bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proposal and validation of a method to classify genetic subtypes of diffuse large B cell lymphoma
Authors: Pedrosa Lucía , Fernández-Miranda Ismael , Pérez-Callejo David , Quero Cristina , Rodríguez Marta , Martín-Acosta Paloma , Gómez Sagrario , González-Rincón Julia , Santos Adrián , Tarin Carlos , García Juan F. , García-Arroyo Francisco R. , Rueda Antonio , Camacho Francisca I. , García-Cosío Mónica , Heredero Ana , Llanos Marta , Mollejo Manuela , Piris-Villaespesa Miguel , Gómez-Codina José , Yanguas-Casás Natalia , Sánchez Antonio , Piris Miguel A. , Provencio Mariano , Sánchez-Beato Margarita 
Published: January 2021

AbstractDiffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease whose prognosis is associated with clinical features, cell-of-origin and genetic aberrations. Recent integrative, multi-omic analyses had led to identifying overlapping genetic DLBCL subtypes. We used targeted massive sequencing to analyze 84 diagnostic samples from a multicenter cohort of patients with DLBCL treated with rituximab-containing therapies and a median follow-up of 6 years. The most frequently mutated genes were IGLL5 (43%), KMT2D (33.3%), CREBBP (28.6%), PIM1 (26.2%), and CARD11 (22.6%). Mutations in CD79B were associated with a higher risk of relapse after treatment, whereas patients with mutations in CD79B, ETS1, and CD58 had a significantly shorter survival. Based on the new genetic DLBCL classifications, we tested and validated a simplified method to classify samples in five genetic subtypes analyzing the mutational status of 26 genes and BCL2 and BCL6 translocations. We propose a two-step genetic DLBCL classifier (2-S), integrating the most significant features from previous algorithms, to classify the samples as N12-S, EZB2-S, MCD2-S, BN22-S, and ST22-S groups. We determined its sensitivity and specificity, compared with the other established algorithms, and evaluated its clinical impact. The results showed that ST22-S is the group with the best clinical outcome and N12-S, the more aggressive one. EZB2-S identified a subgroup with a worse prognosis among GCB-DLBLC cases.
Synthesis, molecular dynamics simulation and adsorption study of different pollutants on functionalized mesosilica
Authors: Pelalak Rasool , Soltani Roozbeh , Heidari Zahra , Malekshah Rahime Eshaghi , Aallaei Mohammadreza , Marjani Azam , Rezakazemi Mashallah , Shirazian Saeed 
Published: January 2021

AbstractExperimental and computational works were carried out on a new type of mesoporous silica. In the experimental section, functionalized hollow mesosilica spheres were prepared via a facile technique and then evaluated using some analytical techniques (FESEM, TEM, L-XRD, FTIR, BET-BJH, and TGA). The obtained results revealed that the synthesized material had hollow structure with a diamino-grafted porous shell. The molecular separation of crystal Violet (CV) and neutral Red (NR) dyes from water were investigated by adsorption process using the synthesized powder. Influence of adsorbent loading was evaluated as adsorption ability and dyes removal efficiency. Also, the obtained modeling results revealed appropriate fitting of data with non-linear Langmuir model. The theoretical studies were employed to study the adsorption and removal mechanism of cationic (CV and NR) and anionic (orange II (OII)) dyes using molecular dynamics calculations. Moreover, the simulation outcomes provided valuable information about quantum chemical properties including the HOMO–LUMO maps, chemical reactivity, global softness (σ) and hardness (η) for silica-linker-water-dyes components.
Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
Authors: Casaburi Giorgio , Duar Rebbeca M. , Brown Heather , Mitchell Ryan D. , Kazi Sufyan , Chew Stephanie , Cagney Orla , Flannery Robin L. , Sylvester Karl G. , Frese Steven A. , Henrick Bethany M. , Freeman Samara L. 
Published: January 2021

