bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial whole-genome sequencing and analysis of the host genetic contribution to COVID-19 severity and susceptibility
Authors: Wang Fang , Huang Shujia , Gao Rongsui , Zhou Yuwen , Lai Changxiang , Li Zhichao , Xian Wenjie , Qian Xiaobo , Li Zhiyu , Huang Yushan , Tang Qiyuan , Liu Panhong , Chen Ruikun , Liu Rong , Li Xuan , Tong Xin , Zhou Xuan , Bai Yong , Duan Gang , Zhang Tao , Xu Xun , Wang Jian , Yang Huanming , Liu Siyang , He Qing , Jin Xin , Liu Lei 
Published: November 2020

AbstractThe COVID-19 pandemic has accounted for millions of infections and hundreds of thousand deaths worldwide in a short-time period. The patients demonstrate a great diversity in clinical and laboratory manifestations and disease severity. Nonetheless, little is known about the host genetic contribution to the observed interindividual phenotypic variability. Here, we report the first host genetic study in the Chinese population by deeply sequencing and analyzing 332 COVID-19 patients categorized by varying levels of severity from the Shenzhen Third People’s Hospital. Upon a total of 22.2 million genetic variants, we conducted both single-variant and gene-based association tests among five severity groups including asymptomatic, mild, moderate, severe, and critical ill patients after the correction of potential confounding factors. Pedigree analysis suggested a potential monogenic effect of loss of function variants in GOLGA3 and DPP7 for critically ill and asymptomatic disease demonstration. Genome-wide association study suggests the most significant gene locus associated with severity were located in TMEM189–UBE2V1 that involved in the IL-1 signaling pathway. The p.Val197Met missense variant that affects the stability of the TMPRSS2 protein displays a decreasing allele frequency among the severe patients compared to the mild and the general population. We identified that the HLA-A*11:01, B*51:01, and C*14:02 alleles significantly predispose the worst outcome of the patients. This initial genomic study of Chinese patients provides genetic insights into the phenotypic difference among the COVID-19 patient groups and highlighted genes and variants that may help guide targeted efforts in containing the outbreak. Limitations and advantages of the study were also reviewed to guide future international efforts on elucidating the genetic architecture of host–pathogen interaction for COVID-19 and other infectious and complex diseases.
Redox-informed models of global biogeochemical cycles
Authors: Zakem Emily J. , Polz Martin F. , Follows Michael J. 
Published: November 2020

AbstractMicrobial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments.“Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keefe
Understanding the metal-to-insulator transition in La1−xSrxCoO3−δ and its applications for neuromorphic computing
Authors: Zhang Shenli , Galli Giulia 
Published: November 2020

AbstractTransition metal oxides that exhibit a metal-to-insulator transition (MIT) as a function of oxygen vacancy concentration are promising systems to realize energy-efficient platforms for neuromorphic computing. However, the current lack of understanding of the microscopic mechanism driving the MIT hinders the realization of effective and stable devices. Here we investigate defective cobaltites and we unravel the structural, electronic, and magnetic changes responsible for the MIT when oxygen vacancies are introduced in the material. We show that, contrary to accepted views, cooperative structural distortions instead of local bonding changes are responsible for the MIT, and we describe the subtle interdependence of structural and magnetic transitions. Finally, we present a model, based on first principles, to predict the required electric bias to drive the transition, showing good agreement with available measurements and providing a paradigm to establish design rules for low-energy cost devices.
Observing photo-induced chiral edge states of graphene nanoribbons in pump-probe spectroscopies
Authors: Chen Yuan , Wang Yao , Claassen Martin , Moritz Brian , Devereaux Thomas P. 
Published: November 2020

AbstractPhoto-induced edge states in low-dimensional materials have attracted considerable attention due to the tunability of topological properties and dispersion. Specifically, graphene nanoribbons have been predicted to host chiral edge modes upon irradiation with circularly polarized light. Here, we present numerical calculations of time-resolved angle resolved photoemission spectroscopy and trRIXS of a graphene nanoribbon. We characterize pump-probe spectroscopic signatures of photo-induced edge states, illustrate the origin of distinct spectral features that arise from Floquet topological edge modes, and investigate the roles of incoming photon energies and finite core–hole lifetime in RIXS. With momentum, energy, and time resolution, pump-probe spectroscopies can play an important role in understanding the behavior of photo-induced topological states of matter.
Mitochondria interaction networks show altered topological patterns in Parkinson’s disease
Authors: Zanin Massimiliano , Santos Bruno F. R. , Antony Paul M. A. , Berenguer-Escuder Clara , Larsen Simone B. , Hanss Zoé , Barbuti Peter A. , Baumuratov Aidos S. , Grossmann Dajana , Capelle Christophe M. , Weber Joseph , Balling Rudi , Ollert Markus , Krüger Rejko , Diederich Nico J. , He Feng Q. 
Published: November 2020

