bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate esters
Authors: Parker Seth J. , Encarnación-Rosado Joel , Hollinshead Kate E. R. , Hollinshead David M. , Ash Leonard J. , Rossi Juan A. K. , Lin Elaine Y. , Sohn Albert S. W. , Philips Mark R. , Jones Drew R. , Kimmelman Alec C. 
Published: August 2021

Abstractα-ketoglutarate (KG), also referred to as 2-oxoglutarate, is a key intermediate of cellular metabolism with pleiotropic functions. Cell-permeable esterified analogs are widely used to study how KG fuels bioenergetic and amino acid metabolism and DNA, RNA, and protein hydroxylation reactions, as cellular membranes are thought to be impermeable to KG. Here we show that esterified KG analogs rapidly hydrolyze in aqueous media, yielding KG that, in contrast to prevailing assumptions, imports into many cell lines. Esterified KG analogs exhibit spurious KG-independent effects on cellular metabolism, including extracellular acidification, arising from rapid hydrolysis and de-protonation of α-ketoesters, and significant analog-specific inhibitory effects on glycolysis or mitochondrial respiration. We observe that imported KG decarboxylates to succinate in the cytosol and contributes minimally to mitochondrial metabolism in many cell lines cultured in normal conditions. These findings demonstrate that nuclear and cytosolic KG-dependent reactions may derive KG from functionally distinct subcellular pools and sources.
Unsupervised discovery of thin-film photovoltaic materials from unlabeled data
Authors: Wang Zhilong , Cai Junfei , Wang Qingxun , Wu SiCheng , Li Jinjin 
Published: August 2021

AbstractQuaternary chalcogenide semiconductors (I2-II-IV-X4) are key materials for thin-film photovoltaics (PVs) to alleviate the energy crisis. Scaling up of PVs requires the discovery of I2-II-IV-X4 with good photoelectric properties; however, the structure search space is significantly large to explore exhaustively. The scarcity of available data impedes even many machine learning (ML) methods. Here, we employ the unsupervised learning (UL) method to discover I2-II-IV-X4 that alleviates the challenge of data scarcity. We screen all the I2-II-IV-X4 from the periodic table as the initial data and finally select eight candidates through UL. As predicted by ab initio calculations, they exhibit good optical conversion efficiency, strong optical responses, and good thermal stabilities at room temperatures. This typical case demonstrates the potential of UL in material discovery, which overcomes the limitation of data scarcity, and shortens the computational screening cycle of I2-II-IV-X4 by ~12.1 years, providing a research avenue for rapid material discovery.
Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
Authors: Shohdy Kyrillus S. , Bareja Rohan , Sigouros Michael , Wilkes David C. , Dorsaint Princesca , Manohar Jyothi , Bockelman Daniel , Xiang Jenny Z. , Kim Rob , Ohara Kentaro , Eng Kenneth , Mosquera Juan Miguel , Elemento Olivier , Sboner Andrea , Alonso Alicia , Faltas Bishoy M. 
Published: August 2021

AbstractThe availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. We performed transcriptomic analysis of 32 FFPE tumor samples from 11 patients using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to the TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. The Spearman’s correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72–0.9,p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88,p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable gene transcripts, includingERBB2, MET, NTRK1, andPPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen’sk = 0.7,p < 0.01). The Agilent and IDT assays detected all the clinically relevant fusions that were initially identified in FF-TruSeq. All FFPE exome capture-based methods had comparable performance and concordance with FF-TruSeq. Our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.
Dog colour patterns explained by modular promoters of ancient canid origin
Authors: Bannasch Danika L. , Kaelin Christopher B. , Letko Anna , Loechel Robert , Hug Petra , Jagannathan Vidhya , Henkel Jan , Roosje Petra , Hytönen Marjo K. , Lohi Hannes , Arumilli Meharji ,   DoGA consortium, Lohi Hannes , Kere Juha , Daub Carsten , Hytönen Marjo , Araujo César L. , Quintero Ileana B. , Kyöstilä Kaisa , Kaukonen Maria , Arumilli Meharji , Salonen Milla , Sarviaho Riika , Niskanen Julia , Hundi Sruthi , Puurunen Jenni , Sulkama Sini , Karjalainen Sini , Sukura Antti , Syrjä Pernilla , Airas Niina , Pekkarinen Henna , Kareinen Ilona , Knuuttila Anna , Nordgren Heli , Hagner Karoliina , Pääkkönen Tarja , Iivanainen Antti , Krjutskov Kaarel , Ezer Sini , Saarinen Auli , Katayama Shintaro , Yoshihara Masahito , Hörtenhuber Matthias , Aljelaify Rasha Fahad , Ross Fiona , Raman Amitha , Stevens Irene , Gusev Oleg , Bannasch Danika L. , Schoenebeck Jeffrey J. , Minor Katie M. , Mickelson James R. , Drögemüller Cord , Barsh Gregory S. , Leeb Tosso 
Published: August 2021

AbstractDistinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.
OPERA tau neutrino charged current interactions
Authors: Agafonova N. , Alexandrov A. , Anokhina A. , Aoki S. , Ariga A. , Ariga T. , Bertolin A. , Bozza C. , Brugnera R. , Buonaura A. , Buontempo S. , Chernyavskiy M. , Chukanov A. , Consiglio L. , D’Ambrosio N. , De Lellis G. , De Serio M. , del Amo Sanchez P. , Di Crescenzo A. , Di Ferdinando D. , Di Marco N. , Dmitrievsky S. , Dracos M. , Duchesneau D. , Dusini S. , Dzhatdoev T. , Ebert J. , Ereditato A. , Fini R. A. , Fornari F. , Fukuda T. , Galati G. , Garfagnini A. , Gentile V. , Goldberg J. , Gorbunov S. , Gornushkin Y. , Grella G. , Guler A. M. , Gustavino C. , Hagner C. , Hara T. , Hayakawa T. , Hollnagel A. , Ishiguro K. , Iuliano A. , Jakovčić K. , Jollet C. , Kamiscioglu C. , Kamiscioglu M. , Kim S. H. , Kitagawa N. , Kliček B. , Kodama K. , Komatsu M. , Kose U. , Kreslo I. , Laudisio F. , Lauria A. , Lavasa A. , Longhin A. , Loverre P. , Malgin A. , Mandrioli G. , Matsuo T. , Matveev V. , Mauri N. , Medinaceli E. , Meregaglia A. , Mikado S. , Miyanishi M. , Mizutani F. , Monacelli P. , Montesi M. C. , Morishima K. , Muciaccia M. T. , Naganawa N. , Naka T. , Nakamura M. , Nakano T. , Niwa K. , Ogawa S. , Okateva N. , Ozaki K. , Paoloni A. , Park B. D. , Pasqualini L. , Pastore A. , Patrizii L. , Pessard H. , Podgrudkov D. , Polukhina N. , Pozzato M. , Pupilli F. , Roda M. , Roganova T. , Rokujo H. , Rosa G. , Ryazhskaya O. , Sato O. , Shakirianova I. , Schembri A. , Shchedrina T. , Shibayama E. , Shibuya H. , Shiraishi T. , Šimko T. , Simone S. , Sirignano C. , Sirri G. , Sotnikov A. , Spinetti M. , Stanco L. , Starkov N. , Stellacci S. M. , Stipčević M. , Strolin P. , Takahashi S. , Tenti M. , Terranova F. , Tioukov V. , Tsanaktsidis I. , Tufanli S. , Ustyuzhanin A. , Vasina S. , Vidal García M. , Vilain P. , Voevodina E. , Votano L. , Vuilleumier J. L. , Wilquet G. , Yoon C. S. 
Published: August 2021

AbstractThe OPERA experiment was designed to discover the vτ appearance in a vμ beam, due to neutrino oscillations. The detector, located in the underground Gran Sasso Laboratory, consisted of a nuclear photographic emulsion/lead target with a mass of about 1.25 kt, complemented by electronic detectors. It was exposed from 2008 to 2012 to the CNGS beam: an almost pure vμ beam with a baseline of 730 km, collecting a total of 1.8·1020 protons on target. The OPERA Collaboration eventually assessed the discovery of vμ→vτ oscillations with a statistical significance of 6.1 σ by observing ten vτ CC interaction candidates. These events have been published on the Open Data Portal at CERN. This paper provides a detailed description of the vτ data sample to make it usable by the whole community.
A new CAM6 + DART reanalysis with surface forcing from CAM6 to other CESM models
Authors: Raeder Kevin , Hoar Timothy J. , El Gharamti Mohamad , Johnson Benjamin K. , Collins Nancy , Anderson Jeffrey L. , Steward Jeff , Coady Mick 
Published: August 2021