AbstractThe gut microbiome plays an important role in early life, protecting newborns from enteric pathogens, promoting immune system development and providing key functions to the infant host. Currently, there are limited data to broadly assess the status of the US healthy infant gut microbiome. To address this gap, we performed a multi-state metagenomic survey and found high levels of bacteria associated with enteric inflammation (e.g. Escherichia, Klebsiella), antibiotic resistance genes, and signatures of dysbiosis, independent of location, age, and diet. Bifidobacterium were less abundant than generally expected and the species identified, including B. breve, B. longum and B. bifidum, had limited genetic capacity to metabolize human milk oligosaccharides (HMOs), while B. infantis strains with a complete capacity for HMOs utilization were found to be exceptionally rare. Considering microbiome composition and functional capacity, this survey revealed a previously unappreciated dysbiosis that is widespread in the contemporary US infant gut microbiome.
Robust MFC anti-windup scheme for LTI systems with norm-bounded uncertainty
Authors: Mo Xiao-Qin , Zhou Mi , Wang Yuan , Guo Shang-Jia 
Published: January 2021

AbstractOn the basic of the fact that all signals in the practical system are always bounded, this paper proposes a 4-degree-of-freedom (DoF) anti-windup scheme for saturated systems with parametric uncertainty. A fairly straightforward tuning rule is introduced to the robust stability analysis for the proposed anti-windup structure under the framework of IQC (Integral Quadratic Constraint). And the sufficient stability conditions are derived to check the reasonable definiteness of the related transfer function. Moreover, the control design for disturbance response and set-point tracking response are two separate part in this proposed scheme. Numerical example demonstrates the effectiveness and the considerable performance improvement of the anti-windup compensator that is designed by the proposed technique.
A deep learning based framework for the registration of three dimensional multi-modal medical images of the head
Authors: Islam Kh Tohidul , Wijewickrema Sudanthi , O’Leary Stephen 
Published: January 2021

AbstractImage registration is a fundamental task in image analysis in which the transform that moves the coordinate system of one image to another is calculated. Registration of multi-modal medical images has important implications for clinical diagnosis, treatment planning, and image-guided surgery as it provides the means of bringing together complimentary information obtained from different image modalities. However, since different image modalities have different properties due to their different acquisition methods, it remains a challenging task to find a fast and accurate match between multi-modal images. Furthermore, due to reasons such as ethical issues and need for human expert intervention, it is difficult to collect a large database of labelled multi-modal medical images. In addition, manual input is required to determine the fixed and moving images as input to registration algorithms. In this paper, we address these issues and introduce a registration framework that (1) creates synthetic data to augment existing datasets, (2) generates ground truth data to be used in the training and testing of algorithms, (3) registers (using a combination of deep learning and conventional machine learning methods) multi-modal images in an accurate and fast manner, and (4) automatically classifies the image modality so that the process of registration can be fully automated. We validate the performance of the proposed framework on CT and MRI images of the head obtained from a publicly available registration database.
Rats sniff out pulmonary tuberculosis from sputum: a diagnostic accuracy meta-analysis
Authors: Kanaan Reem , Farkas Nelli , Hegyi Péter , Soós Alexandra , Hegyi Dávid , Németh Katalin , Horváth Orsolya , Tenk Judit , Mikó Alexandra , Szentesi Andrea , Balaskó Márta , Szakács Zsolt , Vasas Andrea , Csupor Dezső , Gyöngyi Zoltán 
Published: January 2021

AbstractIn Sub-Saharan Africa, African giant pouched rats (Cricetomys gambianus) are trained to identify TB patients by smelling sputum. We conducted a systematic review and meta-analysis of the data to see if this novel method is comparable to traditional laboratory screening and detection methods like Ziehl–Neelsen stain-based assays (ZN) and bacterial culture. The search and data processing strategy is registered at PROSPERO (CRD42019123629). Medline via PubMed, EMBASE, Web of Science, and Cochrane Library databases were systematically searched for the keywords “pouched rat” and “tuberculosis”. Data from 53,181 samples obtained from 24,600 patients were extracted from seven studies. Using sample-wise detection, the sensitivity of the studies was 86.7% [95% CI 80.4–91.2%], while the specificity was 88.4% [95% CI 79.7–93.7%]. For patient-wise detection, the sensitivity was 81.3% [95% CI 64.0–91.4%], while the specificity was 73.4% [95% CI 62.8–81.9%]. Good and excellent classification was assessed by hierarchical summary receiver-operating characteristic analysis for patient-wise and sample-wise detections, respectively. Our study is the first systematic review and meta-analysis of the above relatively inexpensive and rapid screening method. The results indicate that African giant pouched rats can discriminate healthy controls from TB individuals by sniffing sputum with even a higher accuracy than a single ZN screening.
Application of subject-specific adaptive mechanical loading for bone healing in a mouse tail vertebral defect
Authors: Malhotra Angad , Walle Matthias , Paul Graeme R. , Kuhn Gisela A. , Müller Ralph 
Published: January 2021

