bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure
Authors: Arvanitis Marios , Tampakakis Emmanouil , Zhang Yanxiao , Wang Wei , Auton Adam ,   23andMe Research Team, Agee Michelle , Aslibekyan Stella , Bell Robert K. , Bryc Katarzyna , Clark Sarah K. , Elson Sarah L. , Fletez-Brant Kipper , Fontanillas Pierre , Furlotte Nicholas A. , Gandhi Pooja M. , Heilbron Karl , Hicks Barry , Hinds David A. , Huber Karen E. , Jewett Ethan M. , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K. , McCreight Jennifer C. , McIntyre Matthew H. , McManus Kimberly F. , Mountain Joanna L. , Mozaffari Sahar V. , Nandakumar Priyanka , Noblin Elizabeth S. , Northover Carrie A. M. , O’Connell Jared , Pitts Steven J. , Poznik G. David , Sathirapongsasuti J. Fah , Shastri Anjali J. , Shelton Janie F. , Shringarpure Suyash , Tian Chao , Tung Joyce Y. , Tunney Robert J. , Vacic Vladimir , Wang Xin , Zare Amir S. , Dutta Diptavo , Glavaris Stephanie , Keramati Ali , Chatterjee Nilanjan , Chi Neil C. , Ren Bing , Post Wendy S. , Battle Alexis 
Published: February 2020

AbstractHeart failure is a major public health problem affecting over 23 million people worldwide. In this study, we present the results of a large scale meta-analysis of heart failure GWAS and replication in a comparable sized cohort to identify one known and two novel loci associated with heart failure. Heart failure sub-phenotyping shows that a new locus in chromosome 1 is associated with left ventricular adverse remodeling and clinical heart failure, in response to different initial cardiac muscle insults. Functional characterization and fine-mapping of that locus reveal a putative causal variant in a cardiac muscle specific regulatory region activated during cardiomyocyte differentiation that binds to the ACTN2 gene, a crucial structural protein inside the cardiac sarcolemma (Hi-C interaction p-value = 0.00002). Genome-editing in human embryonic stem cell-derived cardiomyocytes confirms the influence of the identified regulatory region in the expression of ACTN2. Our findings extend our understanding of biological mechanisms underlying heart failure.
Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey
Authors: Majka Piotr , Bai Shi , Bakola Sophia , Bednarek Sylwia , Chan Jonathan M. , Jermakow Natalia , Passarelli Lauretta , Reser David H. , Theodoni Panagiota , Worthy Katrina H. , Wang Xiao-Jing , Wójcik Daniel K. , Mitra Partha P. , Rosa Marcello G. P. 
Published: February 2020

AbstractUnderstanding the principles of neuronal connectivity requires tools for efficient quantification and visualization of large datasets. The primate cortex is particularly challenging due to its complex mosaic of areas, which in many cases lack clear boundaries. Here, we introduce a resource that allows exploration of results of 143 retrograde tracer injections in the marmoset neocortex. Data obtained in different animals are registered to a common stereotaxic space using an algorithm guided by expert delineation of histological borders, allowing accurate assignment of connections to areas despite interindividual variability. The resource incorporates tools for analyses relative to cytoarchitectural areas, including statistical properties such as the fraction of labeled neurons and the percentage of supragranular neurons. It also provides purely spatial (parcellation-free) data, based on the stereotaxic coordinates of 2 million labeled neurons. This resource helps bridge the gap between high-density cellular connectivity studies in rodents and imaging-based analyses of human brains.
One-dimensional flat bands in twisted bilayer germanium selenide
Authors: Kennes D. M. , Xian L. , Claassen M. , Rubio A. 
Published: February 2020

