bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-apoptotic enteroblast-specific role of the initiator caspase Dronc for development and homeostasis of the Drosophila intestine
Authors: Lindblad Jillian L. , Tare Meghana , Amcheslavsky Alla , Shields Alicia , Bergmann Andreas 
Published: January 2021

AbstractThe initiator caspase Dronc is the only CARD-domain containing caspase in Drosophila and is essential for apoptosis. Here, we report that homozygous dronc mutant adult animals are short-lived due to the presence of a poorly developed, defective and leaky intestine. Interestingly, this mutant phenotype can be significantly rescued by enteroblast-specific expression of dronc+ in dronc mutant animals, suggesting that proper Dronc function specifically in enteroblasts, one of four cell types in the intestine, is critical for normal development of the intestine. Furthermore, enteroblast-specific knockdown of dronc in adult intestines triggers hyperplasia and differentiation defects. These enteroblast-specific functions of Dronc do not require the apoptotic pathway and thus occur in a non-apoptotic manner. In summary, we demonstrate that an apoptotic initiator caspase has a very critical non-apoptotic function for normal development and for the control of the cell lineage in the adult midgut and therefore for proper physiology and homeostasis.
Linking the oral microbiome and salivary cytokine abundance to circadian oscillations
Authors: Sarkar Anujit , Kuehl Melanie N. , Alman Amy C. , Burkhardt Brant R. 
Published: January 2021

AbstractSaliva has immense potential as a diagnostic fluid for identification and monitoring of several systemic diseases. Composition of the microbiome and inflammation has been associated and reflective of oral and overall health. In addition, the relative ease of collection of saliva further strengthens large-scale diagnostic purposes. However, the future clinical utility of saliva cannot be fully determined without a detailed examination of daily fluctuations that may occur within the oral microbiome and inflammation due to circadian rhythm. In this study, we explored the association between the salivary microbiome and the concentration of IL-1β, IL-6 and IL-8 in the saliva of 12 healthy adults over a period of 24 h by studying the 16S rRNA gene followed by negative binomial mixed model regression analysis. To determine the periodicity and oscillation patterns of both the oral microbiome and inflammation (represented by the cytokine levels), two of the twelve subjects were studied for three consecutive days. Our results indicate that the Operational Taxonomic Units (OTUs) belonging to Prevotella, SR1 and Ruminococcaceae are significantly associated to IL-1β while Prevotella and Granulicatella were associated with IL-8. Our findings have also revealed a periodicity of both the oral microbiome (OTUs) and inflammation (cytokine levels) with identifiable patterns between IL-1β and Prevotella, and IL-6 with Prevotella, Neisseria and Porphyromonas. We believe that this study represents the first measure and demonstration of simultaneous periodic fluctuations of cytokine levels and specific populations of the oral microbiome.
Exploring mobility in Italian Neolithic and Copper Age communities
Authors: De Angelis Flavio , Pellegrini Maura , Martínez-Labarga Cristina , Anzivino Laura , Scorrano Gabriele , Brilli Mauro , Giustini Francesca , Angle Micaela , Calattini Mauro , Carboni Giovanni , Catalano Paola , Ceccaroni Emanuela , Cosentino Serena , Di Giannantonio Stefania , Isola Ilaria , Martini Fabio , Pacciani Elsa , Radina Francesca , Rolfo Mario Federico , Silvestrini Mara , Volante Nicoletta , Zanchetta Giovanni , Sarti Lucia , Rickards Olga 
Published: January 2021

AbstractAs a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (δ18Oca and δ13Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured δ18Oca values suggest a significant role of local sources in the water inputs to the body water, whereas δ13Cca values indicate food resources, principally based on C3 plants. Both δ13Cca and δ18Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas.
Molecular preservation in mammoth bone and variation based on burial environment
Authors: Colleary Caitlin , Lamadrid Hector M. , O’Reilly Shane S. , Dolocan Andrei , Nesbitt Sterling J. 
Published: January 2021