AbstractMethods to repair bone defects arising from trauma, resection, or disease, continue to be sought after. Cyclic mechanical loading is well established to influence bone (re)modelling activity, in which bone formation and resorption are correlated to micro-scale strain. Based on this, the application of mechanical stimulation across a bone defect could improve healing. However, if ignoring the mechanical integrity of defected bone, loading regimes have a high potential to either cause damage or be ineffective. This study explores real-time finite element (rtFE) methods that use three-dimensional structural analyses from micro-computed tomography images to estimate effective peak cyclic loads in a subject-specific and time-dependent manner. It demonstrates the concept in a cyclically loaded mouse caudal vertebral bone defect model. Using rtFE analysis combined with adaptive mechanical loading, mouse bone healing was significantly improved over non-loaded controls, with no incidence of vertebral fractures. Such rtFE-driven adaptive loading regimes demonstrated here could be relevant to clinical bone defect healing scenarios, where mechanical loading can become patient-specific and more efficacious. This is achieved by accounting for initial bone defect conditions and spatio-temporal healing, both being factors that are always unique to the patient.
A nuclear protein, PfMORC confers melatonin dependent synchrony of the human malaria parasite P. falciparum in the asexual stage
Authors: Singh Maneesh K. , Tessarin-Almeida Giulliana , Dias Barbara K. M. , Pereira Pedro Scarpellli , Costa Fahyme , Przyborski Jude M. , Garcia Celia R. S. 
Published: January 2021

AbstractThe host hormone melatonin is known to modulate the asexual cell-cycle of the human malaria parasite Plasmodium falciparum and the kinase PfPK7 is fundamental in the downstream signaling pathways. The nuclear protein PfMORC displays a histidine kinase domain and is involved in parasite cell cycle control. By using a real-time assay, we show a 24 h (h) rhythmic expression of PfMORC at the parasite asexual cycle and the expression is dramatically changed when parasites were treated with 100 nM melatonin for 17 h. Moreover, PfMORC expression was severely affected in PfPK7 knockout (PfPK7−) parasites following melatonin treatment. Parasites expressing 3D7morc-GFP shows nuclear localization of the protein during the asexual stage of parasite development. Although the PfMORC knockdown had no significant impact on the parasite proliferation in vitro it significantly changed the ratio of the different asexual intraerythrocytic stages of the parasites upon the addition of melatonin. Our data reveal that in addition to the upstream melatonin signaling pathways such as IP3 generation, calcium, and cAMP rise, a nuclear protein, PfMORC is essential for the hormone response in parasite synchronization.
The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957
Authors: Miguel-Blanco Celia , Murithi James M. , Benavente Ernest Diez , Angrisano Fiona , Sala Katarzyna A. , van Schalkwyk Donelly A. , Vanaerschot Manu , Schwach Frank , Fuchter Matthew J. , Billker Oliver , Sutherland Colin J. , Campino Susana G. , Clark Taane G. , Blagborough Andrew M. , Fidock David A. , Herreros Esperanza , Gamo Francisco Javier , Baum Jake , Delves Michael J. 
Published: January 2021

