bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paeniclostridium sordellii hemorrhagic toxin targets TMPRSS2 to induce colonic epithelial lesions
Authors: Li Xingxing , He Liuqing , Luo Jianhua , Zheng Yangling , Zhou Yao , Li Danyang , Zhang Yuanyuan , Pan Zhenrui , Li Yanyan , Tao Liang 
Published: July 2022

AbstractHemorrhagic toxin (TcsH) is an important exotoxin produced by Paeniclostridium sordellii, but the exact role of TcsH in the pathogenesis remains unclear, partly due to the lack of knowledge of host receptor(s). Here, we carried out two genome-wide CRISPR/Cas9 screens parallelly with TcsH and identified cell surface fucosylation and TMPRSS2 as host factors contributing to the binding and entry of TcsH. Genetic deletion of either fucosylation biosynthesis enzymes or TMPRSS2 in the cells confers resistance to TcsH intoxication. Interestingly, TMPRSS2 and fucosylated glycans can mediate the binding/entry of TcsH independently, thus serving as redundant receptors. Both TMPRSS2 and fucosylation recognize TcsH through its CROPs domain. By using Tmprss2‒/‒ mice, we show that Tmprss2 is important for TcsH-induced systematic toxicity and colonic epithelial lesions. These findings reveal the importance of TMPRSS2 and surface fucosylation in TcsH actions and further provide insights into host recognition mechanisms for large clostridial toxins.
Notch, RORC and IL-23 signals cooperate to promote multi-lineage human innate lymphoid cell differentiation
Authors: Croft Carys A. , Thaller Anna , Marie Solenne , Doisne Jean-Marc , Surace Laura , Yang Rui , Puel Anne , Bustamante Jacinta , Casanova Jean-Laurent , Di Santo James P. 
Published: July 2022

AbstractInnate lymphoid cells (ILCs) include cytotoxic natural killer cells and distinct groups of cytokine-producing innate helper cells which participate in immune defense and promote tissue homeostasis. Circulating human ILC precursors (ILCP) able to generate all canonical ILC subsets via multi-potent or uni-potent intermediates according to our previous work. Here we show potential cooperative roles for the Notch and IL-23 signaling pathways for human ILC differentiation from blood ILCP using single cell cloning analyses and validate these findings in patient samples with rare genetic deficiencies in IL12RB1 and RORC. Mechanistically, Notch signaling promotes upregulation of the transcription factor RORC, enabling acquisition of Group 1 (IFN-γ) and Group 3 (IL-17A, IL-22) effector functions in multi-potent and uni-potent ILCP. Interfering with RORC or signaling through its target IL-23R compromises ILC3 effector functions but also generally suppresses ILC production from multi-potent ILCP. Our results identify a Notch->RORC- > IL-23R pathway which operates during human ILC differentiation. These observations may help guide protocols to expand functional ILC subsets in vitro with an aim towards novel ILC therapies for human disease.
Evaporation of microwave-shielded polar molecules to quantum degeneracy
Authors: Schindewolf Andreas , Bause Roman , Chen Xing-Yan , Duda Marcel , Karman Tijs , Bloch Immanuel , Luo Xin-Yu 
Published: July 2022

AbstractUltracold polar molecules offer strong electric dipole moments and rich internal structure, which makes them ideal building blocks to explore exotic quantum matter1–9, implement quantum information schemes10–12 and test the fundamental symmetries of nature13. Realizing their full potential requires cooling interacting molecular gases deeply into the quantum-degenerate regime. However, the intrinsically unstable collisions between molecules at short range have so far prevented direct cooling through elastic collisions to quantum degeneracy in three dimensions. Here we demonstrate evaporative cooling of a three-dimensional gas of fermionic sodium–potassium molecules to well below the Fermi temperature using microwave shielding. The molecules are protected from reaching short range with a repulsive barrier engineered by coupling rotational states with a blue-detuned circularly polarized microwave. The microwave dressing induces strong tunable dipolar interactions between the molecules, leading to high elastic collision rates that can exceed the inelastic ones by at least a factor of 460. This large elastic-to-inelastic collision ratio allows us to cool the molecular gas to 21 nanokelvin, corresponding to 0.36 times the Fermi temperature. Such cold and dense samples of polar molecules open the path to the exploration of many-body phenomena with strong dipolar interactions.
Discovery, structure and mechanism of a tetraether lipid synthase
Authors: Lloyd Cody T. , Iwig David F. , Wang Bo , Cossu Matteo , Metcalf William W. , Boal Amie K. , Booker Squire J. 
Published: July 2022

AbstractArchaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values1–5. In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon–carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon–carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)1,2. GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp3-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids6. Structures of the enzyme show the presence of four metallocofactors: three [Fe4S4] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp3–Csp3 bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [Fe4S4] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices7–10.
NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data
Authors: Tan Yuan-De , Guda Chittibabu 
Published: July 2022

