bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global analysis of protein degradation in prion infected cells
Authors: Hutti Charles R. , Welle Kevin A. , Hryhorenko Jennifer R. , Ghaemmaghami Sina 
Published: July 2020

AbstractPrion diseases are rare, neurological disorders caused by the misfolding of the cellular prion protein (PrPC) into cytotoxic fibrils (PrPSc). Intracellular PrPScaggregates primarily accumulate within late endosomes and lysosomes, organelles that participate in the degradation and turnover of a large subset of the proteome. Thus, intracellular accumulation of PrPScaggregates has the potential to globally influence protein degradation kinetics within an infected cell. We analyzed the proteome-wide effect of prion infection on protein degradation rates in N2a neuroblastoma cells by dynamic stable isotopic labeling with amino acids in cell culture (dSILAC) and bottom-up proteomics. The analysis quantified the degradation rates of more than 4,700 proteins in prion infected and uninfected cells. As expected, the degradation rate of the prion protein is significantly decreased upon aggregation in infected cells. In contrast, the degradation kinetics of the remainder of the N2a proteome generally increases upon prion infection. This effect occurs concurrently with increases in the cellular activities of autophagy and some lysosomal hydrolases. The resulting enhancement in proteome flux may play a role in the survival of N2a cells upon prion infection.
Positive effects of grasping virtual objects on memory for novel words in a second language
Authors: Macedonia M. , Lehner A. E. , Repetto C. 
Published: July 2020

AbstractTheories of embodied cognition describe language processing and representation as inherently connected to the sensorimotor experiences collected during acquisition. While children grasp their world, collect bodily experiences and name them, in second language (L2), students learn bilingual word lists. Experimental evidence shows that embodiment by mean of gestures enhances memory for words in L2. However, no study has been conducted on the effects of grasping in L2. In a virtual scenario, we trained 46 participants on 18 two- and three-syllabic words of Vimmi, an artificial corpus created for experimental purposes. The words were assigned concrete meanings of graspable objects. Six words were learned audio-visually, by reading the words projected on the wall and by hearing them. Another 6 words were trained by observation of virtual objects. Another 6 words were learned by observation and additional grasping the virtual objects. Thereafter participants were subministered free, cued recall, and reaction time tests in order to assess the word retention and the word recognition. After 30 days, the recall tests were repeated remotely to assess the memory in the long term. The results show that grasping of virtual objects can lead to superior memory performance and to lower reaction times during recognition.
Interactions of Bunias orientalis plant chemotypes and fungal pathogens with different host specificity in vivo and in vitro
Authors: Tewes Lisa Johanna , Müller Caroline 
Published: July 2020

AbstractWithin several plant species, a high variation in the composition of particular defence metabolites can be found, forming distinct chemotypes. Such chemotypes show different effects on specialist and generalist plant enemies, whereby studies examining interactions with pathogens are underrepresented. We aimed to determine factors mediating the interaction of two chemotypes ofBunias orientalis(Brassicaceae) with two plant pathogenic fungal species of different host range,Alternaria brassicae(narrow host range = specialist) andBotrytis cinerea(broad host-range = generalist) using a combination of controlled bioassays.We found that the specialist, but not the generalist, was sensitive to differences between plant chemotypes in vivo and in vitro. The specialist fungus was more virulent (measured as leaf water loss) on one chemotype in vivo without differing in biomass produced during infection, while extracts from the same chemotype caused strong growth inhibition in that species in vitro. Furthermore, fractions of extracts fromB. orientalishad divergent in vitro effects on the specialist versus the generalist, supporting presumed adaptations to certain compound classes. This study underlines the necessity to combine various experimental approaches to elucidate the complex interplay between plants and different pathogens.
The major effects of health-related quality of life on 5-year survival prediction among lung cancer survivors: applications of machine learning
Authors: Sim Jin-ah , Kim Young Ae , Kim Ju Han , Lee Jong Mog , Kim Moon Soo , Shim Young Mog , Zo Jae Ill , Yun Young Ho 
Published: July 2020

