bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease
Authors: Faber Marc , Shaw Sophie , Yoon Sohye , de Paiva Alves Eduardo , Wang Bei , Qi Zhitao , Okamura Beth , Hartikainen Hanna , Secombes Christopher J. , Holland Jason W. 
Published: January 2021

AbstractThe myxozoan parasite, Tetracapsuloidesbryosalmonae has a two-host life cycle alternating between freshwater bryozoans and salmonid fish. Infected fish can develop Proliferative Kidney Disease, characterised by a gross lymphoid-driven kidney pathology in wild and farmed salmonids. To facilitate an in-depth understanding of T.bryosalmonae-host interactions, we have used a two-host parasite transcriptome sequencing approach in generating two parasite transcriptome assemblies; the first derived from parasite spore sacs isolated from infected bryozoans and the second from infected fish kidney tissues. This approach was adopted to minimize host contamination in the absence of a complete T.bryosalmonae genome. Parasite contigs common to both infected hosts (the intersect transcriptome; 7362 contigs) were typically AT-rich (60–75% AT). 5432 contigs within the intersect were annotated. 1930 unannotated contigs encoded for unknown transcripts. We have focused on transcripts encoding proteins involved in; nutrient acquisition, host–parasite interactions, development, cell-to-cell communication and proteins of unknown function, establishing their potential importance in each host by RT-qPCR. Host-specific expression profiles were evident, particularly in transcripts encoding proteases and proteins involved in lipid metabolism, cell adhesion, and development. We confirm for the first time the presence of homeobox proteins and a frizzled homologue in myxozoan parasites. The novel insights into myxozoan biology that this study reveals will help to focus research in developing future disease control strategies.
Association of serum lipopolysaccharide-binding protein level with sensitization to food allergens in children
Authors: Ha Eun Kyo , Kim Ju Hee , Yon Dong Keon , Lee Seung Won , Kim Mi Ae , Lee Kyung Suk , Sung Myongsoon , Jee Hye Mi , Shin Youn Ho , Han Man Yong 
Published: January 2021

AbstractLipopolysaccharide (LPS)-binding protein (LBP) is an acute-phase reactant that mediates innate immune responses triggered by LPS. Recent studies indicated a positive correlation of circulating LBP level with chronic low-grade inflammation, a condition present in many non-communicable diseases. We determined the association of serum LBP concentration with allergic sensitization in a general pediatric population. Serum LBP was measured in a sample of children (n = 356; mean age = 9.6 ± 0.2 years) in this population-based cross-sectional study. Skin prick tests (SPTs) were performed to assess allergic sensitization to 22 common inhalant and food allergens. One hundred and seven children (30.1%) were nonsensitized, 160 (44.9%) were monosensitized, and 89 (25.0%) were polysensitized. Children who were mono- or polysensitized had a significantly higher median serum LBP level (25.5 ng/mL, inter-quartile range [IQR] 20.3–30.7) than those who were nonsensitized (20.3 ng/mL, IQR = 14.81–25.8,P < 0.0001). Multivariate logistic regression analysis with adjustment for confounders indicated that serum LBP level was positively associated with allergic sensitization overall (adjusted odds ratio [aOR] 1.041; 95% CI 1.007–1.076,P = 0.016), with sensitization to food allergens in particular (aOR 1.080, 95% CI 1.029–1.133,P = 0.002), but not with sensitization to aeroallergens (aOR 1.010, 95% CI 0.982–1.040,P = 0.467). LBP level was not associated with allergic diseases after adjustment. We suggest the possibility of sensitization to food allergens may be related to gut-derived low-grade inflammation, and large sized longitudinal investigations are needed to elucidate the relationship.
Role of the C5a-C5a receptor axis in the inflammatory responses of the lungs after experimental polytrauma and hemorrhagic shock
Authors: Chakraborty Shinjini , Winkelmann Veronika Eva , Braumüller Sonja , Palmer Annette , Schultze Anke , Klohs Bettina , Ignatius Anita , Vater Axel , Fauler Michael , Frick Manfred , Huber-Lang Markus 
Published: January 2021

