bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages
Authors: Weinheimer Alaina R , Aylward Frank O 
Published: March 2022

Abstract
Recent research has underscored the immense diversity and key biogeochemical roles of large DNA viruses in the ocean. Although they are important constituents of marine ecosystems, it is sometimes difficult to detect these viruses due to their large size and complex genomes. This is true for “jumbo” bacteriophages, which have genome sizes &gt;200 kbp and large capsids reaching up to 0.45 µm in diameter. In this study, we sought to assess the genomic diversity and distribution of these bacteriophages in the ocean by generating and analyzing jumbo phage genomes from metagenomes. We recover 85 marine jumbo phages that ranged in size from 201 to 498 kilobases, and we examine their genetic similarities and biogeography together with a reference database of marine jumbo phage genomes. By analyzing Tara Oceans metagenomic data, we show that although most jumbo phages can be detected in a range of different size fractions, 17 of our bins tend to be found in those greater than 0.22 µm, potentially due to their large size. Our network-based analysis of gene-sharing patterns reveals that jumbo bacteriophages belong to five genome clusters that are typified by diverse replication strategies, genomic repertoires, and potential host ranges. Our analysis of jumbo phage distributions in the ocean reveals that depth is a major factor shaping their biogeography, with some phage genome clusters occurring preferentially in either surface or mesopelagic waters, respectively. Taken together, our findings indicate that jumbo phages are widespread community members in the ocean with complex genomic repertoires and ecological impacts that warrant further targeted investigation.
Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels
Authors: Klotz Franziska , Kitzinger Katharina , Ngugi David Kamanda , Büsing Petra , Littmann Sten , Kuypers Marcel M M , Schink Bernhard , Pester Michael 
Published: March 2022

Abstract
Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe’s largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8–39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name “Candidatus Nitrosopumilus limneticus”. Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l‒1 d‒1, corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell−1 d−1. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 109 g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.
A novel prostaglandin E receptor 4 (EP4) small molecule antagonist induces articular cartilage regeneration
Authors: Jin Yunyun , Liu Qianqian , Chen Peng , Zhao Siyuan , Jiang Wenhao , Wang Fanhua , Li Peng , Zhang Yuanjin , Lu Weiqiang , Zhong Tao P. , Ma Xinran , Wang Xin , Gartland Alison , Wang Ning , Shah Karan Mehul , Zhang Hankun , Cao Xu , Yang Lei , Liu Mingyao , Luo Jian 
Published: March 2022

AbstractArticular cartilage repair and regeneration is an unmet clinical need because of the poor self-regeneration capacity of the tissue. In this study, we found that the expression of prostaglandin E receptor 4 (PTGER4 or EP4) was largely increased in the injured articular cartilage in both humans and mice. In microfracture (MF) surgery-induced cartilage defect (CD) and destabilization of the medial meniscus (DMM) surgery-induced CD mouse models, cartilage-specific deletion ofEP4remarkably promoted tissue regeneration by enhancing chondrogenesis and cartilage anabolism, and suppressing cartilage catabolism and hypertrophy. Importantly, knocking outEP4in cartilage enhanced stable mature articular cartilage formation instead of fibrocartilage, and reduced joint pain. In addition, we identified a novel selective EP4 antagonist HL-43 for promoting chondrocyte differentiation and anabolism with low toxicity and desirable bioavailability. HL-43 enhanced cartilage anabolism, suppressed catabolism, prevented fibrocartilage formation, and reduced joint pain in multiple pre-clinical animal models including the MF surgery-induced CD rat model, the DMM surgery-induced CD mouse model, and an aging-induced CD mouse model. Furthermore, HL-43 promoted chondrocyte differentiation and extracellular matrix (ECM) generation, and inhibited matrix degradation in human articular cartilage explants. At the molecular level, we found that HL-43/EP4 regulated cartilage anabolism through the cAMP/PKA/CREB/Sox9 signaling. Together, our findings demonstrate that EP4 can act as a promising therapeutic target for cartilage regeneration and the novel EP4 antagonist HL-43 has the clinical potential to be used for cartilage repair and regeneration.
Pleomorphic rhabdomyosarcoma in a young adult harboring a novel germline MSH2 variant
Authors: Tomida Akimasa , Chiyonobu Tomohiro , Tokuda Shinsaku , Miyachi Mitsuru , Murashima Kyoko , Hirata Makoto , Nakagawa Masanori , Iehara Tomoko , Kuroda Junya , Takayama Koichi 
Published: March 2022

