bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the CAM6 Climate Model Using Cloud Observations at McMurdo Station, Antarctica
Authors: Yip Jackson , Diao Minghui , Barone Tyler , Silber Israel , Gettelman Andrew 
Published: August 2021

AbstractA comparative analysis between observational data from McMurdo Station, Antarctica and the Community Atmosphere Model version 6 (CAM6) simulation is performed focusing on cloud characteristics and their thermodynamic conditions. Ka‐band Zenith Radar (KAZR) and High Spectral Resolution Lidar (HSRL) retrievals are used as the basis of cloud fraction and cloud phase identifications. Radiosondes released at 12‐h increments provide atmospheric profiles for evaluating the simulated thermodynamic conditions. Our findings show that the CAM6 simulation consistently overestimates (underestimates) cloud fraction above (below) 3 km in four seasons of a year. Normalized by total in‐cloud samples, ice and mixed phase occurrence frequencies are underestimated and liquid phase frequency is overestimated by the model at cloud fractions above 0.6, while at cloud fractions below 0.6 ice phase frequency is overestimated and liquid‐containing phase frequency is underestimated by the model. The cloud fraction biases are closely associated with concurrent biases in relative humidity (RH), that is, high (low) RH biases above (below) 2 km. Frequencies of correctly simulating ice and liquid‐containing phase increase when the absolute biases of RH decrease. Cloud fraction biases also show a positive correlation with RH biases. Water vapor mixing ratio biases are the primary contributor to RH biases, and hence, likely a key factor controlling the cloud biases. This diagnosis of the evident shortfalls of representations of cloud characteristics in CAM6 simulation at McMurdo Station brings new insight in improving the governing model physics therein.
Crucial Roles of Eastward Propagating Environments in the Summer MCS Initiation Over the U.S. Great Plains
Authors: Song Fengfei , Feng Zhe , Leung L. Ruby , Pokharel Binod , Wang S.‐Y. Simon , Chen Xingchao , Sakaguchi Koichi , Wang Chi‐chia 
Published: August 2021

AbstractThis study aims to further understand the environments supporting summer mesoscale convective system (MCS) initiation in the U.S. Great Plains. A self‐organizing map analysis is conducted to identify four types of summer MCS initiation environments during 2004–2017: Type‐1 and Type‐2 feature favorable large‐scale environments, Type‐3 has favorable lower‐level and surface conditions but unfavorable upper‐level circulation, while Type‐4 features the most unfavorable large‐scale environments. Despite the unfavorable large‐scale environment, convection‐centered composites reveal the presence of favorable sub‐synoptic scale environments for MCS initiation in Type‐3 and Type‐4. All four types of MCS initiation environments delineate clear eastward propagating features in many meteorological fields, such as potential vorticity, surface pressure, and equivalent potential temperature, upstream up to 25° west of and ∼36 h before MCS initiation. While the propagating environments and local, non‐propagating low‐level moisture are important to MCS initiation at the foothill of the Rocky Mountains, MCS initiation in the Great Plains is supported by the coupled dynamical and moisture anomalies, both associated with eastward propagating waves. Hence, MCSs initiated in the plains can produce more rainfall than those initiated at the foothill due to a more abundant moisture supply. By tracking MCSs and mid‐tropospheric perturbations (MPs), a unique type of sub‐synoptic disturbances with Rocky Mountains origin, it is shown that ∼30% of MPs are associated with MCS initiation, mostly in Type‐4. Although MPs are related to a small fraction of MCS initiation, MCSs that are associated with MPs tend to produce more rainfall in a larger area with a stronger convective intensity.
Spontaneous preterm delivery is reflected in both early neonatal and maternal gut microbiota
Authors: Hiltunen Henni , Collado Maria Carmen , Ollila Helena , Kolari Terhi , Tölkkö Satu , Isolauri Erika , Salminen Seppo , Rautava Samuli 
Published: August 2021