AbstractRapid development of transcriptome sequencing technologies has resulted in a data revolution and emergence of new approaches to study transcriptomic regulation such as alternative splicing, alternative polyadenylation, CRISPR knockout screening in addition to the regular gene expression. A full characterization of the transcriptional landscape of different groups of cells or tissues holds enormous potential for both basic science as well as clinical applications. Although many methods have been developed in the realm of differential gene expression analysis, they all geared towards a particular type of sequencing data and failed to perform well when applied in different types of transcriptomic data. To fill this gap, we offer a negative beta binomial t-test (NBBt-test). NBBt-test provides multiple functions to perform differential analyses of alternative splicing, polyadenylation, CRISPR knockout screening, and gene expression datasets. Both real and large-scale simulation data show superior performance of NBBt-test with higher efficiency, and lower type I error rate and FDR to identify differential isoforms and differentially expressed genes and differential CRISPR knockout screening genes with different sample sizes when compared against the current very popular statistical methods. An R-package implementing NBBt-test is available for downloading from CRAN (https://CRAN.R-project.org/package=NBBttest).
Magnetic field mapping of inaccessible regions using physics-informed neural networks
Authors: Coskun Umit H. , Sel Bilgehan , Plaster Brad 
Published: July 2022

AbstractA difficult problem concerns the determination of magnetic field components within an experimentally inaccessible region when direct field measurements are not feasible. In this paper, we propose a new method of accessing magnetic field components using non-disruptive magnetic field measurements on a surface enclosing the experimental region. Magnetic field components in the experimental region are predicted by solving a set of partial differential equations (Ampere’s law and Gauss’ law for magnetism) numerically with the aid of physics-informed neural networks (PINNs). Prediction errors due to noisy magnetic field measurements and small number of magnetic field measurements are regularized by the physics information term in the loss function. We benchmark our model by comparing it with an older method. The new method we present will be of broad interest to experiments requiring precise determination of magnetic field components, such as searches for the neutron electric dipole moment.
Limited acclimation of early life stages of the coral Seriatopora hystrix from mesophotic depth to shallow reefs
Authors: Prasetia Rian , Sinniger Frederic , Nakamura Takashi , Harii Saki 
Published: July 2022

AbstractMesophotic coral ecosystems (MCEs, reefs between 30 and 150 m depth) have been hypothesized to contribute to shallow reef recovery through the recruitment of larvae. However, few studies have directly examined this. Here we used mesophotic colonies of Seriatopora hystrix, a depth generalist coral, to investigate the effect of light intensity on larval behavior and settlement through ex situ experiments. We also investigated juvenile survival, growth, and physiological acclimation in situ. Bleached larvae and a significant reduction in settlement rates were found when the mesophotic larvae were exposed to light conditions corresponding to shallow depths (5 and 10 m) ex situ. The in situ experiments showed that mesophotic juveniles survived well at 20 and 40 m, with juveniles in shaded areas surviving longer than three months at 3–5 m during a year of mass bleaching in 2016. Juvenile transplants at 20 m showed a sign of physiological acclimation, which was reflected by a significant decline in maximum quantum yield. These results suggest that light is a significant factor for successful recolonization of depth-generalist corals to shallow reefs. Further, recolonization of shallow reefs may only occur in shaded habitats or potentially through multigenerational recruitments with intermediate depths acting as stepping stones.
Construction of a new automatic grading system for jaw bone mineral density level based on deep learning using cone beam computed tomography
Authors: Xiao Yanjun , Liang Qihui , Zhou Lin , He Xuezhi , Lv Lingfeng , Chen Jiang , Endian Su , Jianbin Guo , Wu Dong , Lin Lin 
Published: July 2022

AbstractTo develop and verify an automatic classification method using artificial intelligence deep learning to determine the bone mineral density level of the implant site in oral implant surgery from radiographic data obtained from cone beam computed tomography (CBCT) images. Seventy patients with mandibular dentition defects were scanned using CBCT. These Digital Imaging and Communications in Medicine data were cut into 605 training sets, and then the data were processed with data standardization, and the Hounsfiled Unit (HU) value level was determined as follows: Type 1, 1000–2000; type 2, 700–1000; type 3, 400–700; type 4, 100–400; and type 5, − 200–100. Four trained dental implant physicians manually identified and classified the area of the jaw bone density level in the image using the software LabelMe. Then, with the assistance of the HU value generated by LabelMe, a physician with 20 years of clinical experience confirmed the labeling level. Finally, the HU mean values of various categories marked by dental implant physicians were compared to the mean values detected by the artificial intelligence model to assess the accuracy of artificial intelligence classification. After the model was trained on 605 training sets, the statistical results of the HU mean values of various categories in the dataset detected by the model were almost the same as the HU grading interval on the data annotation. This new classification provides a more detailed solution to guide surgeons to adjust the drilling rate and tool selection during preoperative decision-making and intraoperative hole preparation for oral implant surgery.
Best practices for instrumenting honey bees
Authors: Koenig Phoebe A. , Petersen Kirstin H. 
Published: July 2022

