation bands were found between the induction nitriding layer and matrix. The induction nitriding layer can considerably improve the wear resistance of titanium alloy, but the bonding force between the induction nitriding layer and matrix decreases owing to the segregation band.
Numerical study of the effect of coflow argon jet on a laminar argon thermal plasma jet
Authors: ZHOU Xu , CHEN Xianhui , YE Taohong , ZHU Minming , XIA Weidong 
Published: February 2022

Abstract
The effects of the velocity and width in coflow argon jet inlet on the flow characteristics of laminar argon thermal plasma jet flowing into the cold air have been studied by the large eddy simulation methods. The Kelvin–Helmholtz instability between argon thermal plasma jet and coflow argon jet causes the transition from a laminar jet to a turbulent jet in the presence of coflow argon jet. Moreover, increasing the velocity and width in coflow argon jet inlet can enhance turbulent transport and provoke coherent structure in the downstream of thermal plasma jet. And the mixing characteristics between argon thermal plasma, coflow argon and ambient air are strengthened. In addition, the width in coflow argon jet inlet has a significant effect on the distribution of temperature in the upstream of thermal plasma jet. It was also found that the transition occurs in advance with the increase of velocity and width in coflow argon jet inlet.
Contrasting impacts of net cloud radiative forcing on the surface temperature trends in India
Authors: Banerjee Ayan Kumar , Dutta Soumi , Dey Sagnik 
Published: February 2022

Abstract
The rise of spatial heterogeneity in surface temperature (T

s
) over India cannot be explained by only the direct effect of enhanced greenhouse gas forcing. Here we propose an analytical framework to estimate the impact of the net cloud radiative forcing (CRF) trend on the observed T

s
trend for the duration of 2000–2019. The cloud sensitivity (

λ

c
l
d

) estimated from the satellite observations vary in the range −0.180 to 0.241 K per W m−2 across the seven T

s
homogeneous zones in India. Net average (±1σ) CRFs over the Indian landmass during 2000–2019 in the shortwave and longwave are −15.5 ±11.3 and 12.4 ± 7.4 W m−2, −28.1 ± 22.4 and 24.6 ± 9.8 W m−2, −75.1 ± 20.4 and 55.0 ± 13.8 W m−2 and −23.3 ± 14.9 and 21.6 ± 14.8 W m−2, respectively for the winter (Dec-Feb), pre-monsoon (Mar–May), monsoon (Jun–Sep) and post-monsoon (Oct–Nov) seasons. We find that in some of the T

s
homogeneous regions, seasonal T

s
trends are suppressed, whereas in some other T

s
homogeneous regions, seasonal T

s
trends are accelerated by the net CRF. Our framework can be useful in studying the role of clouds in observed surface warming trends.
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
Authors: Heinken Almut , Thiele Ines 
Published: February 2022

Abstract

Motivation
Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations.

Results
We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.

Availability and implementation
Microbiome Modelling Toolbox and tutorials are freely available as part of the COBRA Toolbox at https://git.io/microbiomeModelingToolbox.
SIRT1 plays an important role in implantation and decidualization during mouse early pregnancy
Authors: Hwang Yeon Jeong , Sung Gi-Jun , Marquardt Ryan , Young Steven L , Lessey Bruce A , Kim Tae Hoon , Cheon Yong-Pil , Jeong Jae-Wook 
Published: February 2022

