bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast and Accurate Computation of Vertical Modes
Authors: Early Jeffrey J. , Lelong M. Pascale , Smith K. Shafer 
Published: February 2020

AbstractThe vertical modes of linearized equations of motion are widely used by the oceanographic community in numerous theoretical and observational contexts. However, the standard approach for solving the generalized eigenvalue problem using second‐order finite difference matrices produces
errors for all but the few lowest modes, and increasing resolution quickly becomes too slow as the computational complexity of eigenvalue algorithms increases as
. Existing methods are therefore inadequate for computing a full spectrum of internal waves, such as needed for initializing a numerical model with a full internal wave spectrum. Here we show that rewriting the eigenvalue problem in stretched coordinates and projecting onto Chebyshev polynomials results in substantially more accurate modes than finite differencing at a fraction of the computational cost. We also compute the surface quasigeostrophic modes using the same methods. All spectral and finite difference algorithms are made available in a suite of Matlab classes that have been validated against known analytical solutions in constant and exponential stratification.
Analog Forecasting of Extreme‐Causing Weather Patterns Using Deep Learning
Authors: Chattopadhyay Ashesh , Nabizadeh Ebrahim , Hassanzadeh Pedram 
Published: February 2020

AbstractNumerical weather prediction models require ever‐growing computing time and resources but, still, have sometimes difficulties with predicting weather extremes. We introduce a data‐driven framework that is based on analog forecasting (prediction using past similar patterns) and employs a novel deep learning pattern‐recognition technique (capsule neural networks, CapsNets) and an impact‐based autolabeling strategy. Using data from a large‐ensemble fully coupled Earth system model, CapsNets are trained on midtropospheric large‐scale circulation patterns (Z500) labeled 0–4 depending on the existence and geographical region of surface temperature extremes over North America several days ahead. The trained networks predict the occurrence/region of cold or heat waves, only using Z500, with accuracies (recalls) of 69–45% (77–48%) or 62–41% (73–47%) 1–5 days ahead. Using both surface temperature and Z500, accuracies (recalls) with CapsNets increase to
80% (88%). In both cases, CapsNets outperform simpler techniques such as convolutional neural networks and logistic regression, and their accuracy is least affected as the size of the training set is reduced. The results show the promises of multivariate data‐driven frameworks for accurate and fast extreme weather predictions, which can potentially augment numerical weather prediction efforts in providing early warnings.
A Regionally Evolving Transpressional Duplex Along the Northern Margin of the Altyn Tagh Fault: New Kinematic and Timing Constraints From the Sanweishan and Nanjieshan, China
Authors: Yang Haibo , Yang Xiaoping , Cunningham Dickson , Hu Zongkai , Huang Xiongnan , Huang Weiliang , Yang Huili , Miao Shuqing , Zhang Ling 
Published: February 2020

AbstractIn this study, we document the kinematics and Late Quaternary slip rates of actively developing faults and folds on the northern side of the Altyn Tagh Fault (ATF) that accommodate uplift and lateral expansion of the northern Tibetan Plateau. Field observations and detailed measurements using Unmanned‐Aerial‐Vehicle Structure‐from‐Motion high‐resolution imagery of offset fan surfaces, gullies, and channel risers coupled with optically stimulated luminescence and 10Be ages constrain the timing and slip rates of the Sanweishan Fault (SWSF) and Nanjieshan Fault (NJSF) systems. The NE striking SWSF is characterized by sinistral strike slip with a top‐to‐the‐NW thrusting component. Offset geomorphic markers and dating results yield Pleistocene strike slip and vertical uplift rates of 0.06–1.25 mm/a and 0.05–0.08 mm/a, respectively. The E‐W trending NJSF is dominated by north and south directed thrusting and km‐scale folding with variable components of sinistral strike slip. The calculated total N‐S shortening rate across the NJSF is ~0.3 mm/a. Low rates of deformation for the SWSF and NJSF account for less than 10% of the total intraplate strain accommodated along the northeasternmost ATF system. Over a 1,000‐km length, the northward expansion of the Tibetan Plateau occurs by progressive northeastward growth of a transpressional duplex rooted SE into the ATF. An assumed crustal strength discontinuity along the northeast trending southern margin of the Tarim Craton focuses oblique convergence along the ATF. Oblique‐slip thrusting and sinistral strike slip along the ATF and to the north accommodate the oblique convergence, consistent with the ENE directed geodetically derived crustal velocity field driven by India's continued indentation 1,500 km to the south.
Dual disruption of aldehyde dehydrogenases 1 and 3 promotes functional changes in the glutathione redox system and enhances chemosensitivity in nonsmall cell lung cancer
Authors: Rebollido-Rios Rocio , Venton Geoffroy , Sánchez-Redondo Sara , Iglesias i Felip Carmela , Fournet Guy , González Elena , Romero Fernández Wilber , Borroto Escuela Dasiel Oscar , Di Stefano Barbara , Penarroche-Díaz Reinier , Martin Guillaume , Ceylan Ismail , Costello Regis , Perez-Alea Mileidys 
Published: February 2020