AbstractThe primary goal of this study was to evaluate the major roles of health-related quality of life (HRQOL) in a 5-year lung cancer survival prediction model using machine learning techniques (MLTs). The predictive performances of the models were compared with data from 809 survivors who underwent lung cancer surgery. Each of the modeling technique was applied to two feature sets: feature set 1 included clinical and sociodemographic variables, and feature set 2 added HRQOL factors to the variables from feature set 1. One of each developed prediction model was trained with the decision tree (DT), logistic regression (LR), bagging, random forest (RF), and adaptive boosting (AdaBoost) methods, and then, the best algorithm for modeling was determined. The models’ performances were compared using fivefold cross-validation. For feature set 1, there were no significant differences in model accuracies (ranging from 0.647 to 0.713). Among the models in feature set 2, the AdaBoost and RF models outperformed the other prognostic models [area under the curve (AUC) = 0.850, 0.898, 0.981, 0.966, and 0.949 for the DT, LR, bagging, RF and AdaBoost models, respectively] in the test set. Overall, 5-year disease-free lung cancer survival prediction models with MLTs that included HRQOL as well as clinical variables improved predictive performance.
Expression and localisation of Rab44 in immune-related cells change during cell differentiation and stimulation
Authors: Tokuhisa Mitsuko , Kadowaki Tomoko , Ogawa Kohei , Yamaguchi Yu , Kido Mizuho A. , Gao Weiqi , Umeda Masahiro , Tsukuba Takayuki 
Published: July 2020

AbstractRab44 is a large Rab GTPase that contains a Rab-GTPase domain and some additional domains, such as EF-hand and coiled-coil domains at the N-terminus. Our previous study showed that Rab44 negatively regulates osteoclast differentiation by modulating intracellular calcium levels; however, aside from those findings, there is little information concerning Rab44 on other cells or tissues. In this study, we showed that Rab44 was highly expressed in bone marrow cells among various mouse tissues. Immunohistochemical studies indicated that Rab44 was detectable by only a small number of cells in the immune-related tissues and that Rab44 was partially detected in CD117-positive cells, but not in Stem cell antigen 1-positive cells in the bone marrow. Rab44 expression levels were decreased during differentiation of immune-related cells, such as neutrophils, macrophages, and dendritic cells compared with bone marrow cells. Although endogenous Rab44 in macrophages was localised in lysosomes, lipopolysaccharide (LPS) stimulation led to partial translocation to early endosomes and the plasma membrane. Moreover, Rab44 expression levels were altered by treatment with various immunomodulators, including LPS. These results indicate that Rab44 expression and localisation in bone marrow cells and macrophages alters with cell differentiation and stimulation.
The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle
Authors: Hu Yongqiang , He Yuyong , Gao Shan , Liao Zhiqiang , Lai Tao , Zhou Haimei , Chen Qianlin , Li Lingyu , Gao Haijun , Lu Wei 
Published: July 2020