AbstractBiomolecules preserved in fossils are expanding our understanding of the biology and evolution of ancient animals. Molecular taphonomy seeks to understand how these biomolecules are preserved and how they can be interpreted. So far, few studies on molecular preservation have considered burial context to understand its impact on preservation or the potentially complementary information from multiple biomolecular classes. Here, we use mass spectrometry and other analytical techniques to detect the remains of proteins and lipids within intact fossil mammoth bones of different ages and varied depositional setting. By combining these approaches, we demonstrate that endogenous amino acids, amides and lipids can preserve well in fossil bone. Additionally, these techniques enable us to examine variation in preservation based on location within the bone, finding dense cortical bone better preserves biomolecules, both by slowing the rate of degradation and limiting the extent of exogenous contamination. Our dataset demonstrates that biomolecule loss begins early, is impacted by burial environment and temperature, and that both exogenous and endogenous molecular signals can be both present and informative in a single fossil.
Spectrum analysis of inborn errors of metabolism for expanded newborn screening in a northwestern Chinese population
Authors: Zhang Ruixue , Qiang Rong , Song Chengrong , Ma Xiaoping , Zhang Yan , Li Fengxia , Wang Rui , Yu Wenwen , Feng Mei , Yang Lihui , Wang Xiaobin , Cai Na 
Published: January 2021

AbstractExpanded newborn screening facilitates early identification and intervention of patients with inborn errors of metabolism (IEMs), There is a lack of disease spectrum data for many areas in China. To determine the disease spectrum and genetic characteristics of IEMs in Xi'an city of Shaanxi province in northwest China, 146152 newborns were screening by MSMS from January 2014 to December 2019 and 61 patients were referred to genetic analysis by next generation sequencing (NGS) and validated by Sanger sequencing. Seventy-five newborns and two mothers were diagnosed with IEMs, with an overall incidence of 1:1898 (1:1949 without mothers). There were 35 newborns with amino acidemias (45.45%, 1:4176), 28 newborns with organic acidurias (36.36%, 1:5220), and 12 newborns and two mothers with FAO disorders (18.18%; 1:10439 or 1:12179 without mothers). Phenylketonuria and methylmalonic acidemia were the two most common disorders, accounting for 65.33% (49/75) of all confirmed newborn. Some hotspot mutations were observed for several IEMs, including PAH gene c.728G>A for phenylketonuria; MMACHC gene c.609G>A and c.567dupT, MMUT gene c.323G>A for methylmalonic acidemia and SLC25A13 gene c.852_855del for citrin deficiency. Our study provides effective clinical guidance for the popularization and application of expanded newborn screening, genetic screening, and genetic counseling of IEMs in this region.
F/OH ratio in a rare fluorine-poor blue topaz from Padre Paraíso (Minas Gerais, Brazil) to unravel topaz’s ambient of formation
Authors: Precisvalle N. , Martucci A. , Gigli L. , Plaisier J. R. , Hansen T. C. , Nobre A. G. , Bonadiman C. 
Published: January 2021

AbstractTopaz [Al2SiO4(F,OH)2] is one of the main fluorine-bearing silicates occurring in environments where variably acidic (F)/aqueous (OH) fluids saturate the silicate system. In this work we fully characterized blue topaz from Padre Paraíso (Minas Gerais, Brazil) by means of in situ synchrotron X-Ray and neutron powder diffraction measurements (temperature range 298–1273 K) combined with EDS microanalyses. Understanding the role of OH/F substitution in topaz is important in order to determine the hydrophilicity and the exchange reactions of fluorine by hydroxyl groups, and ultimately to characterize the environmental redox conditions (H2O/F) required for mineral formation. The fluorine content estimated from neutron diffraction data is ~ 1.03 a.f.u (10.34 wt%), in agreement with the chemical data (on average 10.0 wt%). The XOH [OH/(OH + F)] (0.484) is close to the maximum XOH value (0.5), and represents the OH- richest topaz composition so far analysed in the Minas Gerais district. Topaz crystallinity and fluorine content sharply decrease at 1170 K, while mullite phase starts growing. On the basis of this behaviour, we suggest that this temperature may represent the potential initial topaz’s crystallization temperature from supercritical fluids in a pegmatite system. The log(fH2O/fHF)fluid (1.27 (0.06)) is coherent with the fluorine activity calculated for hydrothermal fluids (pegmatitic stage) in equilibrium with the forming mineral (log(fH2O/fHF)fluid = 1.2–6.5) and clearly different from pure magmatic (granitic) residual melts [log(fH2O/fHF)fluid < 1]. The modelled H2O saturated fluids with the F content not exceeding 1 wt% may represent an anomalous water-dominant / fluorine-poor pegmatite lens of the Padre Paraíso Pegmatite Field.
Effects of integrated biocontrol on bacterial wilt and rhizosphere bacterial community of tobacco
Authors: Hu Yun , Li Yanyan , Yang Xiaoqiong , Li Chunli , Wang Lin , Feng Ji , Chen Shouwen , Li Xihong , Yang Yong 
Published: January 2021