AbstractAldehyde dehydrogenases (ALDHs) are multifunctional enzymes that oxidize diverse endogenous and exogenous aldehydes. We conducted a meta-analysis based on The Cancer Genome Atlas and Gene Expression Omnibus data and detected genetic alterations in ALDH1A1, ALDH1A3, or ALDH3A1, 86% of which were gene amplification or mRNA upregulation, in 31% of nonsmall cell lung cancers (NSCLCs). The expression of these isoenzymes impacted chemoresistance and shortened survival times in patients. We hypothesized that these enzymes provide an oxidative advantage for the persistence of NSCLC. To test this hypothesis, we used genetic and pharmacological approaches with DIMATE, an irreversible inhibitor of ALDH1/3. DIMATE showed cytotoxicity in 73% of NSCLC cell lines tested and demonstrated antitumor activity in orthotopic xenografts via hydroxynonenal-protein adduct accumulation, GSTO1-mediated depletion of glutathione and increased H2O2. Consistent with this result, ALDH1/3 disruption synergized with ROS-inducing agents or glutathione synthesis inhibitors to trigger cell death. In lung cancer xenografts with high to moderate cisplatin resistance, combination treatment with DIMATE promoted strong synergistic responses with tumor regression. These results indicate that NSCLCs with increased expression of ALDH1A1, ALDH1A3, or ALDH3A1 may be targeted by strategies involving inhibitors of these isoenzymes as monotherapy or in combination with chemotherapy to overcome patient-specific drug resistance.
Anti-thyroid antibodies and thyroid echo pattern at baseline as risk factors for thyroid dysfunction induced by anti-programmed cell death-1 antibodies: a prospective study
Authors: Okada Norio , Iwama Shintaro , Okuji Takayuki , Kobayashi Tomoko , Yasuda Yoshinori , Wada Eri , Onoue Takeshi , Goto Motomitsu , Sugiyama Mariko , Tsunekawa Taku , Takagi Hiroshi , Hagiwara Daisuke , Ito Yoshihiro , Suga Hidetaka , Banno Ryoichi , Hase Tetsunari , Morise Masahiro , Kanda Mitsuro , Yokota Kenji , Hashimoto Naozumi , Ando Masahiko , Fujimoto Yasushi , Nagino Masato , Kodera Yasuhiro , Fujishiro Mitsuhiro , Hibi Hideharu , Sone Michihiko , Kiyoi Hitoshi , Gotoh Momokazu , Ando Yuichi , Akiyama Masashi , Hasegawa Yoshinori , Arima Hiroshi 
Published: February 2020

Abstract
Background
Anti-programmed cell death-1 (PD-1) antibodies can cause thyroid dysfunction. However, no predictive biomarkers enabling stratification of thyroid dysfunction risk have been identified.

Methods
A total of 209 patients treated with an anti-PD-1 antibody were evaluated for anti-thyroid antibodies at baseline and prospectively for thyroid function every 6 weeks for 24 weeks after treatment initiation, and then observed until the visits stopped. Thyroid ultrasonography was performed if the patient was positive for anti-thyroid antibodies at baseline.