AbstractHoney bees are vital pollinators and can be used to monitor the landscape. Consequently, interest in mounting technologies onto bees to track foraging behaviors is increasing. The barrier to entry is steep, in part because the methodology for fastening tags to bees, and the success rates, are often missing from publications. We tested six factors suspected to influence the presence and tag retention rates of nurse honey bees after their introduction to hives, and followed bees until foraging age. We also compared reintroducing foragers to their maternal colony using the best method for nurse bees to releasing them in front of their maternal hive and allowing them to fly back unaided. Nurses were most likely to be present in the hive with their tag still attached when introduced using an introduction cage at night. Glue type was important, but may further be influenced by tag material. Foragers were most likely to be present with a tag attached if released in front of their colony. Preparation and introduction techniques influence the likelihood of tagged honey bee survival and of the tags remaining attached, which should be considered when executing honey bee tagging and tracking experiments.
Understanding the spatial distribution and hot spots of collared Bornean elephants in a multi-use landscape
Authors: Abram N. K. , Skara B. , Othman N. , Ancrenaz M. , Mengersen K. , Goossens B. 
Published: July 2022

AbstractIn the Kinabatangan floodplain, Sabah, Malaysian Borneo, oil palm and settlements have reduced and fragmented lowland tropical forests, home to around 200 endangered Bornean elephants (Elephas maximus borneensis). In this region, elephants range within forests, oil palm and community areas. The degree to which elephants are using these areas remains unclear. We used GPS telemetry data from 2010 to 2020 for 14 collared elephants to map their entire known ranges and highly used areas (hot spots) across four land use categories and estimate time spent within these. The use of land use types across elephants varied significantly. Typically, females had strong fidelity to forests, yet many of these forests are threatened with conversion. For the three males, and several females, they heavily used oil palm estates, and this may be due to decreased landscape permeability or foraging opportunities. At the pooled level, the entire range and hot spot extents, constituted 37% and 34% for protected areas, respectively, 8% and 11% for unprotected forests, 53% and 51% for oil palm estates, and 2% for community areas. Protecting all forested habitats and effectively managing areas outside of protected areas is necessary for the long-term survival of this population.
Physical activity and sleep behaviour in women carrying BRCA1/2 mutations
Authors: Galasso Letizia , Castelli Lucia , Roveda Eliana , Oliverio Andreina , Baldassari Ivan , Esposito Fabio , Mulè Antonino , Montaruli Angela , Pasanisi Patrizia , Bruno Eleonora 
Published: July 2022

AbstractThe aim of the present study is to explore the potential association between sleep quality and physical activity (PA) in women carriers of BRCA1/2 mutations. 63 women completed the Pittsburgh Sleep Quality Index (PSQI) and Godin Shepard Leisure-Time Physical Activity Questionnaire (GSL-TPAQ) and were included in the present cross-sectional analysis. Globally, women showed a PSQI score of 7.0 ± 3.6 and a GSL-TPAQ score of 22.8 ± 18.3. Good sleepers (PSQI score ≤ 5) showed significantly higher PA levels compared to bad sleepers (PSQI score > 5). Women in the higher tertile of GSL-TPAQ total score (≥ 27 METs/week) have a prevalence ratio (PR) of being a good sleeper of 2.85 (1.25–6.52, 95% confidence intervals) compared to women in the lower tertile (≤ 11 METs/week). These results were consistent in BRCA1 and BRCA2 women. Considering each single question of PA intensity, the PR of being a good sleeper by unit of increase of MET/week was higher and significant in women engaged in strenuous and moderate intensity PA. These results suggests a direct association between PA and sleep quality in women carriers of BRCA mutations.
Learning based PTSD symptoms in persons with specific learning disabilities
Authors: Grossman Ephraim S. , Hoffman Yaakov S. G. , Shrira Amit 
Published: July 2022