AbstractBacterial wilt as a soil-borne disease was caused byRalstonia solanacearum, and seriously damages the growth of tobacco. Integrated biocontrol method was explored to control bacterial wilt. Nevertheless, the long-term effects of the integrated biocontrol method on soil bacterial community, soil physicochemical properties and the incidence of bacterial wilt are not well understood. In this study,B. amyoliquefaciensZM9, calcium cyanamide and rice bran were applied to tobacco fields in different ways. The disease index and incidence of tobacco bacterial wilt (TBW), soil physicochemical properties, colonization ability ofB. amyoliquefaciensZM9, and rhizopshere bacterial community were investigated. The results showed that the integrated application ofB. amyoliquefaciensZM9, rice bran and calcium cyanamide had the highest control efficiency of TBW and bacteria community diversity. Additionally, the integrated biocontrol method could improve the colonization ability ofB. amyoliquefaciensZM9. Furthermore, the integrated biocontrol method could effectively suppress TBW by regulating soil physicochemical properties, promoting beneficial bacteria and antagonistic bacteria of rhizopshere soil. This strategy has prospect of overcoming the defects in application of a single antagonistic bacteria and provides new insights to understand how to improve the colonization capacity of antagonistic bacteria and control efficacy for TBW.
Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front
Authors: Ramond Pierre , Siano Raffaele , Schmitt Sophie , de Vargas Colomban , Marié Louis , Memery Laurent , Sourisseau Marc 
Published: January 2021

AbstractOceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.
Multiparametric ultrasound imaging for the assessment of normal versus steatotic livers
Authors: Basavarajappa Lokesh , Baek Jihye , Reddy Shreya , Song Jane , Tai Haowei , Rijal Girdhari , Parker Kevin J. , Hoyt Kenneth 
Published: January 2021

AbstractLiver disease is increasing in prevalence across the globe. We present here a multiparametric ultrasound (mpUS) imaging approach for assessing nonalcoholic fatty liver disease (NALFD). This study was performed using rats (N = 21) that were fed either a control or methionine and choline deficient (MCD) diet. A mpUS imaging approach that includes H-scan ultrasound (US), shear wave elastography, and contrast-enhanced US measurements were then performed at 0 (baseline), 2, and 6 weeks. Thereafter, animals were euthanized and livers excised for histological processing. A support vector machine (SVM) was used to find a decision plane that classifies normal and fatty liver conditions. In vivo mpUS results from control and MCD diet fed animals reveal that all mpUS measures were different at week 6 (P < 0.05). Principal component analysis (PCA) showed that the H-scan US data contributed the highest percentage to the classification among the mpUS measurements. The SVM resulted in 100% accuracy for classification of normal and high fat livers and 92% accuracy for classification of normal, low fat, and high fat livers. Histology findings found considerable steatosis in the MCD diet fed animals. This study suggests that mpUS examinations have the potential to provide a comprehensive estimation of the main components of early stage NAFLD.
Deep COVID DeteCT: an international experience on COVID-19 lung detection and prognosis using chest CT
Authors: Lee Edward H. , Zheng Jimmy , Colak Errol , Mohammadzadeh Maryam , Houshmand Golnaz , Bevins Nicholas , Kitamura Felipe , Altinmakas Emre , Reis Eduardo Pontes , Kim Jae-Kwang , Klochko Chad , Han Michelle , Moradian Sadegh , Mohammadzadeh Ali , Sharifian Hashem , Hashemi Hassan , Firouznia Kavous , Ghanaati Hossien , Gity Masoumeh , Doğan Hakan , Salehinejad Hojjat , Alves Henrique , Seekins Jayne , Abdala Nitamar , Atasoy Çetin , Pouraliakbar Hamidreza , Maleki Majid , Wong S. Simon , Yeom Kristen W. 
Published: January 2021