AbstractMitochondrial dysfunction is linked to pathogenesis of Parkinson’s disease (PD). However, individual mitochondria-based analyses do not show a uniform feature in PD patients. Since mitochondria interact with each other, we hypothesize that PD-related features might exist in topological patterns of mitochondria interaction networks (MINs). Here we show that MINs formed nonclassical scale-free supernetworks in colonic ganglia both from healthy controls and PD patients; however, altered network topological patterns were observed in PD patients. These patterns were highly correlated with PD clinical scores and a machine-learning approach based on the MIN features alone accurately distinguished between patients and controls with an area-under-curve value of 0.989. The MINs of midbrain dopaminergic neurons (mDANs) derived from several genetic PD patients also displayed specific changes. CRISPR/CAS9-based genome correction of alpha-synuclein point mutations reversed the changes in MINs of mDANs. Our organelle-interaction network analysis opens another critical dimension for a deeper characterization of various complex diseases with mitochondrial dysregulation.
Curing piglets from diarrhea and preparation of a healthy microbiome with Bacillus treatment for industrial animal breeding
Authors: Yue Shousong , Li Zhentian , Hu Fuli , Picimbon Jean-François 
Published: November 2020

AbstractHigh-throughput farming of animals for an essential purpose such as large scale health and production of hogs is a challenge for the food industry in the modern world. The problem is that the breeding of livestock for fast growth or high yields of meat is often associated with illness and microbial infection that develop under the breeding conditions. Piglet diarrhea is most common pig disease, leading to heavy mortality and thereby economic loss. We proved that chemical drugs can relieve the symptoms of diarrhea in ill piglets, but they do not treat the underlying cause, i.e. significantly altered bacterial gut flora. Using Illumina sequencing of fecal DNA, we showed that the bacterial gut flora of piglets treated with antibiotics remain close to the ill conditions. However, using Illumina sequencing of fecal DNA from piglets treated with a specific Bacillus (Bacillus subtilis Y-15, B. amyloliquefaciens DN6502 and B. licheniformis SDZD02) demonstrated the efficiency of natural bioproducts not only on curing diarrhea, but also on beneficial bacteria to re-establish in the piglet gut. We therefore propose a new natural “medicine” to be explored by the world farm animal agriculture industry, particularly for sustainable improvement of swine livestock production and health.
First sequencing of ancient coral skeletal proteins
Authors: Drake Jeana L. , Whitelegge Julian P. , Jacobs David K. 
Published: November 2020

AbstractHere we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC–MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.
Mir142 loss unlocks IDH2R140-dependent leukemogenesis through antagonistic regulation of HOX genes
Authors: Marshall A. , Kasturiarachchi J. , Datta P. , Guo Y. , Deltcheva E. , James C. , Brown J. , May G. , Anandagoda N. , Jackson I. , Howard J. K. , Ghazaly E. , Brooks S. , Khwaja A. , Araki M. , Araki K. , Linch D. , Lord G. M. , Enver T. , Nimmo R. 
Published: November 2020

AbstractAML is a genetically heterogeneous disease and understanding how different co-occurring mutations cooperate to drive leukemogenesis will be crucial for improving diagnostic and therapeutic options for patients. MIR142 mutations have been recurrently detected in IDH-mutated AML samples. Here, we have used a mouse model to investigate the interaction between these two mutations and demonstrate a striking synergy between Mir142 loss-of-function and IDH2R140Q, with only recipients of double mutant cells succumbing to leukemia. Transcriptomic analysis of the non-leukemic single and leukemic double mutant progenitors, isolated from these mice, suggested a novel mechanism of cooperation whereby Mir142 loss-of-function counteracts aberrant silencing of Hoxa cluster genes by IDH2R140Q. Our analysis suggests that IDH2R140Q is an incoherent oncogene, with both positive and negative impacts on leukemogenesis, which requires the action of cooperating mutations to alleviate repression of Hoxa genes in order to advance to leukemia. This model, therefore, provides a compelling rationale for understanding how different mutations cooperate to drive leukemogenesis and the context-dependent effects of oncogenic mutations.
Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet
Authors: Pujar Mahesh , Gangaprasad S. , Govindaraj Mahalingam , Gangurde Sunil S. , Kanatti A. , Kudapa Himabindu 
Published: November 2020

AbstractPearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.
Modeling and forecasting the early evolution of the Covid-19 pandemic in Brazil
Authors: Bastos Saulo B. , Cajueiro Daniel O. 
Published: November 2020

AbstractWe model and forecast the early evolution of the COVID-19 pandemic in Brazil using Brazilian recent data from February 25, 2020 to March 30, 2020. This early period accounts for unawareness of the epidemiological characteristics of the disease in a new territory, sub-notification of the real numbers of infected people and the timely introduction of social distancing policies to flatten the spread of the disease. We use two variations of the SIR model and we include a parameter that comprises the effects of social distancing measures. Short and long term forecasts show that the social distancing policy imposed by the government is able to flatten the pattern of infection of the COVID-19. However, our results also show that if this policy does not last enough time, it is only able to shift the peak of infection into the future keeping the value of the peak in almost the same value. Furthermore, our long term simulations forecast the optimal date to end the policy. Finally, we show that the proportion of asymptomatic individuals affects the amplitude of the peak of symptomatic infected, suggesting that it is important to test the population.
The influence of induction speed on the frontal (processed) EEG
Authors: Obert D. P. , Sepúlveda P. , Kratzer S. , Schneider G. , Kreuzer M. 
Published: November 2020

AbstractThe intravenous injection of the anaesthetic propofol is clinical routine to induce loss of responsiveness (LOR). However, there are only a few studies investigating the influence of the injection rate on the frontal electroencephalogram (EEG) during LOR. Therefore, we focused on changes of the frontal EEG especially during this period. We included 18 patients which were randomly assigned to a slow or fast induction group and recorded the frontal EEG. Based on this data, we calculated the power spectral density, the band powers and band ratios. To analyse the behaviour of processed EEG parameters we calculated the beta ratio, the spectral entropy, and the spectral edge frequency. Due to the prolonged induction period in the slow injection group we were able to distinguish loss of responsiveness to verbal command (LOvR) from loss of responsiveness to painful stimulus (LOpR) whereas in the fast induction group we could not. At LOpR, we observed a higher relative alpha and beta power in the slow induction group while the relative power in the delta range was lower than in the fast induction group. When concentrating on the slow induction group the increase in relative alpha power pre-LOpR and even before LOvR indicated that frontal EEG patterns, which have been suggested as an indicator of unconsciousness, can develop before LOR. Further, LOvR was best reflected by an increase of the alpha to delta ratio, and LOpR was indicated by a decrease of the beta to alpha ratio. These findings highlight the different spectral properties of the EEG at various levels of responsiveness and underline the influence of the propofol injection rate on the frontal EEG during induction of general anesthesia.
Survival rate dependent variations in retinopathy of prematurity treatment rates in very low birth weight infants
Authors: Park Jae Hyun , Hwang Jong Hee , Chang Yun Sil , Lee Myung Hee , Park Won Soon 
Published: November 2020

AbstractAs increased oxidative stress causes increased mortality and morbidities like bronchopulmonary dysplasia (BPD) and retinopathy of prematurity (ROP) in very low birth weight infants (VLBWIs), the conundrum of improved survival but increased ROP observed with the high oxygen saturation target range of 91–95% is difficult to explain. To determine the survival rate-dependent variation in ROP treatment rate, 6292 surviving eligible VLBWIs registered in the Korean Neonatal Network were arbitrarily grouped according to the survival rate of infants at 23–24 weeks’ gestation as group I (> 70%, n = 1626), group II (40–70%, n = 2984) and group III (< 40%, n = 1682). Despite significantly higher survival and lower BPD rates in group I than in groups II and III, the ROP treatment rate was higher in group I than in groups II and III. However, the adjusted odds ratios for ROP treatment were not significantly different between the study groups, and the ROP treatment rate in the infants at 23–24 weeks’ gestation was 21-fold higher than the infants at ≥ 27 weeks’ gestation. The controversial association between improved survival and reduced BPD reflecting quality improvement of neonatal intensive care but increased ROP treatment rate might be primarily attributed to the improved survival of the most immature infants.
Improving single pixel imaging performance in high noise condition by under-sampling
Authors: Sha Fangyuan , Sahoo Sujit Kumar , Lam Huy Quoc , Ng Beng Koon , Dang Cuong 
Published: November 2020