Abstract
Sirtuin 1 (SIRT1) is a member of the sirtuin family that functions to deacetylate both histones and non-histone proteins. Previous studies have identified significant SIRT1 upregulation in eutopic endometrium from infertile women with endometriosis. However, SIRT1 function in the uterus has not been directly studied. Using immunochemistry analysis, we found SIRT1 to be most strongly expressed at GD4.5 and GD5.5 in decidualized cells and at GD7.5 in secondary decidual cells in mouse. To assess the role of SIRT1 in uterine function, we generated uterine Sirt1 conditional knockout mice (Pgrcre/+Sirt1f/f; Sirt1d/d). A 6-month fertility trial revealed that Sirt1d/d females were subfertile. Implantation site numbers were significantly decreased in Sirt1d/d mice compared with controls at GD5.5. Sirt1d/d implantation sites at GD4.5 could be divided into two groups, Group #1 with luminal closure and nonspecific COX2 expression compared with controls (14/20) and Group #2 with an open lumen and no COX2 (6/20). In Sirt1d/d Group #1, nuclear FOXO1 expression in luminal epithelial cells was significantly decreased. In Sirt1d/d Group #2, nuclear FOXO1 expression was almost completely absent, and there was strong PGR expression in epithelial cells. At GD5.5, stromal PGR and COX2 were significantly decreased in Sirt1d/d uterine in the areas surrounding the embryo compared with controls, indicating defective decidualization. An artificially induced decidualization test revealed that Sirt1d/d females showed defects in decidualization response. All together, these data suggest that SIRT1 is important for decidualization and contributes to preparing a receptive endometrium for successful implantation.
Effects of progesterone and interferon tau on ovine endometrial phosphate, calcium, and vitamin D signaling
Authors: Stenhouse Claire , Halloran Katherine M , Moses Robyn M , Seo Heewon , Gaddy Dana , Johnson Gregory A , Wu Guoyao , Suva Larry J , Bazer Fuller W 
Published: February 2022

Abstract
Given recent reports of expression of postnatal mineral transport regulators at the maternal–conceptus interface during the peri-implantation period, this study tested the hypothesis that progesterone (P4) and interferon tau (IFNT) regulate phosphate, calcium, and vitamin D signaling in the ovine endometrium. Mature Rambouillet ewes (n = 24) were surgically fitted with intrauterine catheters on day 7 of the estrous cycle. Ewes received daily intramuscular injections of 50 mg of P4 in corn oil vehicle and 75 mg of progesterone receptor antagonist (RU486) in corn oil from days 8 to 15, and twice-daily intrauterine injections of either control proteins (CX) or IFNT (25 μg/uterine horn/day) from days 11 to 15 resulting in four treatment groups: P4 + CX; P4 + IFNT; RU486 + P4 + CX; and RU486 + P4 + IFNT. On day 16, ewes were hysterectomized. RU486 + P4 + CX treated ewes had lower concentrations of 25 (OH) D in plasma than P4 + CX treated ewes (P &lt; 0.05). Endometria from ewes treated with IFNT had greater expression of FGF23 (P &lt; 0.01), S100A9 (P &lt; 0.05), and S100A12 (P = 0.05) mRNAs and lower expression of ADAM10 mRNA (P &lt; 0.01) than of ewes treated with CX proteins. Expression of FGF23 mRNA was greater in endometria of ewes that received RU486 + P4 + IFNT than in ewes that received RU486 + P4 + CX (hormone × protein interaction, P &lt; 0.05). The expression of S100G mRNA was greater in endometria of ewes that received P4 + IFNT compared to ewes that received RU486 + P4 + IFNT (P &lt; 0.05; hormone × protein interaction, P &lt; 0.01). These data implicate P4 and IFNT in the regulation of phosphate, calcium, and vitamin D signaling during the peri-implantation period of pregnancy and provide a platform for continued mechanistic investigations.
Chemokine C-X-C receptor 4 mediates recruitment of bone marrow-derived nonhematopoietic and immune cells to the pregnant uterus
Authors: Fang Yuan-Yuan , Lyu Fang , Abuwala Nafeesa , Tal Aya , Chen Alice Y , Taylor Hugh S , Tal Reshef 
Published: February 2022