AbstractThe Coronavirus disease 2019 (COVID-19) presents open questions in how we clinically diagnose and assess disease course. Recently, chest computed tomography (CT) has shown utility for COVID-19 diagnosis. In this study, we developed Deep COVID DeteCT (DCD), a deep learning convolutional neural network (CNN) that uses the entire chest CT volume to automatically predict COVID-19 (COVID+) from non-COVID-19 (COVID−) pneumonia and normal controls. We discuss training strategies and differences in performance across 13 international institutions and 8 countries. The inclusion of non-China sites in training significantly improved classification performance with area under the curve (AUCs) and accuracies above 0.8 on most test sites. Furthermore, using available follow-up scans, we investigate methods to track patient disease course and predict prognosis.
Algorithmic matching of personal protective equipment donations with healthcare facilities during the COVID-19 pandemic
Authors: Bala Ram , Lee Charlotte , Pallant Benjamin , Srinivasan Maahika , Lurie Daniel , Jacob Rohit , Bhagchandani Neeraj , Ranney Megan , He Shuhan 
Published: January 2021

AbstractGetUsPPE.org has built a centralized platform to facilitate matches for PPE donations, with an active role in matching donors with the appropriate recipients. A manual match process was limited by volunteer hours, thus we developed an open-access matching algorithm using a linear programming-based transportation model. From April 14, 2020 to April 27, 2020, the algorithm was used to match 83,136 items of PPE to 135 healthcare facilities in need across the United States with a median of 214.3 miles traveled, 100% of available donations matched, met the full quantity of requested PPE for 67% of recipients matched, and with 46% matches under 30 miles traveled. Compared with the period April 1, 2020 to April 13, 2020, when PPE matching was manual, the algorithm resulted in a 280% increase in matches/day. This publicly available automated algorithm could be deployed in future situations when the healthcare supply chain is insufficient.
Comparative multi-omics analyses reveal differential expression of key genes relevant for parasitism between non-encapsulated and encapsulated Trichinella
Authors: Liu Xiaolei , Feng Yayan , Bai Xue , Wang Xuelin , Qin Rui , Tang Bin , Yu Xinxin , Yang Yong , Liu Mingyuan , Gao Fei 
Published: January 2021

AbstractGenome assemblies provide a powerful basis of comparative multi-omics analyses that offer insight into parasite pathogenicity, host-parasite interactions, and invasion biology. As a unique intracellular nematode, Trichinella consists of two clades, encapsulated and non-encapsulated. Genomic correlation of the distinct differences between the two clades is still unclear. Here, we report an annotated draft reference genome of non-encapsulated Trichinella, T. pseudospiralis, and perform comparative multi-omics analyses with encapsulated T. spiralis. Genome and methylome analyses indicate that, during Trichinella evolution, the two clades of Trichinella exhibit differential expansion and methylation of parasitism-related multi-copy gene families, especially for the DNase II members of the phospholipase D superfamily and Glutathione S-transferases. Further, methylome and transcriptome analyses revealed divergent key excretory/secretory (E/S) genes between the two clades. Among these key E/S genes, TP12446 is significantly more expressed across three life stages in T. pseudospiralis. Overexpression of TP12446 in the mouse C2C12 skeletal muscle cell line could induce inhibition of myotube formation and differentiation, further indicating its key role in parasitism of T. pseudospiralis. This multi-omics study provides a foundation for further elucidation of the mechanism of nurse cell formation and immunoevasion, as well as the identification of pharmacological and diagnostic targets of trichinellosis.
Dipeptidyl peptidase 4 promotes peritoneal fibrosis and its inhibitions prevent failure of peritoneal dialysis
Authors: Li Yi-Chen , Sung Pei-Hsun , Yang Yao-Hsu , Chiang John Y. , Yip Hon-Kan , Yang Chih‐Chao 
Published: January 2021