AbstractSingle-pixel imaging could be a superior solution for imaging applications where the detector array is very expensive or not even available. Sampling order, sampling ratio, noise and type of transforms affect the quality of the reconstructed image. Here, we compare the performance of single pixel imaging (SPI) with Hadamard transform (HT) and discrete cosine transform (DCT) in the presence of noise. The trade-off between adding image information and adding noise in each coefficient measurement results in an optimum number of measurements for reconstruction image quality. In addition, DCT shows higher image quality with fewer measurements than HT does. We then demonstrate our SPI with optimum sampling strategy for a large set of images and lab experiments and finally put forward a quality control technique, which is corroborated by the practical experiments. Our results suggest a practical approach for SPI to improve the speed and achieve the highest possible image quality.
Pyuria, urinary tract infection and renal outcome in patients with chronic kidney disease stage 3–5
Authors: Kuo I-Ching , Lee Jia-Jung , Hwang Daw-Yang , Lim Lee-Moay , Lin Hugo You-Hsien , Hwang Shang-Jyh , Chen Hung-Chun , Hung Chi-Chih 
Published: November 2020

AbstractPyuria is common in chronic kidney disease (CKD), which could be due to either urinary tract infection (UTI) or renal parenchymal inflammation. Only little is known regarding the association of pyuria or UTI with renal outcomes. We investigated 3226 patients with stage 3–5 CKD. Pyuria was defined as ≥ 50 WBC per high-power field (hpf) and was correlated to old age, female, diabetes, hypoalbuminemia, lower eGFR, and higher inflammation status. In Cox regression, patients with more than one episode of pyuria in the first year (11.8%) had increased risks for end-stage renal disease (ESRD) [hazard ratio (95% CI): 1.90 (1.58–2.28); p < 0.001], rapid renal function progression [odds ratio (95% CI): 1.49 (1.13–1.95); p = 0.001], and all-cause mortality [hazard ratio: 1.63 (1.29–2.05); p < 0.001], compared to those without pyuria. In a subgroup analysis, the risk of pyuria for ESRD was modified by CKD stages. We investigated the effects of UTI (urinary symptoms and treated by antibiotics) and pyuria without UTI (urine WBC < 50 to ≥ 10/hpf without any episodes of ≥ 50 WBC/hpf or UTI), while both groups were associated with clinical outcomes. In conclusion, CKD stage 3–5 patients with frequent pyuria or UTI episodes have increased risks of renal outcomes.
The origins of binding specificity of a lanthanide ion binding peptide
Authors: Hatanaka Takaaki , Kikkawa Nobuaki , Matsugami Akimasa , Hosokawa Yoichi , Hayashi Fumiaki , Ishida Nobuhiro 
Published: November 2020

AbstractLanthanide ions (Ln3+) show similar physicochemical properties in aqueous solutions, wherein they exist as + 3 cations and exhibit ionic radii differences of less than 0.26 Å. A flexible linear peptide lanthanide binding tag (LBT), which recognizes a series of 15 Ln3+, shows an interesting characteristic in binding specificity, i.e., binding affinity biphasically changes with an increase in the atomic number, and shows a greater than 60-fold affinity difference between the highest and lowest values. Herein, by combining experimental and computational investigations, we gain deep insight into the reaction mechanism underlying the specificity of LBT3, an LBT mutant, toward Ln3+. Our results clearly show that LBT3-Ln3+ binding can be divided into three, and the large affinity difference is based on the ability of Ln3+ in a complex to be directly coordinated with a water molecule. When the LBT3 recognizes a Ln3+ with a larger ionic radius (La3+ to  Sm3+), a water molecule can interact with Ln3+ directly. This extra water molecule infiltrates the complex and induces dissociation of the Asn5 sidechain (one of the coordinates) from Ln3+, resulting in a destabilizing complex and low affinity. Conversely, with recognition of smaller Ln3+ (Sm3+ to Yb3+), the LBT3 completely surrounds the ions and constructs a stable high affinity complex. Moreover, when the LBT3 recognizes the smallest Ln3+, namely Lu3+, although it completely surrounds Lu3+, an entropically unfavorable phenomenon specifically occurs, resulting in lower affinity than that of Yb3+. Our findings will be useful for the design of molecules that enable the distinction of sub-angstrom size differences.