AbstractImprovement of the food value of rice straw is urgently required in rice crop growing areas to mitigate pollution caused by rice straw burning and enhance the supply of high-quality forages for ruminants. The aims of the present study were to compare the effects of fresh corn Stover and rice straw co-fermented with probiotics and enzymes on rumen fermentation and establish the feasibility of increasing the rice straw content in ruminant diets and, by extension, reducing air pollution caused by burning rice straw. Twenty Simmental hybrid beef cattle were randomly allotted to two groups with ten cattle per group. They were fed diets based either on rice straw co-fermented with probiotics and enzymes or fresh corn Stover for 90 days. Rumen fluid was sampled with an esophageal tube vacuum pump device from each animal on the mornings of days 30, 60, and 90. Bacterial diversity was evaluated by sequencing the V4–V5 region of the 16S rRNA gene. Metabolomes were analyzed by gas chromatography/time-of-flight mass spectrometry (GC–TOF/MS). Compared to cattle fed fresh corn Stover, those fed rice straw co-fermented with probiotics and enzymes had higher (P < 0.05) levels of acetic acid and propionate in rumen liquid at d 60 and d 90 respectively, higher (P < 0.05) abundances of the phyla Bacteroidetes and Fibrobacteres and the generaRuminococcus,Saccharofermentans,Pseudobutyrivibrio,Treponema,Lachnoclostridium, andRuminobacter, and higher (P < 0.05) concentrations of metabolites involved in metabolisms of amino acid, carbohydrate, and cofactors and vitamins. Relative to fresh corn Stover, rice straw co-fermented with probiotics and enzymes resulted in higher VFA concentrations, numbers of complex carbohydrate-decomposing and H2-utilizing bacteria, and feed energy conversion efficiency in the rumen.
No evidence for a relationship between social closeness and similarity in resting-state functional brain connectivity in schoolchildren
Authors: McNabb Carolyn Beth , Burgess Laura Grace , Fancourt Amy , Mulligan Nancy , FitzGibbon Lily , Riddell Patricia , Murayama Kou 
Published: July 2020

AbstractPrevious research suggests that the proximity of individuals in a social network predicts how similarly their brains respond to naturalistic stimuli. However, the relationship between social connectedness and brain connectivity in the absence of external stimuli has not been examined. To investigate whether neural homophily between friends exists at rest we collected resting-state functional magnetic resonance imaging (fMRI) data from 68 school-aged girls, along with social network information from all pupils in their year groups (total 5,066 social dyads). Participants were asked to rate the amount of time they voluntarily spent with each person in their year group, and directed social network matrices and community structure were then determined from these data. No statistically significant relationships between social distance, community homogeneity and similarity of global-level resting-state connectivity were observed. Nor were we able to predict social distance using a regularised regression technique (i.e. elastic net regression based on the local-level similarities in resting-state whole-brain connectivity between participants). Although neural homophily between friends exists when viewing naturalistic stimuli, this finding did not extend to functional connectivity at rest in our population. Instead, resting-state connectivity may be less susceptible to the influences of a person's social environment.
The pervasiveness and policy consequences of medical folk wisdom in the U.S.
Authors: Motta Matthew , Callaghan Timothy 
Published: July 2020

AbstractMedical folk wisdom (MFW) refers to widely held, but factually inaccurate, beliefs about disease, immunity, pregnancy, and other medically-relevant topics. Examples include the idea that fasting when feverish (“starving a fever”) can increase the pace of recovery, or that showering after sex can prevent pregnancy. The pervasiveness of MFW, and whether or not it—like other forms of medically-relevant misinformation—shapes Americans’ health behaviors and policy preferences is an important and under-studied question. We begin this research by proposing and validating a novel measure of MFW; including a short-form scale suitable for administration in public opinion surveys. We find that nearly all Americans—irrespective of socio-economic status, political orientation, and educational background—endorse at least some aspects of MFW. Concerningly, and consistent with the idea that folk wisdom challenges scientific expertise, we additionally find that those highest in MFW tend to place less value on medical expertise and the role experts play in shaping health policy. However, this skepticism does not appear to translate to peoples’ health actions, as MFW appears to have an inconsistent effect on public participation in healthy behaviors.
Electroacupuncture at Zusanli and at Neiguan characterized point specificity in the brain by metabolomic analysis
Authors: Lee Der-Yen , Jiu Yu-Rung , Hsieh Ching-Liang 
Published: July 2020