AbstractBackgroundAberrant gut microbiota composition in preterm neonates is linked to adverse health consequences. Little is known about the impact of perinatal factors or maternal gut microbiota on initial preterm gut colonization.MethodsFecal samples were collected from 55 preterm neonates (<35 gestational weeks), 51 mothers, and 25 full-term neonates during the first 3–4 postpartum days. Gut microbiota composition was assessed using 16S ribosomal RNA gene sequencing.ResultsPreterm neonates exhibited significantly lower gut microbiota alpha diversity and distinct beta diversity clustering compared to term neonates. Spontaneous preterm birth was associated with distinct initial gut microbiota beta diversity as compared to iatrogenic delivery. Gestational age or delivery mode had no impact on the preterm gut microbiota composition. The cause of preterm delivery was also reflected in the maternal gut microbiota composition. The contribution of maternal gut microbiota to initial preterm gut colonization was more pronounced after spontaneous delivery than iatrogenic delivery and not dependent on delivery mode.ConclusionsThe initial preterm gut microbiota is distinct from term microbiota. Spontaneous preterm birth is reflected in the early neonatal and maternal gut microbiota. Transmission of gut microbes from mother to neonate is determined by spontaneous preterm delivery, but not by mode of birth.ImpactThe initial gut microbiota in preterm neonates is distinct from those born full term. Spontaneous preterm birth is associated with changes in the gut microbiota composition of both preterm neonates and their mothers. The contribution of the maternal gut microbiota to initial neonatal gut colonization was more pronounced after spontaneous preterm delivery as compared to iatrogenic preterm delivery and not dependent on delivery mode.Our study provides new evidence regarding the early gut colonization patterns in preterm infants.Altered preterm gut microbiota has been linked to adverse health consequences and may provide a target for early intervention.
The application of CRISPR/Cas9 system in cervical carcinogenesis
Authors: Gao Chun , Wu Ping , Yu Lan , Liu Liting , Liu Hong , Tan Xiangyu , Wang Liming , Huang Xiaoyuan , Wang Hui 
Published: August 2021

AbstractIntegration of high-risk HPV genomes into cellular chromatin has been confirmed to promote cervical carcinogenesis, with HPV16 being the most prevalent high-risk type. Herein, we evaluated the therapeutic effect of the CRISPR/Cas9 system in cervical carcinogenesis, especially for cervical precancerous lesions. In cervical cancer/pre-cancer cell lines, we transfected the HPV16 E7 targeted CRISPR/Cas9, TALEN, ZFN plasmids, respectively. Compared to previous established ZFN and TALEN systems, CRISPR/Cas9 has shown comparable efficiency and specificity in inhibiting cell growth and colony formation and inducing apoptosis in cervical cancer/pre-cancer cell lines, which seemed to be more pronounced in the S12 cell line derived from the low-grade cervical lesion. Furthermore, in xenograft formation assays, CRISPR/Cas9 inhibited tumor formation of the S12 cell line in vivo and affected the corresponding protein expression. In the K14-HPV16 transgenic mice model of HPV-driven spontaneous cervical carcinogenesis, cervical application of CRISPR/Cas9 treatment caused mutations of the E7 gene and restored the expression of RB, E2F1, and CDK2, thereby reversing the cervical carcinogenesis phenotype. In this study, we have demonstrated that CRISPR/Cas9 targeting HPV16 E7 could effectively revert the HPV-related cervical carcinogenesis in vitro, as well as in K14-HPV16 transgenic mice, which has shown great potential in clinical treatment for cervical precancerous lesions.
Puf6 primes 60S pre-ribosome nuclear export at low temperature
Authors: Gerhardy Stefan , Oborská-Oplová Michaela , Gillet Ludovic , Börner Richard , van Nues Rob , Leitner Alexander , Michel Erich , Petkowski Janusz J. , Granneman Sander , Sigel Roland K. O. , Aebersold Ruedi , Panse Vikram Govind 
Published: August 2021

AbstractProductive ribosomal RNA (rRNA) compaction during ribosome assembly necessitates establishing correct tertiary contacts between distant secondary structure elements. Here, we quantify the response of the yeast proteome to low temperature (LT), a condition where aberrant mis-paired RNA folding intermediates accumulate. We show that, at LT, yeast cells globally boost production of their ribosome assembly machinery. We find that the LT-induced assembly factor, Puf6, binds to the nascent catalytic RNA-rich subunit interface within the 60S pre-ribosome, at a site that eventually loads the nuclear export apparatus. Ensemble Förster resonance energy transfer studies show that Puf6 mimics the role of Mg2+ to usher a unique long-range tertiary contact to compact rRNA. At LT, puf6 mutants accumulate 60S pre-ribosomes in the nucleus, thus unveiling Puf6-mediated rRNA compaction as a critical temperature-regulated rescue mechanism that counters rRNA misfolding to prime export competence.
Salmonella effector SopD promotes plasma membrane scission by inhibiting Rab10
Authors: Boddy Kirsten C. , Zhu Hongxian , D’Costa Vanessa M. , Xu Caishuang , Beyrakhova Ksenia , Cygler Miroslaw , Grinstein Sergio , Coyaud Etienne , Laurent Estelle M. N. , St-Germain Jonathan , Raught Brian , Brumell John H. 
Published: August 2021