AbstractMost cases of rhabdomyosarcoma (RMS) are sporadic and not associated with the Lynch syndrome (LS) spectrum. We report a young adult patient with RMS and a family history of colorectal cancer. Comprehensive cancer genomic profiling (CGP) of his tumor revealed a likely pathogenic variant of MSH2, NM_000251.3:c.1741delA (p.I581Lfs*9), which was also present in his blood sample. The widespread use of CGP may reveal that RMS can be a rare manifestation of LS.
Full-spin-wave-scaled stochastic micromagnetism for mesh-independent simulations of ferromagnetic resonance and reversal
Authors: Oezelt Harald , Qu Luman , Kovacs Alexander , Fischbacher Johann , Gusenbauer Markus , Beigelbeck Roman , Praetorius Dirk , Yano Masao , Shoji Tetsuya , Kato Akira , Chantrell Roy , Winklhofer Michael , Zimanyi Gergely T. , Schrefl Thomas 
Published: March 2022

AbstractIn this paper, we address the problem that standard stochastic Landau-Lifshitz-Gilbert (sLLG) simulations typically produce results that show unphysical mesh-size dependence. The root cause of this problem is that the effects of spin-wave fluctuations are ignored in sLLG. We propose to represent the effect of these fluctuations by a full-spin-wave-scaled stochastic LLG, or FUSSS LLG method. In FUSSS LLG, the intrinsic parameters of the sLLG simulations are first scaled by scaling factors that integrate out the spin-wave fluctuations up to the mesh size, and the sLLG simulation is then performed with these scaled parameters. We developed FUSSS LLG by studying the Ferromagnetic Resonance (FMR) in Nd2Fe14B cubes. The nominal scaling greatly reduced the mesh size dependence relative to sLLG. We then performed three tests and validations of our FUSSS LLG with this modified scaling. (1) We studied the same FMR but with magnetostatic fields included. (2) We simulated the total magnetization of the Nd2Fe14B cube. (3) We studied the effective, temperature- and sweeping rate-dependent coercive field of the cubes. In all three cases, we found that FUSSS LLG delivered essentially mesh-size-independent results, which tracked the theoretical expectations better than unscaled sLLG. Motivated by these successful validations, we propose that FUSSS LLG provides marked, qualitative progress towards accurate, high precision modeling of micromagnetics in hard, permanent magnets.
Corrosion fatigue behavior of electron beam melted iron in simulated body fluid
Authors: Wackenrohr Steffen , Torrent Christof Johannes Jaime , Herbst Sebastian , Nürnberger Florian , Krooss Philipp , Ebbert Christoph , Voigt Markus , Grundmeier Guido , Niendorf Thomas , Maier Hans Jürgen 
Published: March 2022

AbstractPure iron is very attractive as a biodegradable implant material due to its high biocompatibility. In combination with additive manufacturing, which facilitates great flexibility of the implant design, it is possible to selectively adjust the microstructure of the material in the process, thereby control the corrosion and fatigue behavior. In the present study, conventional hot-rolled (HR) pure iron is compared to pure iron manufactured by electron beam melting (EBM). The microstructure, the corrosion behavior and the fatigue properties were studied comprehensively. The investigated sample conditions showed significant differences in the microstructures that led to changes in corrosion and fatigue properties. The EBM iron showed significantly lower fatigue strength compared to the HR iron. These different fatigue responses were observed under purely mechanical loading as well as with superimposed corrosion influence and are summarized in a model that describes the underlying failure mechanisms.
The relative contributions of insight and neurocognition to intrinsic motivation in schizophrenia
Authors: Brasso Claudio , Bellino Silvio , Bozzatello Paola , Cardillo Simona , Montemagni Cristiana , Rocca Paola 
Published: March 2022