Abstract
Bone marrow-derived progenitor cells (BMDPCs) are mobilized to the circulation in pregnancy and get recruited to the pregnant decidua where they contribute functionally to decidualization and successful implantation. However, the molecular mechanisms underlying BMDPCs recruitment to the decidua are unknown. CXCL12 ligand and its CXCR4 receptor play crucial roles in the mobilization and homing of stem/progenitor cells to various tissues. To investigate the role of CXCL12–CXCR4 axis in BMDPCs recruitment to decidua, we created transgenic GFP mice harboring CXCR4 gene susceptible to tamoxifen-inducible Cre-mediated ablation. These mice served as BM donors into wild-type C57BL/6 J female recipients using a 5-fluorouracil-based nongonadotoxic submyeloablation to achieve BM-specific CXCR4 knockout (CXCR4KO). Successful CXCR4 ablation was confirmed by RT-PCR and in vitro cell migration assays. Flow cytometry and immunohistochemistry showed a significant increase in GFP+ BM-derived cells (BMDCs) in the implantation site as compared to the nonpregnant uterus of control (2.7-fold) and CXCR4KO (1.8-fold) mice. This increase was uterus-specific and was not observed in other organs. This pregnancy-induced increase occurred in both hematopoietic (CD45+) and nonhematopoietic (CD45–) uterine BMDCs in control mice. In contrast, in CXCR4KO mice there was no increase in nonhematopoietic BMDCs in the pregnant uterus. Moreover, decidual recruitment of myeloid cells but not NK cells was diminished by BM CXCR4 deletion. Immunofluorescence showed the presence of nonhematopoietic GFP+ cells that were negative for CD45 (panleukocyte) and DBA (NK) markers in control but not CXCR4KO decidua. In conclusion, we report that CXCR4 expression in nonhematopoietic BMDPCs is essential for their recruitment to the pregnant decidua.
Prostaglandin E2 receptor 3 promotes M1 macrophages polarization in unexplained recurrent pregnancy loss
Authors: Ye Yao , Peng Lin , Chelariu-Raicu Anca , Kuhn Christina , Dong Xi , Jeschke Udo , von Schönfeldt Viktoria 
Published: February 2022

Abstract
Unexplained recurrent pregnancy loss (uRPL) is associated with macrophage polarization, which can be modulated by prostaglandin E2 (PGE2). Our previous study demonstrated that PGE2 receptor 3 (EP3) signaling is induced in the first-trimester placentas of uRPL patients compared with its expression in healthy controls. However, whether EP3 plays a role in macrophage polarization at the maternal-fetal interface of uRPL women remains unknown. The positive expression of EP3 in decidual macrophages was confirmed by double immunofluorescence staining in the first-trimester placentas collected from uRPL patients and healthy controls. Antibodies CD68, iNOS, and CD163 were used as immunofluorescence marker for decidual macrophages, M1, and M2 macrophages. To clarify the effects of EP3 on macrophage polarization, THP-1 monocyte cells were applied as M0 macrophages after phorbol 12-myristate 13-acetate (PMA) treatment for in vitro study. The mRNA levels of representative M1 markers (interleukin-1β and interleukin-6) and M2 markers (interleukin-10 and arginase-1) were quantified with qPCR in M0 macrophages being stimulated with sulprostone (an EP3 agonist) or L-798,106 (an EP3 antagonist). We found that EP3 expression was upregulated in the decidual macrophages of first-trimester placentas from uRPL patients compared with healthy controls. Furthermore, EP3 expression was increased in M1 macrophages compared with that in M2 macrophages in first-trimester placentas of uRPL patients. Sulprostone intensified the mRNA levels of IL-6 together with interferon-γ, whereas L-798,106 stimulated the mRNA expression of IL-10 and Arg-1 in a dose-dependent manner.
ActivatingRAC1variants in the switch II region cause a developmental syndrome and alter neuronal morphology
Authors: Banka Siddharth , Bennington Abigail , Baker Martin J , Rijckmans Ellen , Clemente Giuliana D , Ansor Nurhuda Mohamad , Sito Hilary , Prasad Pritha , Anyane-Yeboa Kwame , Badalato Lauren , Dimitrov Boyan , Fitzpatrick David , Hurst Anna C E , Jansen Anna C , Kelly Melissa A , Krantz Ian , Rieubland Claudine , Ross Meredith , Rudy Natasha L , Sanz Javier , Stouffs Katrien , Xu Zhuo Luan , Malliri Angeliki , Kazanietz Marcelo G , Millard Tom H 
Published: February 2022