AbstractSingular blockade of C5a in experimental models of sepsis is known to confer protection by rescuing lethality and decreasing pro-inflammatory responses. However, the role of inhibiting C5a has not been evaluated in the context of sterile systemic inflammatory responses, like polytrauma and hemorrhagic shock (PT + HS). In our presented study, a novel and highly specific C5a L-aptamer, NoxD21, was used to block C5a activity in an experimental murine model of PT + HS. The aim of the study was to assess early modulation of inflammatory responses and lung damage 4 h after PT + HS induction. NoxD21-treated PT + HS mice displayed greater polymorphonuclear cell recruitment in the lung, increased pro-inflammatory cytokine levels in the bronchoalveolar lavage fluids (BALF) and reduced myeloperoxidase levels within the lung tissue. An in vitro model of the alveolar-capillary barrier was established to confirm these in vivo observations. Treatment with a polytrauma cocktail induced barrier damage only after 16 h, and NoxD21 treatment in vitro did not rescue this effect. Furthermore, to test the exact role of both the cognate receptors of C5a (C5aR1 and C5aR2), experimental PT + HS was induced in C5aR1 knockout (C5aR1 KO) and C5aR2 KO mice. Following 4 h of PT + HS, C5aR2 KO mice had significantly reduced IL-6 and IL-17 levels in the BALF without significant lung damage, and both, C5aR1 KO and C5aR2 KO PT + HS animals displayed reduced MPO levels within the lungs. In conclusion, the C5aR2 could be a putative driver of early local inflammatory responses in the lung after PT + HS.
Quantifying the hydroxyapatite orientation near the ossification front in a piglet femoral condyle using X-ray diffraction tensor tomography
Authors: Mürer Fredrik K. , Chattopadhyay Basab , Madathiparambil Aldritt Scaria , Tekseth Kim Robert , Di Michiel Marco , Liebi Marianne , Lilledahl Magnus B. , Olstad Kristin , Breiby Dag W. 
Published: January 2021

AbstractWhile a detailed knowledge of the hierarchical structure and morphology of the extracellular matrix is considered crucial for understanding the physiological and mechanical properties of bone and cartilage, the orientation of collagen fibres and carbonated hydroxyapatite (HA) crystallites remains a debated topic. Conventional microscopy techniques for orientational imaging require destructive sample sectioning, which both precludes further studies of the intact sample and potentially changes the microstructure. In this work, we use X-ray diffraction tensor tomography to image non-destructively in 3D the HA orientation in a medial femoral condyle of a piglet. By exploiting the anisotropic HA diffraction signal, 3D maps showing systematic local variations of the HA crystallite orientation in the growing subchondral bone and in the adjacent mineralized growth cartilage are obtained. Orientation maps of HA crystallites over a large field of view (~ 3 × 3 × 3 mm3) close to the ossification (bone-growth) front are compared with high-resolution X-ray propagation phase-contrast computed tomography images. The HA crystallites are found to predominantly orient with their crystallite c-axis directed towards the ossification front. Distinct patterns of HA preferred orientation are found in the vicinity of cartilage canals protruding from the subchondral bone. The demonstrated ability of retrieving 3D orientation maps of bone-cartilage structures is expected to give a better understanding of the physiological properties of bones, including their propensity for bone-cartilage diseases.
Configurational diffusion transport of water and oil in dual continuum shales
Authors: Siddiqui Mohammed Abdul Qadeer , Salvemini Filomena , Ramandi Hamed Lamei , Fitzgerald Paul , Roshan Hamid 
Published: January 2021