AbstractIntrinsic motivation was described as the mental process of pursuing a task or an action because it is enjoyable or interesting in itself and was found to play a central role in the determination of the functional outcome of schizophrenia. Neurocognition is one of the most studied determinants of intrinsic motivation in clinically stable schizophrenia while little is known about the role of insight. Following this need we decided to focus on the contribution of different aspects of insight and of neurocognition to intrinsic motivation in a large sample (n = 176) of patients with stable schizophrenia. We performed three hierarchical linear regressions from which resulted that, among different insight aspects, the ability to correctly attribute signs and symptoms to the mental disorder made the strongest contribution to intrinsic motivation. Neurocognition, also, was significantly related to intrinsic motivation when analyzed simultaneously with insight. Moreover, even after accounting for sociodemographic and clinical variables significantly correlated with intrinsic motivation, the relationship between insight and neurocognition and intrinsic motivation remained statistically significant. These findings put the emphasis on the complex interplay between insight, neurocognition, and intrinsic motivation suggesting that interventions targeting both insight and neurocognition might possibly improve this motivational deficit in stable schizophrenia should.
A vaccine targeting the L9 epitope of the malaria circumsporozoite protein confers protection from blood-stage infection in a mouse challenge model
Authors: Jelínková Lucie , Flores-Garcia Yevel , Shapiro Sarah , Roberts Bryce T. , Petrovsky Nikolai , Zavala Fidel , Chackerian Bryce 
Published: March 2022

AbstractPre-erythrocytic malaria vaccines that induce high-titer, durable antibody responses can potentially provide protection from infection. Here, we engineered a virus-like particle (VLP)-based vaccine targeting a recently described vulnerable epitope at the N-terminus of the central repeat region of the Plasmodium falciparum circumsporozoite protein that is recognized by the potently inhibitory monoclonal antibody L9 and show that immunization with L9 VLPs induces strong antibody responses that provide protection from blood-stage malaria in a mouse infection model.
Spatio-temporal analysis identifies marine mammal stranding hotspots along the Indian coastline
Authors: Dudhat Sohini , Pande Anant , Nair Aditi , Mondal Indranil , Srinivasan Mridula , Sivakumar Kuppusamy 
Published: March 2022

AbstractMarine mammal strandings provide vital information on species’ life histories, population health and status of marine ecosystems. Opportunistic reporting of strandings also serve as a powerful low-cost tool for monitoring these elusive mammals. We collated data over ~ 270 years available through various open access databases, reports and publications. Annual strandings along the Indian coast (mean = 11.25 ± SE 9.1) increased in the last two years of the study (2015–2017, mean = 27.66 ± SE 8.5 strandings /year). We found that stranding events spike during June—September along the west coast and during December–January along the east coast. We identified several sections of the coastline, such as Mumbai (0.38 strandings/km), Kozhikode (0.28 strandings/km), Tuticorin (0.4 strandings/km), Rameswaram (1.82 strandings/km), Chennai (0.32 strandings/km) and Bhubaneshwar (0.26 strandings/km) with a higher number of stranded animals reported. Emerging Hotspot Analysis located new and consecutive hotspots along the north-west coast, and sporadic hotspots along the south-east coast. We recommend establishing regional stranding response centres at the identified hotspots coordinated by a National Stranding Centre with adequately trained personnel and central funding support. Regular stranding response training programs for field veterinarians, and frontline personnel of State Forest Departments near stranding hotspots would provide an improved understanding of marine mammal health and threats in Indian waters. Further, the suggested National Stranding Centre needs to maintain a ‘National Stranding Database’ for long-term marine mammal conservation planning in India.
Triacontanol regulates morphological traits and enzymatic activities of salinity affected hot pepper plants
Authors: Sarwar Mubeen , Anjum Sumreen , Alam Muhammad Waqar , Ali Qurban , Ayyub C. M. , Haider Muhammad Saleem , Ashraf M. Irfan , Mahboob Wajid 
Published: March 2022