AbstractAn ensemble Kalman filter reanalysis has been archived in the Research Data Archive at the National Center for Atmospheric Research. It used a CAM6 configuration of the Community Earth System Model (CESM), several million observations per day, and the Data Assimilation Research Testbed (DART). The data saved from this global, $$\sim 1^\circ $$

∼

1
∘

resolution, 80 member ensemble span 2011–2019. They include ensembles of: sub-daily, real world, atmospheric forcing for use by all of the nonatmospheric models of CESM; weekly, CAM6, restart file sets; 6 hourly, prior hindcast estimates of the assimilated observations; 6 hourly, land model, plant growth variables, and 6 hourly, ensemble mean, gridded, atmospheric analyses. This data can be used for hindcast studies and data assimilation using component models of CESM; CAM6, CLM5, CICE5, POP2. MOM6, MOSART, and CISM; and non-CESM Earth system models. This large dataset (~ 120 Tb) has a unique combination of a large ensemble, high frequency, and multiyear time span, which provides opportunities for robust statistical analysis and use as a machine learning training dataset.
Moisture variation inferred from tree rings in north central China and its links with the remote oceans
Authors: Zheng Zeyu , Jin Liya , Li Jinjian , Chen Jie , Zhang Xiaojian , Wang Zhenqian 
Published: August 2021

AbstractIn this study we presented a composite standard chronology, spanning 1635–2018 to reconstruct May–July moisture variation in north central China. Our reconstruction revealed four severe dry epochs and five pronounced wet epochs. Additionally, spatial correlation analysis of our reconstruction with the actual self-calibrating Palmer drought severity index showed that our reconstruction was representative of large-scale May–July moisture changes. Both the severe dry and pronounced wet epochs showed one-to-one correspondence with other reconstructions nearby during their common periods, which demonstrated the reliability of our reconstruction backwards in time. Spectral analysis showed that significant spectral peaks were found at 2.1–3.8 years, which fell within the overall bandwidth of the El Niño-Southern Oscillations (ENSO). The spatial correlation patterns between our reconstruction and sea surface temperature (SST) in the equatorial eastern Pacific further confirmed the link between regional moisture and ENSO, with warm-phase ENSO resulting in low moisture and vice-versa. However, this link was time-dependent during the past four centuries, and was modulated by different phases of SST in the tropical Indian Ocean. Additionally, significant peaks at 24.9–46.5 years and spatial correlation patterns indicated that the Pacific Decadal Oscillation and the North Atlantic Oscillation may be the possible forcing factors of regional moisture at lower frequencies.
The first dinosaurs from the Early Cretaceous Hami Pterosaur Fauna, China
Authors: Wang Xiaolin , Bandeira Kamila L. N. , Qiu Rui , Jiang Shunxing , Cheng Xin , Ma Yingxia , Kellner Alexander W. A. 
Published: August 2021

AbstractThe Early Cretaceous Hami Pterosaur Fauna in Northwest China preserves a large number of specimens of the sexually dimorphic pteranodontoid pterosaurHamipterus tianshanensis, including 3D eggs and embryos. During the last decade, several more fossils have been collected in this area, including three somphospondylan sauropod specimens. The first isSilutitan sinensisgen. et sp. nov., which consists of an articulated middle to posterior cervical vertebrae series. The second,Hamititan xinjiangensisgen. et sp. nov., consists of an incomplete articulated caudal sequence that could be assigned to lithostrotian titanosaurs based on the strongly procoelous caudal vertebrae with lateral concave surface, as well as marked ventrolateral ridges. The third specimen consists of four sacral vertebral elements, apparently unfused, with exposed camellate internal bone and regarded as somphospondylan. Cladistic analyses based on different datasets recoveredSilutitan sinensisas an euhelopodid closely related toEuhelopusandHamititan xinjiangensisas a titanosaur. Besides the pterosaurHamipterusand one theropod tooth,these dinosaurs are the first vertebrates reported in this region, increasing the diversity of the fauna as well as the information on Chinese sauropods, further supporting a widespread diversification of somphospondylans during the Early Cretaceous of Asia.
JNK activation in TA and EDL muscle is load-dependent in rats receiving identical excitation patterns
Authors: Eftestøl Einar , Franchi Martino V. , Kasper Stephanie , Flück Martin 
Published: August 2021