AbstractExperimental advances in the fabrication and characterization of few-layer materials stacked at a relative twist of small angle have recently shown the emergence of flat energy bands. As a consequence electron interactions become relevant, providing inroads into the physics of strongly correlated two-dimensional systems. Here, we demonstrate by combining large scale ab initio simulations with numerically exact strong correlation approaches that an effective one-dimensional system emerges upon stacking two twisted sheets of GeSe, in marked contrast to all moiré systems studied so far. This not only allows to study the necessarily collective nature of excitations in one dimension, but can also serve as a promising platform to scrutinize the crossover from two to one dimension in a controlled setup by varying the twist angle, which provides an intriguing benchmark with respect to theory. We thus establish twisted bilayer GeSe as an intriguing inroad into the strongly correlated physics of lowdimensional systems.
Rift Valley fever virus vaccination induces long-lived, antigen-specific human T cell responses
Authors: Harmon Jessica R. , Barbeau Dominique J. , Nichol Stuart T. , Spiropoulou Christina F. , McElroy Anita K. 
Published: February 2020

AbstractRift Valley fever virus (RVFV) is a zoonotic arbovirus of clinical significance in both livestock and humans. A formalin-inactivated virus preparation was initially developed for human use and tested in laboratory workers in the 1960s. Vaccination resulted in generation of neutralizing antibody titers in most recipients, but neutralization titers waned over time, necessitating frequent booster doses. In this study, T cell-based immune responses to the formalin-inactivated vaccine were examined in a cohort of seven individuals who received between 1 and 6 doses of the vaccine. RVFV-specific T cell responses were detectable up to 24 years post vaccination. Peripheral blood mononuclear cells from this cohort of individuals were used to map out the viral epitopes targeted by T cells in humans. These data provide tools for assessing human RVFV-specific T cell responses and are thus a valuable resource for future human RVFV vaccine efforts.
Kinetics of Photo-Oxidation of Oxazole and its Substituents by Singlet Oxygen
Authors: Zeinali Nassim , Oluwoye Ibukun , Altarawneh Mohammednoor , Dlugogorski Bogdan Z. 
Published: February 2020

AbstractOxazole has critical roles not only in heterocycle (bio)chemistry research, but also as the backbone of many active natural and medicinal species. These diverse and specialised functions can be attributed to the unique physicochemical properties of oxazole. This contribution investigates the reaction of oxazole and its derivatives with singlet oxygen, employing density functional theory DFT-B3LYP calculations. The absence of allylic hydrogen in oxazole eliminates the ene-mode addition of singlet oxygen to the aromatic ring. Therefore, the primary reaction pathway constitutes the [4 + 2]-cycloaddition of singlet oxygen to oxazole ring, favouring an energetically accessible corridor of 57 kJ/mol to produce imino-anhydride which is postulated to convert to triamide end-product in subsequent steps. The pseudo-first-order reaction rate for substituted oxazole (e.g., 4-methyl-2,5-diphenyloxazole, 1.14 × 106 M−1 s−1) appears slightly higher than that of unsubstituted oxazole (0.94 × 106 M−1 s−1) considering the same initial concentration of the species at 300 K, due to the electronic effect of the functional groups. The global reactivity descriptors have justified the relative influence of the functional groups along with their respective physiochemical properties.
Exploring the temporal dynamics of speech production with EEG and group ICA
Authors: Janssen Niels , Meij Maartje van der , López-Pérez Pedro Javier , Barber Horacio A. 
Published: February 2020

AbstractSpeech production is a complex skill whose neural implementation relies on a large number of different regions in the brain. How neural activity in these different regions varies as a function of time during the production of speech remains poorly understood. Previous MEG studies on this topic have concluded that activity proceeds from posterior to anterior regions of the brain in a sequential manner. Here we tested this claim using the EEG technique. Specifically, participants performed a picture naming task while their naming latencies and scalp potentials were recorded. We performed group temporal Independent Component Analysis (group tICA) to obtain temporally independent component timecourses and their corresponding topographic maps. We identified fifteen components whose estimated neural sources were located in various areas of the brain. The trial-by-trial component timecourses were predictive of the naming latency, implying their involvement in the task. Crucially, we computed the degree of concurrent activity of each component timecourse to test whether activity was sequential or parallel. Our results revealed that these fifteen distinct neural sources exhibit largely concurrent activity during speech production. These results suggest that speech production relies on neural activity that takes place in parallel networks of distributed neural sources.
Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential
Authors: Golz Julia C. , Epping Lennard , Knüver Marie-Theres , Borowiak Maria , Hartkopf Felix , Deneke Carlus , Malorny Burkhard , Semmler Torsten , Stingl Kerstin 
Published: February 2020

AbstractCampylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.
Documentation of a new hypotrich species in the family Amphisiellidae, Lamtostyla gui n. sp. (Protista, Ciliophora) using a multidisciplinary approach
Authors: Liao Wanying , Gong Zhiwei , Ni Bing , Fan Xinpeng , Petroni Giulio 
Published: February 2020

AbstractAn integrated approach considering both morphologic and molecular data is now required to improve biodiversity estimations and provide more robust systematics interpretations in hypotrichs, a highly differentiated group of ciliates. In present study, we document a new hypotrich species, Lamtostyla gui n. sp., collected from Chongming wetland, Shanghai, China, based on investigations using living observation, protargol staining, scanning and transmission electron microscopy, and gene sequencing. The new species is mainly recognized by having a short amphisiellid median cirral row composed of four cirri, three frontoventral cirri, three dorsal kinetids, four to eight macronuclear nodules, and small colorless cortical granules distributed as rosettes around dorsal bristles. Transmission electron microscope observation finds the associated microtubules of cirri and pharyngeal discs of L. gui are distinct from those in other hypotrichs. Morphogenesis of this species indicates that parental adoral membranelles retained intact or partial renewed is a potential feature to separate Lamtostyla granulifera-group and Lamtostyla lamottei-group. Phylogenetic analysis based on small subunit ribosomal RNA (rRNA) gene shows that this molecular marker is not useful to resolve phylogenetic relationships of the genus Lamtostyla, as well as many other hypotrichous taxa. We additionally characterize the internal transcribed spacers (ITS) region and the almost complete large subunit rRNA, which will be essential for future studies aimed at solving phylogenetic problems of Lamtostyla, or even the family Amphisiellidae. As a final remark, the critical screening of GenBank using ITS genes of our organism allows us to recognize a large amount of hypotrichous sequences have been misclassified as fungi. This observation suggests that hypotrichs could be frequently found in fungi-rich environment and overlooked by fungal specialists.
Comparison of outcomes of four different treatment modalities for diabetic vitreous haemorrhage
Authors: Taskintuna Ibrahim , Elsayed Maram E. A. Abdalla , Taskintuna Kaan , Ahmad Khabir , Khandekar Rajiv , Schatz Patrik , Kozak Igor 
Published: February 2020

AbstractWe compared outcomes of four different management modalities for diabetic VH. Patients with diabetic VH were identified in this retrospective study undertaken at King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia. Eyes were grouped based on the treatment received: control (observation only), intravitreal bevacizumab (IVB) injection(s), pars plana vitrectomy (PPV), and preoperative single IVB injection before PPV. Best-corrected visual acuity (BCVA) and status of VH were noted at baseline and the last follow up (Minimum: 6 months, maximum: 29 months). The proportion of eyes with Snellen BCVA improvement by two lines or more and VH clearance at the last follow up were compared between groups. The four groups – Control, IVB, PPV, and IVB-before-PPV had 23, 29, 17, and 20 eyes, respectively. The proportion of eyes gaining ≥2 lines was substantially higher in the IVB-before-PPV and PPV groups (90% and 77%, respectively) compared with IVB and observation groups (41% and 22%, respectively). Surgical treatment was associated with a 2.38 times higher likelihood of gaining ≥2 lines than the non-surgical one (incidence ratio: 2.38, 95% CI 1.19, 4.78 P = 0.015) after adjusting for age, hyperglycemia and BCVA at presentation. Less invasive treatment such as IVB injections did not result in the same amount of improvement in vision as did PPV. Prospective randomized studies are needed to better define the role of IVB injections in the management of diabetic VH.
Automated volumetric radiomic analysis of breast cancer vascularization improves survival prediction in primary breast cancer
Authors: Dietzel Matthias , Schulz-Wendtland Rüdiger , Ellmann Stephan , Zoubi Ramy , Wenkel Evelyn , Hammon Matthias , Clauser Paola , Uder Michael , Runnebaum Ingo B. , Baltzer Pascal A. T. 
Published: February 2020