AbstractNew antimalarial therapeutics are needed to ensure that malaria cases continue to be driven down, as both emerging parasite resistance to frontline chemotherapies and mosquito resistance to current insecticides threaten control programmes.Plasmodium, the apicomplexan parasite responsible for malaria, causes disease pathology through repeated cycles of invasion and replication within host erythrocytes (the asexual cycle). Antimalarial drugs primarily target this cycle, seeking to reduce parasite burden within the host as fast as possible and to supress recrudescence for as long as possible. Intense phenotypic drug screening efforts have identified a number of promising new antimalarial molecules. Particularly important is the identification of compounds with new modes of action within the parasite to combat existing drug resistance and suitable for formulation of efficacious combination therapies. Here we detail the antimalarial properties of DDD01034957—a novel antimalarial molecule which is fast-acting and potent against drug resistant strains in vitro, shows activity in vivo, and possesses a resistance mechanism linked to the membrane transporter PfABCI3. These data support further medicinal chemistry lead-optimization of DDD01034957 as a novel antimalarial chemical class and provide new insights to further reduce in vivo metabolic clearance.
Changes in metabolic syndrome status affect the incidence of end-stage renal disease in the general population: a nationwide cohort study
Authors: Koh Eun Sil , Do Han Kyung , Kim Mee Kyoung , Kim Eun Sook , Lee Min-Kyung , Nam Ga Eun , Hong Oak-Kee , Kwon Hyuk-Sang 
Published: January 2021

AbstractFew studies have investigated the impact of a change in metabolic syndrome (MetS) components on clinical renal outcomes in the general population. Using nationally representative data from the Korean National Health Insurance System, 13,310,924 subjects who underwent two health examinations over 2 years and were free from end-stage renal disease (ESRD) from 2009 to 2012 were followed to the end of 2016. The subjects were divided into four groups according to the change in MetS components between the two visits over 2 years: no MetS (–/–), post-MetS (–/+), pre-MetS (+/–), and both MetS (+/+). After a median follow up of 5.11 years, 18,582 incident ESRD cases were identified. In the multivariate adjusted model, the hazard ratio (HR) and 95% confidence interval (CI) for the development of ESRD in the both-MetS (+/+) group compared with the no-MetS (–/–) group was 5.65 (95% CI, 5.42–5.89), which was independent of age, sex, and baseline estimated glomerular filtration rate. Additionally, the HR for the pre-MetS (+/–) group versus the no-MetS (–/–) group was 2.28 (2.15–2.42). In subgroup analysis according to renal function, the impact of a change in MetS on the incidence of ESRD was more pronounced in individuals with advanced renal dysfunction. Subjects with resolved MetS components had a decreased risk of ESRD, but not as low as those that never had MetS components. This provides evidence supporting the strategy of modulating MetS in the general population to prevent the development of ESRD.
Heat dissipation in subterranean rodents: the role of body region and social organisation
Authors: Vejmělka František , Okrouhlík Jan , Lövy Matěj , Šaffa Gabriel , Nevo Eviatar , Bennett Nigel Charles , Šumbera Radim 
Published: January 2021

AbstractThe relatively warm and very humid environment of burrows presents a challenge for thermoregulation of its mammalian inhabitants. It was found that African mole-rats dissipate body heat mainly through their venter, and social mole-rats dissipate more body heat compared to solitary species at lower temperatures. In addition, the pattern of the ventral surface temperature was suggested to be homogeneous in social mole-rats compared to a heterogeneous pattern in solitary mole-rats. To investigate this for subterranean rodents generally, we measured the surface temperatures of seven species with different degrees of sociality, phylogeny, and climate using infrared thermography. In all species, heat dissipation occurred mainly through the venter and the feet. Whereas the feet dissipated body heat at higher ambient temperatures and conserved it at lower ambient temperatures, the ventral surface temperature was relatively high in all temperatures indicating that heat dissipation to the environment through this body region is regulated mainly by behavioural means. Solitary species dissipated less heat through their dorsum than social species, and a tendency for this pattern was observed for the venter. The pattern of heterogeneity of surface temperature through the venter was not related to sociality of the various species. Our results demonstrate a general pattern of body heat exchange through the three studied body regions in subterranean rodents. Besides, isolated individuals of social species are less able to defend themselves against low ambient temperatures, which may handicap them if staying alone for a longer period, such as during and after dispersal events.
Opposite correlation of 25-hydroxy-vitamin D- and 1,25-dihydroxy-vitamin D-metabolites with gestational age, bone- and lipid-biomarkers in pregnant women
Authors: Tsuprykov Oleg , Elitok Saban , Buse Claudia , Chu Chang , Krämer Bernhard Karl , Hocher Berthold 
Published: January 2021