AbstractUnderstanding fluid flow in shale rocks is critical for the recovery of unconventional energy resources. Despite the extensive research conducted on water and oil flow in shales, significant uncertainties and discrepancies remain in reported experimental data. The most noted being that while oil spreads more than water on shale surfaces in an inviscid medium, its uptake by shale pores is much less than water during capillary flow. This leads to misjudgement of wettability and the underlying physical phenomena. In this study, therefore, we performed a combined experimental and digital rock investigation on an organic-rich shale including contact angle and spontaneous imbibition, X-ray and neutron computed tomography, and small angle X-ray scattering tests to study the potential physical processes. We also used non-equilibrium thermodynamics to theoretically derive constitutive equations to support our experimental observations. The results of this study indicate that the pre-existing fractures (first continuum) imbibe more oil than water consistent with contact angle measurements. The overall imbibition is, however, higher for water than oil due to greater water diffusion into the shale matrix (second continuum). It is shown that more water uptake into shale is controlled by pore size and accessibility in addition to capillary or osmotic forces i.e. configurational diffusion of water versus oil molecules. While the inorganic pores seem more oil-wet in an inviscid medium, they easily allow passage of water molecules compared to oil due to the incredibly small size of water molecules that can pass through such micro-pores. Contrarily, these strongly oil-wet pores possessing strong capillarity are restricted to imbibe oil simply due to its large molecular size and physical inaccessibility to the micro-pores. These results provide new insights into the previously unexplained discrepancy regarding water and oil uptake capacity of shales.
Cysteine: an overlooked energy and carbon source
Authors: Göbbels Luise , Poehlein Anja , Dumnitch Albert , Egelkamp Richard , Kröger Cathrin , Haerdter Johanna , Hackl Thomas , Feld Artur , Weller Horst , Daniel Rolf , Streit Wolfgang R. , Schoelmerich Marie Charlotte 
Published: January 2021

AbstractBiohybrids composed of microorganisms and nanoparticles have emerged as potential systems for bioenergy and high-value compound production from CO2 and light energy, yet the cellular and metabolic processes within the biological component of this system are still elusive. Here we dissect the biohybrid composed of the anaerobic acetogenic bacterium Moorella thermoacetica and cadmium sulphide nanoparticles (CdS) in terms of physiology, metabolism, enzymatics and transcriptomic profiling. Our analyses show that while the organism does not grow on l-cysteine, it is metabolized to acetate in the biohybrid system and this metabolism is independent of CdS or light. CdS cells have higher metabolic activity, despite an inhibitory effect of Cd2+ on key enzymes, because of an intracellular storage compound linked to arginine metabolism. We identify different routes how cysteine and its oxidized form can be innately metabolized by the model acetogen and what intracellular mechanisms are triggered by cysteine, cadmium or blue light.
Examination of permittivity for depolarization field of ferroelectric by ab initio calculation, suggesting hidden mechanisms
Authors: Watanabe Yukio 
Published: January 2021

AbstractElectrostatics of depolarization field Ed in relation to the polarization is studied. In particular, the value of permittivity for Ed (εd) in prototypical situations of ferroelectrics, including Mehta formula, is examined by ab initio calculations. By using spontaneous polarization PS corresponding to accurate experiment ones, we show εd = 1, which suggests that the results of εd ≫ 1 indicate hidden mechanisms; εd = 1 suggests that the effect of Ed is significant to induce intriguing important phenomena overlooked by εd ≫ 1. A bridge between εd = 1 and εd ≫ 1, i.e. the consistency of εd = 1 with conventional results is presented. The exact electrostatic equality of head-to-head–tail-to-tail domains to free-standing ferroelectrics is deduced. Hence, most stoichiometric clean freestanding monodomain ferroelectrics and head-to-head–tail-to-tail domains are shown unstable regardless of size, unless partially metallic. This verifies the previous results in a transparent manner. This conclusion is shown consistent with a recent hyperferroelectric LiBeSb and “freestanding” monolayer ferroelectrics, of which origin is suggested to be adsorbates. In addition, this restriction is suggested to break in externally strained ultrathin ferroelectrics. The macroscopic formulas of Ed are found valid down to a several unit-cells, when electronic and atomic-scale surface effects are unimportant and accurate PS is used.
Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium
Authors: Jain Abhiney , Gralnick Jeffrey A. 
Published: January 2021

AbstractNeutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative “omics” studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the molecular and biochemical understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy in M. ferrooxydans, a metabolism that has been speculated but not experimentally validated. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.
Micropatterning biomineralization with immobilized mother of pearl proteins
Authors: White Kristopher A. , Cali Vincent J. , Olabisi Ronke M. 
Published: January 2021