AbstractSalmonellautilizes translocated virulence proteins (termed effectors) to promote host cell invasion. The effector SopD contributes to invasion by promoting scission of the plasma membrane, generatingSalmonella-containing vacuoles. SopD is expressed in allSalmonellalineages and plays important roles in animal models of infection, but its host cell targets are unknown. Here we show that SopD can bind to and inhibit the small GTPase Rab10, through a C-terminal GTPase activating protein (GAP) domain. During infection, Rab10 and its effectors MICAL-L1 and EHBP1 are recruited to invasion sites. By inhibiting Rab10, SopD promotes removal of Rab10 and recruitment of Dynamin-2 to drive scission of the plasma membrane. Together, our study uncovers an important role for Rab10 in regulating plasma membrane scission and identifies the mechanism used by a bacterial pathogen to manipulate this function during infection.
Sessile drops in weightlessness: an ideal playground for challenging Young’s equation
Authors: Medale Marc , Brutin David 
Published: August 2021

AbstractSessile drop creation in weightlessness is critical for designing scientific instruments for space applications and for manipulating organic or biological liquids, such as whole human blood or DNA drops. It requires perfect control of injection, spreading, and wetting; however, the simple act of creating a drop on a substrate is more complex than it appears. A new macroscopic model is derived to better understand this related behavior. We find that, for a given set of substrate, liquid, and surrounding gas properties, when the ratio of surface free energies to contact line free energy is on the macroscopic scale, the macroscopic contact angle can vary at static equilibrium over a broad volume range. It can increase or decrease against volume depending on the sign of this ratio up to an asymptotic value. Consequently, our model aims to explore configurations that challenge the faithful representativity of the classical Young’s equation and extends the present understanding of wetting.
Unique chemical parameters and microbial activity lead to increased archaeological preservation at the Roman frontier site of Vindolanda, UK
Authors: Orr C. H. , Williams R. , Halldórsdóttir H. H. , Birley A. , Greene E. , Nelson A. , Ralebitso-Senior T. K. , Taylor G. 
Published: August 2021

AbstractWaterlogged burial conditions impact upon artefact preservation. One major determinant of preservation is presence and behaviour of microorganisms, however, unravelling the mechanisms, especially in waterlogged conditions is challenging. In this study, we analysed elemental composition, bacterial diversity and community structure from excavation trenches at the Roman Site of Vindolanda, Northumberland, UK, using pXRF and 16S rRNA gene amplicon sequencing. Excavation trenches provide information of different occupation periods. The results indicated that microbial communities were dominated by Firmicutes, BacteroidetesandProteobacteriaat a phylum level. Samples which also had visible vivianite presence showed that there were marked increases inMethylophilus.Methylophilusmight be associated with favourable preservation in these anaerobic conditions. More research is needed to clearly link the presence ofMethylophiluswith vivianite production. The study emphasises the need for further integration of chemical and microbiome approaches, especially in good preservation areas, to explore microbial and chemical degradation mechanisms.
Changes in surface water drive the movements of Shoebills
Authors: Acácio Marta , Mullers Ralf H. E. , Franco Aldina M. A. , Willems Frank J. , Amar Arjun 
Published: August 2021