Abstract25-Hydroxyvitamin D (25OHD) and 1,25-dihydroxyvitamin D (1,25(OH)2D) need to be bound to carrier proteins to be transported to their target cells. The majority of either 25OHD or 1,25(OH)2D is bound to vitamin D-binding protein (DBP), a smaller fraction is bound to albumin and only very small amounts of 25OHD or 1,25(OH)2D are free. Albumin-bound 25OHD or 1,25(OH)2D is relatively easily available after dissociation from albumin. Thus, the sum of free and albumin-bound forms is called bioavailable 25OHD and bioavailable 1,25(OH)2D. Total 25OHD and 1,25(OH)2D are defined as the sum of free, albumin-bound and DBP-bound 25OHD and 1,25(OH)2D, respectively. This cross-sectional study in 427 pregnant women compared the correlation of the six vitamin D compounds with biomarkers of bone health, lipid metabolism, kidney function, endocrine parameters, and group B water-soluble vitamins. Among the 25OHD metabolites analysed, total 1,25(OH)2D showed clearly the best correlation with calcium, bone-specific alkaline phosphatase, adiponectin, LDL, HDL, urea, thyroxine, and group B water-soluble vitamins. When comparing the three 25OHD metabolites, both free 25OHD and bioavailable 25OHD showed overall good correlations with calcium, bone-specific alkaline phosphatase, adiponectin, LDL, HDL, urea, thyroxine, triiodothyronine, and group B water-soluble vitamins, The correlations of 1,25(OH)2D and 25OHD metabolites went always in opposite directions. Only PTH correlates always inversely with all six vitamin D compounds. In conclusion, free 25(OH)D and bioavailable 25(OH)D are more precise determinants of the vitamin D status than total 25(OH)D in normal pregnancy, whereas total 1,25(OH)2D is superior to free and bioavailable 1,25(OH)2D. Except for PTH, correlations of 25(OH)D and 1,25(OH)2D metabolites with typical clinical chemistry readouts go in opposite directions.
Thermoelectricity of near-resonant tunnel junctions and their relation to Carnot efficiency
Authors: Popp Matthias A. , Erpenbeck André , Weber Heiko B. 
Published: January 2021

AbstractWe present a conceptual study motivated by electrical and thermoelectrical measurements on various near-resonant tunnel junctions. The squeezable nano junction technique allows the quasi-synchronous measurement of conductance G, I(V) characteristics and Seebeck coefficient S. Correlations between G and S are uncovered, in particular boundaries for S(G). We find the simplest and consistent description of the observed phenomena in the framework of the single level resonant tunneling model within which measuring I(V) and S suffice for determining all model parameters. We can further employ the model for assigning thermoelectric efficiencies $$\eta $$
η
without measuring the heat flow. Within the ensemble of thermoelectric data, junctions with assigned $$\eta $$
η
close to the Carnot limit can be identified. These insights allow providing design rules for optimized thermoelectric efficiency in nanoscale junctions.
More than redox, biological organic ligands control iron isotope fractionation in the riparian wetland
Authors: Lotfi-Kalahroodi Elaheh , Pierson-Wickmann Anne-Catherine , Rouxel Olivier , Marsac Rémi , Bouhnik-Le Coz Martine , Hanna Khalil , Davranche Mélanie 
Published: January 2021

AbstractAlthough redox reactions are recognized to fractionate iron (Fe) isotopes, the dominant mechanisms controlling the Fe isotope fractionation and notably the role of organic matter (OM) are still debated. Here, we demonstrate how binding to organic ligands governs Fe isotope fractionation beyond that arising from redox reactions. The reductive biodissolution of soil Fe(III) enriched the solution in light Fe isotopes, whereas, with the extended reduction, the preferential binding of heavy Fe isotopes to large biological organic ligands enriched the solution in heavy Fe isotopes. Under oxic conditions, the aggregation/sedimentation of Fe(III) nano-oxides with OM resulted in an initial enrichment of the solution in light Fe isotopes. However, heavy Fe isotopes progressively dominate the solution composition in response to their binding with large biologically-derived organic ligands. Confronted with field data, these results demonstrate that Fe isotope systematics in wetlands are controlled by the OM flux, masking Fe isotope fractionation arising from redox reactions. This work sheds light on an overseen aspect of Fe isotopic fractionation and calls for a reevaluation of the parameters controlling the Fe isotopes fractionation to clarify the interpretation of the Fe isotopic signature.