AbstractPeritoneal dialysis (PD) possesses multiple advantages for end stage renal disease. However, long-term PD triggers peritoneal fibrosis (PF). From the nationwide analysis of diabetic PD patients (n = 19,828), we identified the incidence of PD failure was significantly lower in diabetic patients treated with dipeptidyl peptidase 4 (DPP4) inhibitors. Experimental study further showed high concentration of glucose remarkably enhanced DPP4 to promote epithelial-mesenchymal transition (EMT) in the mesothelial cells. In chlorhexidine gluconate (CG)-induced PF model of rats, DPP4 expression was enriched at thickening peritoneum. Moreover, as to CG-induced PF model, DPP4 deficiency (F344/DuCrlCrlj strain), sitagliptin and exendin-4 treatments significantly inhibited DPP4 to reverse the EMT process, angiogenesis, oxidative stress, and inflammation, resulting in the protection from PF, preservation of peritoneum and the corresponding functional integrity. Furthermore, DPP4 activity was significantly correlated with peritoneal dysfunction. Taken together, DPP4 caused peritoneal dysfunction/PF, whereas inhibition of DPP4 protected the PD patients against PD failure.
DeepLabStream enables closed-loop behavioral experiments using deep learning-based markerless, real-time posture detection
Authors: Schweihoff Jens F. , Loshakov Matvey , Pavlova Irina , Kück Laura , Ewell Laura A. , Schwarz Martin K. 
Published: January 2021

AbstractIn general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Most of the available current technologies focus on offline pose estimation with high spatiotemporal resolution. However, to correlate behavior with neuronal activity it is often necessary to detect and react online to behavioral expressions. Here we present DeepLabStream, a versatile closed-loop tool providing real-time pose estimation to deliver posture dependent stimulations. DeepLabStream has a temporal resolution in the millisecond range, can utilize different input, as well as output devices and can be tailored to multiple experimental designs. We employ DeepLabStream to semi-autonomously run a second-order olfactory conditioning task with freely moving mice and optogenetically label neuronal ensembles active during specific head directions.
Colonization and genetic diversification processes of Leishmania infantum in the Americas
Authors: Schwabl Philipp , Boité Mariana C. , Bussotti Giovanni , Jacobs Arne , Andersson Bjorn , Moreira Otacilio , Freitas-Mesquita Anita L. , Meyer-Fernandes Jose Roberto , Telleria Erich L. , Traub-Csekö Yara , Vaselek Slavica , Leštinová Tereza , Volf Petr , Morgado Fernanda N. , Porrozzi Renato , Llewellyn Martin , Späth Gerald F. , Cupolillo Elisa 
Published: January 2021

AbstractLeishmania infantum causes visceral leishmaniasis, a deadly vector-borne disease introduced to the Americas during the colonial era. This non-native trypanosomatid parasite has since established widespread transmission cycles using alternative vectors, and human infection has become a significant concern to public health, especially in Brazil. A multi-kilobase deletion was recently detected in Brazilian L. infantum genomes and is suggested to reduce susceptibility to the anti-leishmanial drug miltefosine. We show that deletion-carrying strains occur in at least 15 Brazilian states and describe diversity patterns suggesting that these derive from common ancestral mutants rather than from recurrent independent mutation events. We also show that the deleted locus and associated enzymatic activity is restored by hybridization with non-deletion type strains. Genetic exchange appears common in areas of secondary contact but also among closely related parasites. We examine demographic and ecological scenarios underlying this complex L. infantum population structure and discuss implications for disease control.