AbstractAs the excitation–contraction coupling is inseparable during voluntary exercise, the relative contribution of the mechanical and neural input on hypertrophy-related molecular signalling is still poorly understood. Herein, we use a rat in-vivo strength exercise model with an electrically-induced standardized excitation pattern, previously shown to induce a load-dependent increase in myonuclear number and hypertrophy, to study acute effects of load on molecular signalling. We assessed protein abundance and specific phosphorylation of the four protein kinases FAK, mTOR, p70S6K and JNK after 2, 10 and 28 min of a low- or high-load contraction, in order to assess the effects of load, exercise duration and muscle-type on their response to exercise. Specific phosphorylation of mTOR, p70S6K and JNK was increased after 28 min of exercise under the low- and high-load protocol. Elevated phosphorylation of mTOR and JNK was detectable already after 2 and 10 min of exercise, respectively, but greatest after 28 min of exercise, and JNK phosphorylation was highly load-dependent. The abundance of all four kinases was higher in TA compared to EDL muscle, p70S6K abundance was increased after exercise in a load-independent manner, and FAK and JNK abundance was reduced after 28 min of exercise in both the exercised and control muscles. In conclusion, the current study shows that JNK activation after a single resistance exercise is load-specific, resembling the previously reported degree of myonuclear accrual and muscle hypertrophy with repetition of the exercise stimulus.
Predicted limited redistribution of T cells to secondary lymphoid tissue correlates with increased risk of haematological malignancies in asplenic patients
Authors: Kmieciak Aleksandra E. , Brown Liam V. , Coles Mark C. , Wagg Jonathan , Phipps Alex , Gaffney Eamonn A. 
Published: August 2021

AbstractThe spleen, a secondary lymphoid tissue (SLT), has an important role in generation of adaptive immune responses. Although splenectomy remains a common procedure, recent studies reported poor prognosis and increased risk of haematological malignancies in asplenic patients. The high baseline trafficking of T lymphocytes to splenic tissue suggests splenectomy may lead to loss of blood-borne malignant immunosurveillance that is not compensated for by the remaining SLT. To date, no quantitative analysis of the impact of splenectomy on the human T cell trafficking dynamics and tissue localisation has been reported. We developed a quantitative computational model that describes organ distribution and trafficking of human lymphocytes to explore the likely impact of splenectomy on immune cell distributions. In silico splenectomy resulted in an average reduction of T cell numbers in SLT by 35% (95%CI 0.12–0.97) and a comparatively lower, 9% (95%CI 0.17–1.43), mean decrease of T cell concentration in SLT. These results suggest that the surveillance capacity of the remaining SLT insufficiently compensates for the absence of the spleen. This may, in part, explain haematological malignancy risk in asplenic patients and raises the question of whether splenectomy has a clinically meaningful impact on patient responses to immunotherapy.
Transcriptomic profiling of Gh/Igf system reveals a prompted tissue-specific differentiation and novel hypoxia responsive genes in gilthead sea bream
Authors: Naya-Català F. , Simó-Mirabet P. , Calduch-Giner J. , Pérez-Sánchez J. 
Published: August 2021

AbstractA customized PCR-array was used for the simultaneous gene expression of the Gh/Igf system and related markers of muscle growth, and lipid and energy metabolism during early life stages of gilthead sea bream (60–127 days posthatching). Also, transcriptional reprogramming by mild hypoxia was assessed in fingerling fish with different history trajectories on O2 availability during the same time window. In normoxic fish, the expression of almost all the genes in the array varied over time with a prompted liver and muscle tissue-specific differentiation, which also revealed temporal changes in the relative expression of markers of the full gilthead sea bream repertoire of Gh receptors, Igfs and Igf-binding proteins. Results supported a different contribution through development of ghr and igf subtypes on the type of action of GH via systemic or direct effects at the local tissue level. This was extensive to Igfbp1/2/4 and Igfbp3/5/6 clades that clearly evolved through development as hepatic and muscle Igfbp subtypes, respectively. This trade-off is however very plastic to cope changes in the environment, and ghr1 and igfbp1/3/4/5 emerged as hypoxic imprinting genes during critical early developmental windows leading to recognize individuals with different history trajectories of oxygen availability and metabolic capabilities later in life.
Direct numerical simulations of three-dimensional surface instability patterns in thin film-compliant substrate structures
Authors: Nikravesh Siavash , Ryu Donghyeon , Shen Yu-Lin 
Published: August 2021