AbstractPotential role of triacontanol applied as a foliar treatment to ameliorate the adverse effects of salinity on hot pepper plants was evaluated. In this pot experiment, hot pepper plants under 75 mM NaCl stress environment were subjected to foliar application of 25, 50, and 75 µM triacontanol treatments; whereas, untreated plants were taken as control. Salt stress had a significant impact on morphological characteristics, photosynthetic pigments, gas exchange attributes, MDA content, antioxidants activities, electrolytes leakage, vitamin C, soluble protein, and proline contents. All triacontanol treatments significantly mitigated the adversative effects of salinity on hot pepper plants; however, foliar application triacontanol at 75 µM had considerably improved the growth of hot pepper plants in terms of plant height, shoot length, leaf area, plant fresh/dry biomasses by modulating above mentioned physio-biochemical traits. While, improvement in gas exchange properties, chlorophyll, carotenoid contents, increased proline contents coupled with higher SOD and CAT activities were observed in response to 75 µM triacontanol followed by 50 µM triacontanol treatment. MDA and H2O2 contents were decreased significantly in hot pepper plants sprayed with 75 µM triacontanol followed by 50 µM triacontanol foliar treatment. Meanwhile, root and shoot lengths were maximum in 50 µM triacontanol sprayed hot pepper plants along with enhanced APX activity on exposure to salt stress. In crux, exogenous application triacontanol treatments improved hot pepper performance under salinity, however,75 µM triacontanol treatment evidently was more effective in mitigating the lethal impact of saline stress via controlling the ROS generation and increment in antioxidant enzyme activities.
GaWRDenMap: a quantitative framework to study the local variation in cell–cell interactions in pancreatic disease subtypes
Authors: Krishnan Santhoshi N. , Mohammed Shariq , Frankel Timothy L. , Rao Arvind 
Published: March 2022