AbstractDifferent point stimulations can induce brain activity in specific regions, and however whether these stimulations affect unique neurotransmitter transmission remains unknown. Therefore, we aimed to investigate the effect of point specificity to the brain by resolving the metabolite profiles. Eighteen Sprague–Dawley rats were randomly divided into three groups: (1) the sham group: sham acupuncture at Zusanli (ST36) without electric stimulation; (2) the Zusanli (ST36) group: electroacupuncture (EA) at ST36; and (3) the Neiguan (PC6) group: EA at PC6. Then, the metabolites from rat brain samples were measured by LC–ESI–MS. The results of a partial least squares discriminant analysis revealed the differences among the sham, ST36, and PC6 groups regarding the relative content of metabolites in the cerebral cortex, hippocampus, and hypothalamus. EA at PC6 resulted in downregulation of adenosine, adrenaline, γ-aminobutyric acid, glycine, and glutamate majorly in hippocampus, and then in cerebral cortex. Otherwise, EA at ST6 resulted in upregulation of adrenaline and arginine in hippocampus, and all stimulations showed barely change of identified neurotransmitters in hypothalamus. These differential metabolite and neurotransmitter profiles prove that brain areas can be modulated by point specificity and may provide a maneuver to understand more details of meridian.
Demonstration of a pseudo-magnetization based simultaneous write and read operation in a Co60Fe20B20/Pb(Mg1/3Nb2/3)0.7Ti0.3O3 heterostructure
Authors: Shen Tingting , Ostwal Vaibhav , Camsari Kerem Y. , Appenzeller Joerg 
Published: July 2020

AbstractTaking advantage of the magnetoelectric and its inverse effect, this article demonstrates strain-mediated magnetoelectric write and read operations simultaneously in Co60Fe20B20/Pb(Mg1/3Nb2/3)0.7Ti0.3O3 heterostructures based on a pseudo-magnetization µ ≡ mx2 − my2. By applying an external DC-voltage across a (011)-cut PMN-PT substrate, the ferroelectric polarization is re-oriented, which results in an anisotropic in-plane strain that transfers to the CoFeB thin film and changes its magnetic anisotropy Hk. The change in Hk in-turn results in a 90° rotation of the magnetic easy axis for sufficiently high voltages. Simultaneously, the inverse effect is employed to read changes of the magnetic properties. The change of magnetization in ferromagnetic (FM) layer induces an elastic stress in the piezoelectric (PE) layer, which generates a PE potential that can be used to readout the magnetic state of the FM layer. The experimental results are in excellent qualitative agreement with an equivalent circuit model that considers how magnetic properties are electrically controlled in such a PE/FM heterostructure and how a back-voltage is generated due to changing magnetic properties in a self-consistent model. We demonstrated that a change of easy axis of magnetization due to an applied voltage can be directly used for information processing, which is essential for future ME based devices.
Technological characterization of gold jewellery from the Sogdian tomb of Shi Jun (d. 579 CE) in Xi’an, Shaanxi Province
Authors: Tan Panpan , Yang Junchang , Liu Yan , Zheng Yaozheng , Yang Junkai 
Published: July 2020

AbstractNorthern dynasties (386–581 CE) of China witnessed extensive cultural contacts with the outside world. Several gold objects of this period indicate multiple culture influences. However, very few of them were testified by metallurgic analysis. The gold jewellery including a finger ring and an earring with exotic features were uncovered from the joint elite Sogdian tomb of Shi Jun and his wife of the Northern Zhou dynasty (557–581 CE) in Xi'an. The current study applied multiple non-destructive analyses to investigate the decorative techniques and materials of the two objects. The results showed that both ornaments were made of refined gold. Autogenous welding and brazing were employed for joining the granules of the earring, indicating different technical choices. More interestingly, niello made of silver sulfide was identified as an innovative technology to decorate the finger ring, presenting the earliest evidence of niello inlay in ancient China. It is noteworthy that powders of silver and sulfur were applied separately, deferring from the traditional method of silver sulfide being synthesised prior to being used. These findings help us gain insights into understanding the technical features of early Medieval gold jewellery, as well as the goldsmith’s methods and intentions.
miRNAs involved in transcriptome remodeling during pollen development and heat stress response in Solanum lycopersicum
Authors: Keller Mario , Schleiff Enrico , Simm Stefan 
Published: July 2020