AbstractTo investigate whether automated volumetric radiomic analysis of breast cancer vascularization (VAV) can improve survival prediction in primary breast cancer. 314 consecutive patients with primary invasive breast cancer received standard clinical MRI before the initiation of treatment according to international recommendations. Diagnostic work-up, treatment, and follow-up was done at one tertiary care, academic breast-center (outcome: disease specific survival/DSS vs. disease specific death/DSD). The Nottingham Prognostic Index (NPI) was used as the reference method with which to predict survival of breast cancer. Based on the MRI scans, VAV was accomplished by commercially available, FDA-cleared software. DSD served as endpoint. Integration of VAV into the NPI gave NPIVAV. Prediction of DSD by NPIVAV compared to standard NPI alone was investigated (Cox regression, likelihood-test, predictive accuracy: Harrell’s C, Kaplan Meier statistics and corresponding hazard ratios/HR, confidence intervals/CI). DSD occurred in 35 and DSS in 279 patients. Prognostication of the survival outcome by NPI (Harrell’s C = 75.3%) was enhanced by VAV (NPIVAV: Harrell’s C = 81.0%). Most of all, the NPIVAV identified patients with unfavourable outcome more reliably than NPI alone (hazard ratio/HR = 4.5; confidence interval/CI = 2.14-9.58; P = 0.0001). Automated volumetric radiomic analysis of breast cancer vascularization improved survival prediction in primary breast cancer. Most of all, it optimized the identification of patients at higher risk of an unfavorable outcome. Future studies should integrate MRI as a “gate keeper” in the management of breast cancer patients. Such a “gate keeper” could assist in selecting patients benefitting from more advanced diagnostic procedures (genetic profiling etc.) in order to decide whether are a more aggressive therapy (chemotherapy) is warranted.
Peripartum issues in the inflammatory arthritis patient: A survey of the RAPPORT registry
Authors: Dissanayake T. D. , Maksymowych W. P. , Keeling S. O. 
Published: February 2020

AbstractChildbearing women with rheumatoid (RA) and psoriatic arthritis (PsA) have significant peripartum issues. A retrospective anonymous RedCAP survey of peripartum period in females with RA/PsA in the RAPPORT registry was performed. Completed analyses included descriptive statistics, Chi-square and Fisher’s exact test. 162 patients (133 RA/29 PsA) completed the survey (103 women having 234 pregnancies), 164 pregnancies occurring before and 70 pregnancies occurring after diagnosis. Pregnancy outcomes from 103 patients included: 96% live births, 1.9% stillbirths, 23% miscarriages, and 15% therapeutic abortions. A third of patients had fewer children than desired due to disease activity, medications and other reasons. For 63 pregnancies after diagnosis: (1) 49% of pregnancies received pre-conception counseling; (2) 65% described good disease control during pregnancy but 74% flared in the first 3 months postpartum; (3) 79% of pregnancies discontinued IA medications; (4) 35% of pregnancies occurred on biologic therapy at or prior to conception. Gestational age at time of delivery was 37–40 weeks in 58% (33/57) post-arthritis vs 66% (83/126) pre-arthritis pregnancies. No statistically significant differences occurred between pregnancies before or after RA/PsA diagnosis for: pregnancy planning, fertility treatment, pregnancy and labour/delivery complications, birth defect frequency or neonatal complications. Neonatal ICU admissions were significantly lower in pre- compared to post-arthritis pregnancies (3.2% vs 14.5%). No pregnancy complications were noted in 24/54 pregnancies on medications compared to 6/9 pregnancies not on medications. The impact of RA/PsA before, during and after pregnancy varied considerably in this cohort emphasizing the importance of informed-decision making at all stages.
Corals reveal ENSO-driven synchrony of climate impacts on both terrestrial and marine ecosystems in northern Borneo
Authors: Krawczyk Hedwig , Zinke Jens , Browne Nicola , Struck Ulrich , McIlwain Jennifer , O’Leary Michael , Garbe-Schönberg Dieter 
Published: February 2020