AbstractA comprehensive numerical study of three-dimensional surface instability patterns is presented. The formation of wrinkles is a consequence of deformation instability when a thin film, bonded to a compliant substrate, is subject to in-plane compressive loading. We apply a recently developed computational approach to directly simulate complex surface wrinkling from pre-instability to post-instability in a straightforward manner, covering the entire biaxial loading spectrum from pure uniaxial to pure equi-biaxial compression. The simulations use embedded imperfections with perturbed material properties at the film-substrate interface. This approach not only triggers the first bifurcation mode but also activates subsequent post-buckling states, thus capable of predicting the temporal evolution of wrinkle patterns in one simulation run. The state of biaxiality is found to influence the surface pattern significantly, and each bifurcation mode can be traced back to certain abrupt changes in the overall load–displacement response. Our systematic study reveals how the loading condition dictates the formation of various instability modes including one-dimensional (1D) sinusoidal wrinkles, herringbone, labyrinth, and checkerboard.
Fatty liver index as a predictor for type 2 diabetes in subjects with normoglycemia in a nationwide cohort study
Authors: García-Escobar E. , Valdés S. , Soriguer F. , Vendrell J. , Urrutia-Etxebarria I. M. , Maldonado-Araque C. , Ortega E. , Ocón P. , Montanya E. , Menéndez E. , Lago-Sampedro A. , González-Frutos T. , Gomis R. , Goday A. , García-Serrano S. , Galán-García J. L. , Castell C. , Bordiú E. , Badía R. , Aguilera-Venegas G. , Girbés J. , Gaztambide S. , Delgado E. , Chaves F. J. , Castaño L. , Calle-Pascual A. , Rojo-Martínez G. , Franch-Nadal J. 
Published: August 2021

AbstractOur aim was to evaluate whether fatty liver index (FLI) is associated with the risk of type 2 diabetes (T2DM) development within the Spanish adult population and according to their prediabetes status; additionally, to examine its incremental predictive value regarding traditional risk factors. A total of 2260 subjects (Prediabetes: 641 subjects, normoglycemia: 1619 subjects) from the Di@bet.es cohort study were studied. Socio-demographic, anthropometric, clinical data and survey on habits were recorded. An oral glucose tolerance test was performed and fasting determinations of glucose, lipids and insulin were made. FLI was calculated and classified into three categories: Low (< 30), intermediate (30–60) and high (> 60). In total, 143 people developed diabetes at follow-up. The presence of a high FLI category was in all cases a significant independent risk factor for the development of diabetes. The inclusion of FLI categories in prediction models based on different conventional T2DM risk factors significantly increase the prediction power of the models when all the population was considered. According to our results, FLI might be considered an early indicator of T2DM development even under normoglycemic condition. The data also suggest that FLI could provide additional information for the prediction of T2DM in models based on conventional risk factors.
Extended in vivo transcriptomes of two ascoviruses with different tissue tropisms reveal alternative mechanisms for enhancing virus reproduction in hemolymph
Authors: Zaghloul Heba A. H. , Hice Robert H. , Arensburger Peter , Bideshi Dennis K. , Federici Brian A. 
Published: August 2021

AbstractAscoviruses are large dsDNA viruses characterized by the extraordinary changes they induce in cellular pathogenesis and architecture whereby after nuclear lysis and extensive hypertrophy, each cell is cleaved into numerous vesicles for virion reproduction. However, the level of viral replication and transcription in vesicles compared to other host tissues remains uncertain. Therefore, we applied RNA-Sequencing to compare the temporal transcriptome of Spodoptera frugiperda ascovirus (SfAV) and Trichoplusia ni ascovirus (TnAV) at 7, 14, and 21 days post-infection (dpi). We found most transcription occurred in viral vesicles, not in initial tissues infected, a remarkably novel reproduction mechanism compared to all other viruses and most other intracellular pathogens. Specifically, the highest level of viral gene expression occurred in hemolymph, for TnAV at 7 dpi, and SfAV at 14 dpi. Moreover, we found that host immune genes were partially down-regulated in hemolymph, where most viral replication occurred in highly dense accumulations of vesicles.