AbstractIn response to the drawbacks of autograft donor-site morbidity and bone morphogenetic protein type 2 (BMP2) carcinogenesis and ectopic bone formation, there has been an increased research focus towards developing alternatives capable of achieving spatial control over bone formation. Here we show for the first time both osteogenic differentiation and mineralization (from solution or mediated by cells) occurring within predetermined microscopic patterns. Our results revealed that both PEGylated BMP2 and nacre proteins induced stem cell osteodifferentiation in microscopic patterns when these proteins were covalently bonded in patterns onto polyethylene glycol diacrylate (PEGDA) hydrogel substrates; however, only nacre proteins induced mineralization localized to the micropatterns. These findings have broad implications on the design and development of orthopedic biomaterials and drug delivery.
Intracellular alpha-fetoprotein interferes with all-trans retinoic acid induced ATG7 expression and autophagy in hepatocellular carcinoma cells
Authors: Wang Shanshan , Feng Rilu , Shi Ying , Chen Dexi , Weng Honglei , Ding Huiguo , Zhang Chenguang 
Published: January 2021

AbstractRetinoic acid and retinoid acid receptor (RA-RAR) signaling exhibits suppressive functions in the progression of hepatocellular carcinoma (HCC) through multiple mechanisms. However, whether RA-RAR signaling induces autophagy that contributes its anti-tumor activity in HCC remains elusive. In the current study, the effects of RA-RAR pathway on autophagy were investigated in two HCC cell lines: alpha-fetoprotein (AFP) positive PLC/PRF/5 and AFP negative HLE cells. Cell autophagy was analyzed with western blot for detection of LC3 conversion and p62/SQSTM1 degradation while autophagy flux was assayed using the mRFP-GFP-LC3 reporter. Cell apoptosis and viability were analyzed by caspase-3 activity, TdT-mediated dUTP nick end labeling (TUNEL) assay, and Cell Counting Kit (CCK)-8, respectively. Chromatin immunoprecipitation (ChIP) was employed to detect the binding of RAR onto the promoter of autophagy-relevant 7 (ATG7), and co-immunoprecipitation (CoIP) was used to analyze the interaction of AFP and RAR. The results showed that ATRA dosage and time-dependently induced high levels of cell autophagy in both the PLC/PRF/5 and HLE cells, which was accompanied with up-regulation of ATG7. ChIP assay showed that RAR was able to bind to its responsive elements on ATG7 promoter. Impairment of ATG7 induction or blockade of autophagy with chloroquine aggravated ATRA induced apoptosis of HCC cells. Furthermore, intracellular AFP was able to complex with RAR in PLC/PRF/5 cells. Knockdown of AFP in PLC/PRF/5 cells augmented the up-regulation of ATG7 by ATRA while overexpression of AFP in HLE cells attenuated ATRA induced ATG7 expression and autophagy. Thus, ATRA induced ATG7 and autophagy participated in its cytotoxicity on HCC cells and AFP interfere with the induction of ATG7 and autophagy through forming complex with RAR.
Cluster strong lensing with hierarchical inference
Authors: Bergamini P. , Agnello A. , Caminha G. B. 
Published: January 2021

Context. Lensing by galaxy clusters is a versatile probe of cosmology and extragalactic astrophysics, but the accuracy of some of its predictions is limited by the simplified models adopted to reduce the (otherwise intractable) number of degrees of freedom.
Aims. We aim to explore cluster lensing models in which the parameters of all cluster member galaxies are free to vary around some common scaling relations with non-zero scatter and deviate significantly from these relations if, and only if, the data require this.
Methods. We devised a Bayesian hierarchical inference framework that enables the determination of all lensing parameters and the scaling relation hyperparameters, including intrinsic scatter, from lensing constraints and (if given) stellar kinematic measurements. We achieve this through BAYESLENS, a purpose-built wrapper around common parametric lensing codes that can sample the full posterior on parameters and hyperparameters; we release BAYESLENS with this paper.
Results. We ran functional tests of our code against simple mock cluster lensing datasets with realistic uncertainties. The parameters and hyperparameters are recovered within their 68% credibility ranges and the positions of all the “observed” multiple images are accurately reproduced by the BAYELENS best-fit model, without over-fitting.
Conclusions. We have shown that an accurate description of cluster member galaxies is attainable, despite a large number of degrees of freedom, through fast and tractable inference. This extends beyond the most updated cluster lensing models. The precise impact on studies of cosmography, galaxy evolution, and high-redshift galaxy populations can then be quantified on real galaxy clusters. While other sources of systematics exist and may be significant in real clusters, our results show that the contribution of intrinsic scatter in cluster member populations can now be controlled.
Probing the internal magnetism of stars using asymptotic magneto-asteroseismology
Authors: Mathis S. , Bugnet L. , Prat V. , Augustson K. , Mathur S. , Garcia R. A. 
Published: January 2021