AbstractAnimal movement is mainly determined by spatial and temporal changes in resource availability. For wetland specialists, the seasonal availability of surface water may be a major determinant of their movement patterns. This study is the first to examine the movements of Shoebills (Balaeniceps rex), an iconic and vulnerable bird species. Using GPS transmitters deployed on six immature and one adult Shoebills over a 5-year period, during which four immatures matured into adults, we analyse their home ranges and distances moved in the Bangweulu Wetlands, Zambia. We relate their movements at the start of the rainy season (October to December) to changes in Normalized Difference Water Index (NDWI), a proxy for surface water. We show that Shoebills stay in the Bangweulu Wetlands all year round, moving less than 3 km per day on 81% of days. However, average annual home ranges were large, with high individual variability, but were similar between age classes. Immature and adult Shoebills responded differently to changes in surface water; sites that adults abandoned became drier, while sites abandoned by immatures became wetter. However, there were no differences in NDWI of areas used by Shoebills before abandonment and newly selected sites, suggesting that Shoebills select areas with similar surface water. We hypothesise that the different responses to changes in surface water by immature and adult Shoebills are related to age-specific optimal foraging conditions and fishing techniques. Our study highlights the need to understand the movements of Shoebills throughout their life cycle to design successful conservation actions for this emblematic, yet poorly known, species.
Deciphering the biology of KIR2DL3+ T lymphocytes that are associated to relapse in haploidentical HSCT
Authors: David Gaëlle , Willem Catherine , Legrand Nolwenn , Djaoud Zakia , Mérieau Pierre , Walencik Alexandre , Guillaume Thierry , Gagne Katia , Chevallier Patrice , Retière Christelle 
Published: August 2021

AbstractKIR are mainly expressed on NK cells and to a lesser extent on T lymphocytes. Although the KIR NK cell repertoire was well explored in haploidentical Hematopoietic Stem Cell Transplantation (HSCT), KIR T cell compartment remains to be investigated in this context. In this study, the investigation of NK receptors on T lymphocytes during immune reconstitution after T-cell-replete haploidentical HSCT with Post-Transplant Cyclophosphamide (PTCy) has shown a significant increase of KIR2DL2/3+T cell frequency at day 25. This was especially observed at day 30 in recipients who relapsed. IL-15 but not IL-12 increased in vitro KIR+T cell expansion suggesting that the raised IL-15 serum concentration observed after PTCy in haploidentical HSCT might increase KIR+T cell frequency. Moreover, investigations from healthy blood donors showed a higher inhibiting effect of KIR2DL3 on CMV specific T cell response against allogeneic than autologous C1+target cells. The association of KIR+T cell subset with relapse may suggest that inhibitory KIR2DL2/3 limit anti-leukemic effect of specific T lymphocytes at this early step of immune reconstitution. Further phenotypic and mechanistic investigations on this cell subset from a broader cohort of HSCT recipients should clarify its potential implication in relapse occurrence. Our results demonstrate that KIR-HLA interactions known to modulate NK cell functions also modulate T cell immune responses in the context of allogeneic HSCT.
Deep learning for pulmonary embolism detection on computed tomography pulmonary angiogram: a systematic review and meta-analysis
Authors: Soffer Shelly , Klang Eyal , Shimon Orit , Barash Yiftach , Cahan Noa , Greenspana Hayit , Konen Eli 
Published: August 2021

AbstractComputed tomographic pulmonary angiography (CTPA) is the gold standard for pulmonary embolism (PE) diagnosis. However, this diagnosis is susceptible to misdiagnosis. In this study, we aimed to perform a systematic review of current literature applying deep learning for the diagnosis of PE on CTPA. MEDLINE/PUBMED were searched for studies that reported on the accuracy of deep learning algorithms for PE on CTPA. The risk of bias was evaluated using the QUADAS-2 tool. Pooled sensitivity and specificity were calculated. Summary receiver operating characteristic curves were plotted. Seven studies met our inclusion criteria. A total of 36,847 CTPA studies were analyzed. All studies were retrospective. Five studies provided enough data to calculate summary estimates. The pooled sensitivity and specificity for PE detection were 0.88 (95% CI 0.803–0.927) and 0.86 (95% CI 0.756–0.924), respectively. Most studies had a high risk of bias. Our study suggests that deep learning models can detect PE on CTPA with satisfactory sensitivity and an acceptable number of false positive cases. Yet, these are only preliminary retrospective works, indicating the need for future research to determine the clinical impact of automated PE detection on patient care. Deep learning models are gradually being implemented in hospital systems, and it is important to understand the strengths and limitations of these algorithms.
Genome-wide association studies for production, respiratory disease, and immune-related traits in Landrace pigs
Authors: Uemoto Yoshinobu , Ichinoseki Kasumi , Matsumoto Toshimi , Oka Nozomi , Takamori Hironori , Kadowaki Hiroshi , Kojima-Shibata Chihiro , Suzuki Eisaku , Okamura Toshihiro , Aso Hisashi , Kitazawa Haruki , Satoh Masahiro , Uenishi Hirohide , Suzuki Keiichi 
Published: August 2021