AbstractSpecific learning disorders (SLD) persist into adulthood. Persons with SLD frequently experience emotional and social difficulties. Following qualitative descriptions of individuals with SLD who experienced learning, as traumatic, we hypothesized that individuals reporting SLD would report higher levels of learning-based post-traumatic-stress-disorder (PTSD) symptoms. In Study 1 (N = 216), participants responded to questionnaires concerning SLD and learning-based PTSD. A separate sample (N = 43) was queried about adjustment disorder symptoms. Study 2 (N = 176) examined if current psychological distress was predicted by levels of learning-based PTSD at each developmental stage (elementary/high-school/post-high-school) and whether SLD links to current psychological distress. Finally, we assessed if SLD-psychological distress associations are mediated by cumulative levels of learning-based PTSD across these school periods. In Study 1 individuals reporting SLD displayed higher learning-based PTSD levels than those without SLD. SLD-PTSD associations held beyond adjustment disorder symptom levels. In Study 2, SLD was linked with psychological distress, mediated by accumulated learning-based PTSD symptom levels across school periods. These results suggest that in individuals with SLD, learning experiences may be associated with learning-based PTSD symptoms. Further, persons with SLD may be scarred by their traumatic learning experiences linking with current psychological distress, a link mediated by cumulative difficulties experienced over school years.
Microwave-assisted extraction of pectin from grape pomace
Authors: Spinei Mariana , Oroian Mircea 
Published: July 2022

AbstractThe utilization of microwave technique for the pectin extraction from grape pomace (Fetească Neagră and Rară Neagră), its influence on yield, galacturonic acid content, degree of esterification and molecular weight of pectin were analyzed. The optimal conditions of the extraction process were microwave power of 560 W, pH of 1.8 for 120 s. The pectin samples extracted by MAE in optimal conditions were analyzed by comparing with commercial apple and citrus pectin based on FT-IR analysis, thermal behavior, rheological characteristics and microstructure. The FT-IR analysis established the presence of different functional groups which are attributed to the finger print region of extracted pectin, while the rheological behavior presented a good viscoelasticity of pectin solutions. The obtained data assumes that grape pomace has a great potential to be a valuable source of pectin which can be extracted by simple and quick techniques, while maintaining analogous quality to conventional sources of pectin.
Lung cancer CT image generation from a free-form sketch using style-based pix2pix for data augmentation
Authors: Toda Ryo , Teramoto Atsushi , Kondo Masashi , Imaizumi Kazuyoshi , Saito Kuniaki , Fujita Hiroshi 
Published: July 2022

AbstractArtificial intelligence (AI) applications in medical imaging continue facing the difficulty in collecting and using large datasets. One method proposed for solving this problem is data augmentation using fictitious images generated by generative adversarial networks (GANs). However, applying a GAN as a data augmentation technique has not been explored, owing to the quality and diversity of the generated images. To promote such applications by generating diverse images, this study aims to generate free-form lesion images from tumor sketches using a pix2pix-based model, which is an image-to-image translation model derived from GAN. As pix2pix, which assumes one-to-one image generation, is unsuitable for data augmentation, we propose StylePix2pix, which is independently improved to allow one-to-many image generation. The proposed model introduces a mapping network and style blocks from StyleGAN. Image generation results based on 20 tumor sketches created by a physician demonstrated that the proposed method can reproduce tumors with complex shapes. Additionally, the one-to-many image generation of StylePix2pix suggests effectiveness in data-augmentation applications.
Integral effects of brassinosteroids and timber waste biochar enhances the drought tolerance capacity of wheat plant
Authors: Lalarukh Irfana , Amjad Syeda F. , Mansoora Nida , Al-Dhumri Sami A. , Alshahri Abdullah H. , Almutari Mohammad M. , Alhusayni ‏Fatimah S. , Al-Shammari Wasimah B. , Poczai Peter , Abbas Mohamed H. H. , Elghareeb Doaa , Kubra Khadija tul , Abdelhafez Ahmed A. 
Published: July 2022

AbstractDrought stress is among the major threats that affect negatively crop productivity in arid and semi-arid regions. Probably, application of some additives such as biochar and/or brassinosteroids could mitigate this stress; however, the mechanism beyond the interaction of these two applications is not well inspected. Accordingly, a greenhouse experiment was conducted on wheat (a strategic crop) grown under deficit irrigation levels (factor A) i.e., 35% of the water holding capacity (WHC) versus 75% of WHC for 35 days while considering the following additives, i.e., (1) biochar [BC, factor B, 0, 2%] and (2) the foliar application of 24-epibrassinolide [BR, factor C, 0 (control treatment, C), 1 (BR1) or 3 (BR2) μmol)]. All treatments were replicated trice and the obtained results were statistically analyzed via the analyses of variance. Also, heat-map conceits between measured variables were calculated using the Python software. Key results indicate that drought stress led to significant reductions in all studied vegetative growth parameters (root and shoot biomasses) and photosynthetic pigments (chlorophyll a, b and total contents) while raised the levels of oxidative stress indicators. However, with the application of BC and/or BR, significance increases occurred in the growth attributes of wheat plants, its photosynthetic pigments, especially the combined additions. They also upraised the levels of enzymatic and non-enzymatic antioxidants while decreased stress indicators. Furthermore, they increased calcium (Ca), phosphorus (P) and potassium (K) content within plants. It can therefore be deduced that the integral application of BR and BC is essential to mitigate drought stress in plants.