AbstractCellular transitions during development and stress response depend on coordinated transcriptomic and proteomic alterations. Pollen is particular because its development is a complex process that includes meiotic and mitotic divisions which causes a high heat sensitivity of these cells. Development and stress response are accompanied by a reprogramming of the transcriptome, e.g. by post-transcriptional regulation via miRNAs. We identified known and potentially novel miRNAs in the transcriptome of developing and heat-stressed pollen of Solanum lycopersicum (tomato). The prediction of target mRNAs yielded an equal number of predicted target-sites in CDS and 3′UTR regions of target mRNAs. The result enabled the postulation of a possible link between miRNAs and a fine-tuning of transcription factor abundance during pollen development. miRNAs seem to play a role in the pollen heat stress response as well. We identified several heat stress transcription factors and heat shock proteins as putative targets of miRNAs in response to heat stress, thereby placing these miRNAs as important elements of thermotolerance. Moreover, for members of the AP2, SBP and ARF family members we could predict a miRNA-mediated regulation during development via the miR172, mir156 and mir160-family strengthening the current concept of a cross-connection between development and stress response in plants.
Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis
Authors: Liu Jiangang , Cho Yong Beom , Hong Hye Kyung , Wu Song , Ebert Philip J. , Bray Steven M. , Wong Swee Seong , Ting Jason C. , Calley John N. , Whittington Catherine F. , Bhagwat Shripad V. , Reinhard Christoph , Wild Robert , Nam Do-Hyun , Aggarwal Amit , Lee Woo Yong , Peng Sheng-Bin 
Published: July 2020

AbstractMetastasis is the primary cause of cancer mortality. The primary tumors of colorectal cancer (CRC) often metastasize to the liver. In this study, we have collected 122 samples from 45 CRC patients. Among them, 32 patients have primary tumors, adjacent normal tissues, and matched liver metastases. Thirteen patients have primary tumors without distant metastasis and matched normal tissues. Characterization of these samples was conducted by whole-exome and RNA sequencing and SNP6.0 analysis. Our results revealed no significant difference in genetic alterations including common oncogenic mutations, whole genome mutations and copy number variations between primary and metastatic tumors. We then assembled gene co-expression networks and identified metastasis-correlated gene networks of immune-suppression, epithelial–mesenchymal transition (EMT) and angiogenesis as the key events and potentially synergistic drivers associated with CRC metastasis. Further independent cohort validation using published datasets has verified that these specific gene networks are up regulated throughout the tumor progression. The gene networks of EMT, angiogenesis, immune-suppression and T cell exhaustion are closely correlated with the poor patient outcome and intrinsic anti-PD-1 resistance. These results offer insights of combinational strategy for the treatment of metastatic CRC.
Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology
Authors: Bazaga Adrián , Leggate Dan , Weisser Hendrik 
Published: July 2020

AbstractA major cause of failed drug discovery programs is suboptimal target selection, resulting in the development of drug candidates that are potent inhibitors, but ineffective at treating the disease. In the genomics era, the availability of large biomedical datasets with genome-wide readouts has the potential to transform target selection and validation. In this study we investigate how computational intelligence methods can be applied to predict novel therapeutic targets in oncology.
We compared different machine learning classifiers applied to the task of drug target classification for nine different human cancer types. For each cancer type, a set of “known” target genes was obtained and equally-sized sets of “non-targets” were sampled multiple times from the human protein-coding genes. Models were trained on mutation, gene expression (TCGA), and gene essentiality (DepMap) data. In addition, we generated a numerical embedding of the interaction network of protein-coding genes using deep network representation learning and included the results in the modeling. We assessed feature importance using a random forests classifier and performed feature selection based on measuring permutation importance against a null distribution. Our best models achieved good generalization performance based on the AUROC metric. With the best model for each cancer type, we ran predictions on more than 15,000 protein-coding genes to identify potential novel targets. Our results indicate that this approach may be useful to inform early stages of the drug discovery pipeline.