AbstractSpatial pattern modelling concepts are being increasingly used in capturing disease heterogeneity. Quantification of heterogeneity in the tumor microenvironment is extremely important in pancreatic ductal adenocarcinoma (PDAC), which has been shown to co-occur with other pancreatic diseases and neoplasms with certain attributes that make visual discrimination difficult. In this paper, we propose the GaWRDenMap framework, that utilizes the concepts of geographically weighted regression (GWR) and a density function-based classification model, and apply it to a cohort of multiplex immunofluorescence images from patients belonging to six different pancreatic diseases. We used an internal cohort of 228 patients comprised of 34 Chronic Pancreatitis (CP), 71 PDAC, 70 intraductal papillary mucinous neoplasm (IPMN), 16 mucinous cystic neoplasm (MCN), 29 pancreatic intraductal neoplasia (PanIN) and 8 IPMN-associated PDAC patients. We utilized GWR to model the relationship between epithelial cells and immune cells on a spatial grid. The GWR model estimates were used to generate density signatures which were used in subsequent pairwise classification models to distinguish between any two pairs of disease groups. Image-level, as well as subject-level analysis, were performed. When applied to this dataset, our classification model showed significant discrimination ability in multiple pairwise comparisons, in comparison to commonly used abundance-based metrics, like the Morisita-Horn index. The model was able to best discriminate between CP and PDAC at both the subject- and image-levels. It was also able to reasonably discriminate between PDAC and IPMN. These results point to a potential difference in the spatial arrangement of epithelial and immune cells between CP, PDAC and IPMN, that could be of high diagnostic significance. Further validation on a more comprehensive dataset would be warranted.
Association between prehospital fluid resuscitation with crystalloids and outcome of trauma patients in Asia by a cross-national multicenter cohort study
Authors: Sung Chih-Wei , Sun Jen-Tang , Huang Edward Pei-Chuan , Shin Sang Do , Song Kyoung Jun , Hong Ki Jeong , Jamaluddin Sabariah Faizah , Son Do Ngoc , Hsieh Ming-Ju , Ma Matthew Huei-Ming , Hsu Li-Min , Chiang Wen-Chu ,   The PATOS Clinical Research Network, Rao Ramana , Abraham George P. , Ramakrishnan T. V. , Jamaluddin Sabariah Faiwah , Mohidin Mohd Amin Bin , Saim Al-Hilmi , Kean Lim Chee , Anthonysamy Cecilia , Yssof Shah Jahan Din Mohd , Ji Kang Wen , Kheng Cheah Phee , Ali Shamila Bt Mohamad , Ramanathan Periyanayaki , Yang Chia Boon , Chia Hon Woei , Hamad Hafidahwati Binti , Ismail Samsu Ambia , Abdullah Wan Rasydan B. Wan , Tanaka Hideharu , Kimura Akio , Velasco Bernadett , Gundran Carlos D. , Convocar Pauline , Sabarre Nerissa G. , Tiglao Patrick Joseph , Hong Ki Jeong , Song Kyoung Jun , Jeong Joo , Moon Sung Woo , Kim Joo-yeong , Cha Won Chul , Lee Seung Chul , Ahn Jae Yun , Lee Kang Hyeon , Yeom Seok Ran , Ryu Hyeon Ho , Kim Su Jin , Kim Sang Chul , Hu Ray-Heng , Sun Jen Tang , Wang Ruei-Fang , Hsieh Shang-Lin , Kao Wei-Fong , Riyapan Sattha , Tianwibool Parinya , Buaprasert Phudit , Akaraborworn Osaree , Sakaf Omer Ahmed Al , Fares Saleh , Huy Le Bao , Son Do Ngoc , Van Dai Nguyen 
Published: March 2022

AbstractPrehospital fluid resuscitation with crystalloids in patients following trauma remain controversial. This study aimed to investigate the association between prehospital fluid resuscitation and outcomes of trauma patients in Asia. We conducted a retrospective cohort study of trauma patients between 2016 and 2018 using data from the Pan-Asia Trauma Outcomes Study (PATOS) database. Prehospital fluid resuscitation was defined as any administration of intravenous crystalloid fluid on the ambulance before arrival to hospitals. The outcomes were in-hospital mortality and poor functional outcomes, defined as Modified Rankin Scale ≥ 4. Propensity score matching (PSM) was used to equalize potential prognostic factors in both groups. This study included 31,735 patients from six countries in Asia, and 4318 (13.6%) patients had ever received prehospital fluid resuscitation. The patients receiving prehospital fluid resuscitation had a higher risk of in-hospital mortality, with an adjusted odds ratio (aOR) of 2.02, 95% confidence interval (CI) 1.32–3.10, p = 0.001 in PSM analysis. Prehospital fluid resuscitation was also associated with poor functional outcomes, with an OR 1.73, 95% CI: 1.48–2.03, p < 0.001 in PSM analysis. Prehospital fluid resuscitation in patients with major trauma (injury severity score ≥ 16) presented a higher risk of poor functional outcomes (aOR = 2.65, 95% CI: 1.89–3.73 in PSM analysis, pinteraction = 0.006) via subgroup analysis. Prehospital fluid resuscitation of trauma patients is associated with higher in-hospital mortality and poor functional outcomes in the subgroup in countries studied.
Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation
Authors: Noll D. , Leon F. , Brandt D. , Pistorius P. , Le Bohec C. , Bonadonna F. , Trathan P. N. , Barbosa A. , Rey A. Raya , Dantas G. P. M. , Bowie R. C. K. , Poulin E. , Vianna J. A. 
Published: March 2022

AbstractAlthough mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.