Results
Of the 209 patients, 19 (9.1%) developed thyroid dysfunction (destructive thyroiditis or hypothyroidism). The cumulative incidence of thyroid dysfunction was significantly higher in patients who were positive vs. negative for anti-thyroid antibodies (15/44 [34.1%] vs. 4/165 [2.4%], p < 0.001). Forty-two patients positive for anti-thyroid antibodies at baseline were divided into two groups according to the presence of an irregular echo pattern. The cumulative incidence of thyroid dysfunction was significantly higher in those with an irregular vs. a regular echo pattern (13/23 [56.5%] vs. 1/19 [5.3%], p = 0.001). None of the patients developed thyroid dysfunction after the initial 24-week period.

Conclusions
The risk of thyroid dysfunction induced by anti-PD-1 antibodies can be predicted by evaluation of anti-thyroid antibodies and the thyroid echo pattern at baseline.

Trial registration
UMIN000019024.
A20 targets PFKL and glycolysis to inhibit the progression of hepatocellular carcinoma
Authors: Feng Yilu , Zhang Ye , Cai Yi , Liu Ruijie , Lu Miaolong , Li Tangzhiming , Fu Ying , Guo Ming , Huang Huichao , Ou Yifu , Chen Yongheng 
Published: February 2020

AbstractAbnormal expression of the E3 ubiquitin ligase A20 has been found in some malignant cancers, including hepatocellular carcinoma (HCC). Here, we discovered that A20 is an E3 ubiquitin ligase for phosphofructokinase, liver type (PFKL) in HCC A20 interacts with PFKL and promotes its degradation, therefore inhibiting glycolysis in HCC cell lines. Downregulation of A20 in HCC cells promotes proliferation, migration, and glycolysis, all of which can be inhibited by targeting PFKL with RNA interference. Importantly, A20 is downregulated in advanced HCC tissues and inversely correlated with PFKL expression. Thus, our findings establish A20 as a critical regulator of glycolysis and reveal a novel mechanism for A20 in tumor suppression and PFKL regulation. Given that an increased level of glycolysis is linked with HCC, this study also identifies potential therapeutic targets for HCC treatment.
SIVA-1 regulates apoptosis and synaptic function by modulating XIAP interaction with the death receptor antagonist FAIM-L
Authors: Coccia Elena , Planells-Ferrer Laura , Badillos-Rodríguez Raquel , Pascual Marta , Segura Miguel F. , Fernández-Hernández Rita , López-Soriano Joaquin , Garí Eloi , Soriano Eduardo , Barneda-Zahonero Bruna , Moubarak Rana S. , Pérez-García M. Jose , Comella Joan X. 
Published: February 2020

AbstractThe long isoform of Fas apoptosis inhibitory molecule (FAIM-L) is a neuron-specific death receptor antagonist that modulates apoptotic cell death and mechanisms of neuronal plasticity. FAIM-L exerts its antiapoptotic action by binding to X-linked inhibitor of apoptosis protein (XIAP), an inhibitor of caspases, which are the main effectors of apoptosis. XIAP levels are regulated by the ubiquitin-proteasome pathway. FAIM-L interaction with XIAP prevents the ubiquitination and degradation of the latter, thereby allowing it to inhibit caspase activation. This interaction also modulates non-apoptotic functions of caspases, such as the endocytosis of AMPA receptor (AMPAR) in hippocampal long-term depression (LTD). The molecular mechanism of action exerted by FAIM-L is unclear since the consensus binding motifs are still unknown. Here, we performed a two-hybrid screening to discover novel FAIM-L-interacting proteins. We found a functional interaction of SIVA-1 with FAIM-L. SIVA-1 is a proapoptotic protein that has the capacity to interact with XIAP. We describe how SIVA-1 regulates FAIM-L function by disrupting the interaction of FAIM-L with XIAP, thereby promoting XIAP ubiquitination, caspase-3 activation and neuronal death. Furthermore, we report that SIVA-1 plays a role in receptor internalization in synapses. SIVA-1 is upregulated upon chemical LTD induction, and it modulates AMPAR internalization via non-apoptotic activation of caspases. In summary, our findings uncover SIVA-1 as new functional partner of FAIM-L and demonstrate its role as a regulator of caspase activity in synaptic function.
Hepatocyte apoptosis is tumor promoting in murine nonalcoholic steatohepatitis
Authors: Hirsova Petra , Bohm Friederike , Dohnalkova Ester , Nozickova Barbora , Heikenwalder Mathias , Gores Gregory J. , Weber Achim 
Published: February 2020