AbstractIdentification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits.
Comparison of corneal irregular astigmatism by the type of corneal regular astigmatism
Authors: Ueno Yuta , Nomura Risa , Hiraoka Takahiro , Kinoshita Katsuhito , Ohara Mutsuko , Oshika Tetsuro 
Published: August 2021

AbstractWe investigated the relation between corneal regular and irregular astigmatism in normal human eyes. In 951 eyes of 951 patients, corneal irregular astigmatism, such as asymmetry and higher-order irregularity components, was calculated using the Fourier harmonic analysis of corneal topography data within the central 3-mm zone of the anterior corneal surface. The eyes were classified by the type of corneal regular astigmatism into four groups; minimum (< 0.75 diopters), with-the-rule (WTR), against-the-rule (ATR), and oblique astigmatism. The mean age was significantly different among the four groups (P < 0.001); patients with WTR astigmatism were the youngest, followed by those with minimum, oblique, and ATR astigmatism. Significant inter-group differences were found among the four groups in asymmetry (P = 0.005) and higher-order irregularity components (P < 0.001); the largest was in eyes with oblique astigmatism, followed by ATR, WTR, and minimum astigmatism. The stepwise multiple regression analysis revealed that corneal regular astigmatism pattern significantly influenced the amount of corneal irregular astigmatism after controlling for confounding factors (P < 0.001). Corneal irregular astigmatism, such as asymmetry and higher order irregularity components, was the largest in eyes with oblique astigmatism, followed by those with ATR, WTR, and minimum astigmatism, even after adjustment for age of subjects.
Magnetic single atom catalyst in C2N to induce adsorption selectivity toward oxidizing gases
Authors: Mushtaq Muhammad , Tit Nacir 
Published: August 2021

AbstractDensity functional theory (DFT) method is used to study the effect of single-atom catalyst (SAC) of Mn embedded in C2N nanoribbon (C2N-NR) on the adsorption properties as an attempt to achieve selectivity. Many gases (e.g., CO, CO2, H2, H2O, H2S, N2 and O2) of interest to energy and environmental applications were tested. The results show that SAC-Mn alters chemisorption processes with all gas molecules except N2. Clear adsorption selectivity is obtained towards oxidizing CO, CO2 and O2 molecules as evidenced by the enhancements in binding energy and charge transfer and the reduction in magnetization. While the SAC-Mn contributes predominantly to Fermi-energy region with spin-down states, the strong binding to oxidizing molecules introduces there more spin-up states to compromise and reduce the magnetization. Hence, C2N-NR:Mn is proposed to be used as platform for gas sensor (if combined with magnetic sensor) to yield high selectivity toward these latter gases.
Efficient Ohmic contacts and built-in atomic sublayer protection in MoSi2N4 and WSi2N4 monolayers
Authors: Wang Qianqian , Cao Liemao , Liang Shi-Jun , Wu Weikang , Wang Guangzhao , Lee Ching Hua , Ong Wee Liat , Yang Hui Ying , Ang Lay Kee , Yang Shengyuan A. , Ang Yee Sin 
Published: August 2021

AbstractMetal contacts to two-dimensional (2D) semiconductors are often plagued by the strong Fermi level pinning (FLP) effect which reduces the tunability of the Schottky barrier height (SBH) and degrades the performance of 2D semiconductor devices. Here, we show that MoSi2N4 and WSi2N4 monolayers—an emerging 2D semiconductor family with exceptional physical properties—exhibit strongly suppressed FLP and wide-range tunable SBH. An exceptionally large SBH slope parameter of S ≈ 0.7 is obtained which outperforms the vast majority of other 2D semiconductors. Such intriguing behavior arises from the septuple-layered morphology of MoSi2N4 and WSi2N4 monolayers in which the semiconducting electronic states are protected by the outlying Si–N sublayer. We identify Ti, Sc, and Ni as highly efficient Ohmic contacts to MoSi2N4 and WSi2N4 with zero interface tunneling barrier. Our findings reveal the potential of MoSi2N4 and WSi2N4 as a practical platform for designing high-performance and energy-efficient 2D semiconductor electronic devices.