AbstractExtreme climate events, such as the El Niños in 1997/1998 and 2015/16, have led to considerable forest loss in the Southeast Asian region following unprecedented drought and wildfires. In Borneo, the effects of extreme climate events have been exacerbated by rapid urbanization, accelerated deforestation and soil erosion since the 1980s. However, studies quantifying the impact of interannual and long-term (>3 decades) climatic and anthropogenic change affecting Borneo’s coastal and coral reef environments are lacking. Here, we used coral cores collected in Miri-Sibuti Coral Reefs National Park, Sarawak (Malaysia) to reconstruct the spatio-temporal dynamics of sea surface temperature and oxygen isotopic composition of seawater from 1982 to 2016, based on paired oxygen isotope and Sr/Ca measurements. The results revealed rising sea surface temperatures of 0.26 ± 0.04 °C per decade since 1982. Reconstructed δ18Osw displayed positive excursion during major El Niño events of 1983, 1997/98 and 2015/16, indicating drought conditions with less river runoff, rainfall and higher ocean salinities. La Niñas were generally associated with lower δ18Osw. We observed a long-term shift from more saline conditions between 1982 and 1995 towards less saline conditions after 1995, which are in agreement with the regional freshening trend, punctuated by saline excursion during El Niños. The decadal shifts were found to be driven by the Pacific Decadal Oscillation (PDO). This study provides the first long-term data on El Niño Southern Oscillation (ENSO)-driven synchrony of climate impacts on both terrestrial and marine ecosystems in northern Borneo. Our results suggest that coral records from northern Borneo are invaluable archives to detect regional ENSO and PDO impacts, and their interaction with the Asian-Australian monsoon, on the hydrological balance in the southern South China Sea beyond the past three decades.
An investigation of pre-crystalline order, ruling out Pauli crystals and introducing Pauli anti-crystals
Authors: Fremling Mikael , Slingerland J. K. 
Published: February 2020

AbstractFluid states of matter can locally exhibit characteristics of the onset of crystalline order. Traditionally this has been theoretically investigated using multipoint correlation functions. However new measurement techniques now allow multiparticle configurations of cold atomic systems to be observed directly. This has led to a search for new techniques to characterize the configurations that are likely to be observed. One of these techniques is the configuration density (CD), which has been used to argue for the formation of “Pauli crystals” by non-interacting electrons in e.g. a harmonic trap. We show here that such Pauli crystals do not exist, but that other other interesting spatial structures can occur in the form of an “anti-Crystal”, where the fermions preferentially avoid a lattice of positions surrounding any given fermion. Further, we show that configuration densities must be treated with great care as naive application can lead to the identification of crystalline structures which are artifacts of the method and of no physical significance. We analyze the failure of the CD and suggest methods that might be more suitable for characterizing multiparticle correlations which may signal the onset of crystalline order. In particular, we introduce neighbour counting statistics (NCS), which is the full counting statistics of the particle number in a neighborhood of a given particle. We test this on two dimensional systems with emerging triangular and square crystal structures.
First evidence of production of the lantibiotic nisin P
Authors: Garcia-Gutierrez Enriqueta , O’Connor Paula M. , Saalbach Gerhard , Walsh Calum J. , Hegarty James W. , Guinane Caitriona M. , Mayer Melinda J. , Narbad Arjan , Cotter Paul D. 
Published: February 2020

AbstractNisin P is a natural nisin variant, the genetic determinants for which were previously identified in the genomes of twoStreptococcusspecies, albeit with no confirmed evidence of production. Here we describeStreptococcus agalactiaeDPC7040, a human faecal isolate, which exhibits antimicrobial activity against a panel of gut and food isolates by virtue of producing nisin P. Nisin P was purified, and its predicted structure was confirmed by nanoLC-MS/MS, with both the fully modified peptide and a variant without rings B and E being identified. Additionally, we compared its spectrum of inhibition and minimum inhibitory concentration (MIC) with that of nisin A and its antimicrobial effect in a faecal fermentation in comparison with nisin A and H. We found that its antimicrobial activity was less potent than nisin A and H, and we propose a link between this reduced activity and the peptide structure.