AbstractNonalcoholic fatty liver disease is the most common chronic liver disease and may progress to nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). The molecular determinants of this pathogenic progression, however, remain largely undefined. Since liver tumorigenesis is driven by apoptosis, we examined the effect of overt hepatocyte apoptosis in a mouse model of NASH using mice lacking myeloid cell leukemia 1 (Mcl1), a pro-survival member of the BCL-2 protein family. Hepatocyte-specific Mcl1 knockout (Mcl1∆hep) mice and control littermates were fed chow or FFC (high saturated fat, fructose, and cholesterol) diet, which induces NASH, for 4 and 10 months. Thereafter, liver injury, inflammation, fibrosis, and tumor development were evaluated biochemically and histologically. Mcl1∆hep mice fed with the FFC diet for 4 months displayed a marked increase in liver injury, hepatocyte apoptosis, hepatocyte proliferation, macrophage-associated liver inflammation, and pericellular fibrosis in contrast to chow-fed Mcl1∆hep and FFC diet-fed Mcl1-expressing littermates. After 10 months of feeding, 78% of FFC diet-fed Mcl1∆hep mice developed liver tumors compared to 38% of chow-fed mice of the same genotype. Tumors in FFC diet-fed Mcl1∆hep mice were characterized by cytologic atypia, altered liver architecture, immunopositivity for glutamine synthetase, and histologically qualified as HCC. In conclusion, this study provides evidence that excessive hepatocyte apoptosis exacerbates the NASH phenotype with enhancement of tumorigenesis in mice.
A new coronavirus associated with human respiratory disease in China
Authors: Wu Fan , Zhao Su , Yu Bin , Chen Yan-Mei , Wang Wen , Song Zhi-Gang , Hu Yi , Tao Zhao-Wu , Tian Jun-Hua , Pei Yuan-Yuan , Yuan Ming-Li , Zhang Yu-Ling , Dai Fa-Hui , Liu Yi , Wang Qi-Min , Zheng Jiao-Jiao , Xu Lin , Holmes Edward C. , Zhang Yong-Zhen 
Published: February 2020

AbstractEmerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Authors: Zhou Peng , Yang Xing-Lou , Wang Xian-Guang , Hu Ben , Zhang Lei , Zhang Wei , Si Hao-Rui , Zhu Yan , Li Bei , Huang Chao-Lin , Chen Hui-Dong , Chen Jing , Luo Yun , Guo Hua , Jiang Ren-Di , Liu Mei-Qin , Chen Ying , Shen Xu-Rui , Wang Xi , Zheng Xiao-Shuang , Zhao Kai , Chen Quan-Jiao , Deng Fei , Liu Lin-Lin , Yan Bing , Zhan Fa-Xian , Wang Yan-Yi , Xiao Geng-Fu , Shi Zheng-Li 
Published: February 2020

AbstractSince the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1–4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5–7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of . In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.
LiB13: A New Member of Tetrahedral-Typed B13 Ligand Half-Surround Cluster
Authors: Shi Hongxiao , Kuang Xiaoyu , Lu Cheng 
Published: February 2020

AbstractIt will get entirely unusual derivatives with gratifying chemical bonding schemes for boron clusters by doping with lithium, the lightest alkalis. The geometric structures and electronic properties of the LiBn0/− (n = 10−20) clusters have been studied through Crystal structure AnaLYsis by Particle Swarm Optimization (CALYPSO) structural search approach along with the density functional theory (DFT) calculations. The low-lying candidates of LiBn0/− (n = 10–20) are reoptimized at the B3LYP functional in conjunction with 6–311 + G(d) basis set. Three forms of geometric configurations are identified for the ground-state structures of LiBn0/− clusters: half-sandwich-type, quasi-planar and drum-type structures. The photoelectron spectra (PES) of the LiBn− clusters have been calculated through time-dependent density functional theory (TD-DFT). A promising LiB13 with tetrahedral-typed B13 ligand half-surround cluster and robust stability is uncovered. The molecular orbital and adaptive natural density partitioning (AdNDP) analysis show that B-B bonds in the B13 moiety combined with the interaction between the B13 shell and Li atom stabilize the C2v LiB13 cluster. Our results advance the fundamental understanding about the alkali metal doped boron clusters.
Emergence of life in an inflationary universe
Authors: Totani Tomonori 
Published: February 2020

AbstractAbiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40–100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random reactions seems statistically unlikely. However, our universe, created by a single inflation event, likely includes more than 10100 Sun-like stars. If life can emerge at least once in such a large volume, it is not in contradiction with our observations of life on Earth, even if the expected number of abiogenesis events is negligibly small within the observable universe that contains only 1022 stars. Here, a quantitative relation is derived between the minimum RNA length lmin required to be the first biological polymer, and the universe size necessary to expect the formation of such a long and active RNA by randomly adding monomers. It is then shown that an active RNA can indeed be produced somewhere in an inflationary universe, giving a solution to the abiotic polymerization problem. On the other hand, lmin must be shorter than ~20 nucleotides for the abiogenesis probability close to unity on a terrestrial planet, but a self-replicating activity is not expected for such a short RNA. Therefore, if extraterrestrial organisms of a different origin from those on Earth are discovered in the future, it would imply an unknown mechanism at work to polymerize nucleotides much faster than random statistical processes.
Controlled edge dependent stacking of WS2-WS2 Homo- and WS2-WSe2 Hetero-structures: A Computational Study
Authors: Ghatak Kamalika , Kang Kyung Nam , Yang Eui-Hyeok , Datta Dibakar 
Published: February 2020

AbstractTransition Metal Dichalcogenides (TMDs) are one of the most studied two-dimensional materials in the last 5–10 years due to their extremely interesting layer dependent properties. Despite the presence of vast research work on TMDs, the complex relation between the electro-chemical and physical properties make them the subject of further research. Our main objective is to provide a better insight into the electronic structure of TMDs. This will help us better understand the stability of the bilayer post growth homo/hetero products based on the various edge-termination, and different stacking of the two layers. In this regard, two Tungsten (W) based non-periodic chalcogenide flakes (sulfides and selenides) were considered. An in-depth analysis of their different edge termination and stacking arrangement was performed via Density Functional Theory method using VASP software. Our finding indicates the preference of chalcogenide (c-) terminated structures over the metal (m-) terminated structures for both homo and heterobilayers, and thus strongly suggests the nonexistence of the m-terminated TMDs bilayer products.
S100A12 is a promising biomarker in papillary thyroid cancer
Authors: Wang Xiaojie , Sun Zhenxiang , Tian Wei , Piao Chenghao , Xie Xiaochen , Zang Jin , Peng Shiqiao , Yu Xiaohui , Wang Yiwei 
Published: February 2020

AbstractS100A12 belongs to the S100 family and acts as a vital regulator in different types of tumors. However, the function of S100A12 in thyroid carcinoma has not yet been investigated. In this study, we analyzed the expression of S100A12 in human papillary thyroid cancer (PTC) samples and two PTC cell lines. In addition, we explored the effects of S100A12 on PTC cell progression in vitro and in vivo. Our results showed that S100A12 was significantly upregulated in PTC specimens. Moreover, silencing S100A12 markedly inhibited PTC cell proliferation, migration, invasion and cell cycle progression. In addition, knockdown of S100A12 significantly reduced the expression of CyclinD1, CDK4 and p-ERK in PTC cells. An in vivo study also showed that silencing S100A12 dramatically suppressed tumor cell growth and decreased Ki67 expression in a xenograft mouse model. This study provides novel evidence that S100A12 serves as an oncogene in PTC. Knockdown of S100A12 suppressed PTC cell proliferation, migration, and invasion and induced G0/G1 phase arrest via the inhibition of the ERK signaling pathway. Therefore, S100A12 may be a potent therapeutic target for PTC.