Context. Our knowledge of the dynamics of stars has undergone a revolution through the simultaneous large amount of high-quality photometric observations collected by space-based asteroseismology and ground-based high-precision spectropolarimetry. They allowed us to probe the internal rotation of stars and their surface magnetism in the whole Hertzsprung-Russell diagram. However, new methods should still be developed to probe the deep magnetic fields in these stars.
Aims. Our goal is to provide seismic diagnoses that allow us to probe the internal magnetism of stars.
Methods. We focused on asymptotic low-frequency gravity modes and high-frequency acoustic modes. Using a first-order perturbative theory, we derived magnetic splittings of their frequencies as explicit functions of stellar parameters.
Results. As in the case of rotation, we show that asymptotic gravity and acoustic modes can allow us to probe the different components of the magnetic field in the cavities in which they propagate. This again demonstrates the high potential of using mixed-modes when this is possible.
LKMA Evaluation Formed from PUAP Program in Overcoming Farming Financing in Rural Areas (Case study: Magelang Regency)
Authors: Darwis Valeriana , Ashari  , Muslim Chairul 
Published: January 2021

Rural Agribusiness Development (PUAP) is a program to provide capital for smallholder in the agricultural sector. The final goal of this program is to format Agribusiness Micro Credit Institutions (LKMA) in rural. In the implementation 6,887 LKMAs have been formed, including in Magelang Regency. The purpose of this paper is to evaluate the LKMA and its benefit for farmers’ capital fulfillment. The survey was conducted in July 2019 using the FGD method with administrators and interviews with the farmer using a questionnaire. The evaluation focused on the institutional, business, and capital development aspects. The data analyzed through the ranking method to determine the LKMA rank. Of the 9 LKMA, the best LKMA is Ngudi Luhur LKMA, with criteria (i) the institutional aspect is already incorporated, has an office, employees with a fixed monthly salary; (ii) business aspects: saving and loan business carried out based on SOP of financial institutions and (iii) of capital development have reached 3.3 billion. However, loans only cover less than 30% of farmers’ needs due to the limited availability of LKMA capital.
Therefore, it is recommended to assist capital loan assistance to LKMA, which will then be transmitted to farmmers.
Empowering communities for resolving the environmental crisis in forest and land fires in Riau Province
Authors: Rosilawati Yeni , Dewi Asri 
Published: January 2021

The issue of the environment is becoming more complex.
Regarding industry development, the impact of pollution, waste, infrastructure, and social pollution is getting worse. Especially in Riau Province, known for its disastrous peatland fires in recent years. This paper aims to identify the community development to address the environmental crisis in forest and land fires implemented in Kampung Jawa, Riau Province. This study utilized participatory observation and in-depth interviews with the local community. Secondary data were collected in the form of information on programs from the newspaper clippings and reports. The research discovered that local communities initiated the community development program to change the image of peatlands previously known as the source of haze disaster, which also has economic potential. The community development conducted by the local communities consisted of (i) Masyarakat Peduli Api (MPA)—a community volunteering to deal with disasters and suppress forest fires, (ii) pineapple farm and pineapple product processing, and (iii) peat Arboretum. This study also disclosed that community development carried out proactive dialogue and engagement with stakeholders, including farmers’ communities, local communities, NGOs, and local government.