AbstractRAC1 is a highly conserved Rho GTPase critical for many cellular and developmental processes. De novo missense RAC1 variants cause a highly variable neurodevelopmental disorder. Some of these variants have previously been shown to have a dominant negative effect. Most previously reported patients with this disorder have either severe microcephaly or severe macrocephaly.Here, we describe eight patients with pathogenic missense RAC1 variants affecting residues between Q61 and R68 within the switch II region of RAC1. These patients display variable combinations of developmental delay, intellectual disability, brain anomalies such as polymicrogyria and cardiovascular defects with normocephaly or relatively milder micro- or macrocephaly. Pulldown assays, NIH3T3 fibroblast spreading assays and staining for activated PAK1/2/3 and WAVE2 suggest that these variants increase RAC1 activity and over-activate downstream signalling targets. Axons of neurons isolated from Drosophila embryos expressing the most common of the activating variants are significantly shorter, with an increased density of filopodial protrusions. In vivo, these embryos exhibit frequent defects in axonal organization. Class IV dendritic arborization neurons expressing this variant exhibit a significant reduction in the total area of the dendritic arbour, increased branching and failure of self-avoidance. RNAi knock down of the WAVE regulatory complex component Cyfip significantly rescues these morphological defects.These results establish that activating substitutions affecting residues Q61–R68 within the switch II region of RAC1 cause a developmental syndrome. Our findings reveal that these variants cause altered downstream signalling, resulting in abnormal neuronal morphology and reveal the WAVE regulatory complex/Arp2/3 pathway as a possible therapeutic target for activating RAC1 variants. These insights also have the potential to inform the mechanism and therapy for other disorders caused by variants in genes encoding other Rho GTPases, their regulators and downstream effectors.
Controversy over the temporal cortical terminations of the left arcuate fasciculus: a reappraisal
Authors: Giampiccolo Davide , Duffau Hugues 
Published: February 2022

Abstract
The arcuate fasciculus has been considered a major dorsal fronto-temporal white matter pathway linking frontal language production regions with auditory perception in the superior temporal gyrus, the so-called Wernicke’s area. In line with this tradition, both historical and contemporary models of language function have assigned primacy to superior temporal projections of the arcuate fasciculus. However, classical anatomical descriptions and emerging behavioural data are at odds with this assumption. On one hand, fronto-temporal projections to Wernicke’s area may not be unique to the arcuate fasciculus. On the other hand, dorsal stream language deficits have been reported also for damage to middle, inferior and basal temporal gyri that may be linked to arcuate disconnection. These findings point to a reappraisal of arcuate projections in the temporal lobe. Here, we review anatomical and functional evidence regarding the temporal cortical terminations of the left arcuate fasciculus by incorporating dissection and tractography findings with stimulation data using cortico–cortical evoked potentials and direct electrical stimulation mapping in awake patients. First, we discuss the fibres of the arcuate fasciculus projecting to the superior temporal gyrus and the functional rostro-caudal gradient in this region where both phonological encoding and auditory-motor transformation may be performed. Caudal regions within the temporoparietal junction may be involved in articulation and associated with temporoparietal projections of the third branch of the superior longitudinal fasciculus, while more rostral regions may support encoding of acoustic phonetic features, supported by arcuate fibres. We then move to examine clinical data showing that multimodal phonological encoding is facilitated by projections of the arcuate fasciculus to superior, but also middle, inferior and basal temporal regions. Hence, we discuss how projections of the arcuate fasciculus may contribute to acoustic (middle-posterior superior and middle temporal gyri), visual (posterior inferior temporal/fusiform gyri comprising the visual word form area) and lexical (anterior-middle inferior temporal/fusiform gyri in the basal temporal language area) information in the temporal lobe to be processed, encoded and translated into a dorsal phonological route to the frontal lobe. Finally, we point out surgical implications for this model in terms of the prediction and avoidance of neurological deficit.
SR-A neutralizing antibody: potential drug candidate for ameliorating osteoclastogenesis in rheumatoid arthritis
Authors: Xie Yang , Jiang Xiang , Wang Ping , Zheng Xi , Song Jing , Bai Mingxin , Tang Yundi , Fang Xiangyu , Jia Yuan , Li Zhanguo , Hu Fanlei 
Published: February 2022

Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by proliferative synovitis with deterioration of cartilage and bone. Osteoclasts (OCs) are the active participants in the bone destruction of RA. Although with great advances, most current therapeutic strategies for RA have limited effects on bone destruction. Macrophage scavenger receptor A (SR-A) is a class of pattern recognition receptors (PRRs) involved in bone metabolism and OC differentiation. More recently, our study revealed the critical role of SR-A in RA diagnosis and pathogenesis. Here, we further demonstrated that serum SR-A levels were positively correlated with bone destruction in patients with RA. Anti-SR-A neutralizing antibodies significantly inhibited OC differentiation and bone absorption in vitro in patients with RA, but not in healthy individuals, dampening the expression of OC-specific genes such as tartrate-resistant acid phosphatase (TRAP), cathepsin K (CTSK), and matrix metalloproteinase-9 (MMP-9). Similar results were also seen in collagen-induced arthritis (CIA) mice in vitro. Moreover, the anti-SR-A neutralizing antibody could further ameliorate osteoclastogenesis in vivo and ex vivo in CIA mice, accompanied by decreased serum levels of C-terminal telopeptide and IL-6, exhibiting potential protective effects. These results suggest that blockade of SR-A using anti-SR-A neutralizing antibodies might provide a promising therapeutic strategy for bone destruction in the RA.
Differential expression of insulin-like growth factor type 1 receptor identifies heterogeneous intrahepatic regulatory T subsets in mouse hepatocellular carcinoma
Authors: Huang Yabing , Huang Ling , Zhu Jiling , Wu Yin , Shi Jinzhi , Dai Kai 
Published: February 2022

Abstract
Understanding regulatory T-cell (Treg)-mediated tumor tolerance is critical for designing immunotherapy against hepatocellular carcinoma (HCC). In this study, we characterized the expression of insulin-like growth factor type 1 receptor (IGF1R) in intrahepatic Tregs in a chemical-induced mouse HCC model. We found two intrahepatic Treg subsets with differential IGF1R expression: IGF1Rhi Tregs and IGF1Rlo/– Tregs. Functional assays indicated that compared with IGF1Rlo/– Tregs, IGF1Rhi Tregs produced more TGF-β and IL-10 and were more proliferative in vivo. Furthermore, IGF1Rhi Tregs exhibited higher phosphorylation of the mammalian target of the rapamycin complex 1 (mTORC1) in vivo. However, in vitro stimulation and immunosuppression assay revealed that the immunosuppressive capacity of the two Treg subsets was equivalent, as evidenced by comparable cytokine production and immunosuppressive effect over conventional T cells. The transcriptome sequencing analysis revealed up-regulation of genes that encode proteins essential for glycolysis, oxidative phosphorylation, and electron transport chain in IGF1Rhi Tregs. Consistently, IGF1Rhi Tregs produces more adenosine triphosphate (ATP), lactate, and reactive oxygen species (ROS). Furthermore, malignant cells in the tumor nodules induced IGF1R down-regulation in Tregs at the mRNA level. In summary, we identified the heterogeneity of intrahepatic Tregs in HCC which might play significant roles in tumor immunity.