bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age-dependent deterioration of nuclear pore assembly in mitotic cells decreases transport dynamics
Authors: Rempel I.L. , Crane M.M. , Mishra A. , Jansen D.P.M. , Janssens G.E. , Popken P. , Kaeberlein M. , Van der Giessen E. , Onck P.R. , Steen A. , Veenhoff L.M. 
Published: November 2018

AbstractNuclear transport is facilitated by the Nuclear Pore Complex (NPC) and is essential for life in eukaryotes. The NPC is a long-lived and exceptionally large structure. We asked whether NPC function is compromised in ageing mitotic cells. By imaging of single yeast cells during ageing, we show that the abundance of several NPC components and NPC assembly factors decreases while signs of misassembled NPCs appear. Consequently, nuclear permeability decreases, resulting in decreased dynamics of transcription factor shuttling and increased nuclear compartmentalisation. In support that declining NPC quality control is important in mitotic ageing, we find that the transport kinetics observed in ageing is mimicked in an NPC assembly mutant. Additionally, the single cell life histories reveal that cells that better maintain NPC function are longer lived. We conclude that assembly and quality control of NPCs are major challenges for ageing mitotic cells.
Live-cell single RNA imaging reveals bursts of translational frameshifting
Authors: Lyon Kenneth , Aguilera Luis U. , Morisaki Tatsuya , Munsky Brian , Stasevich Timothy J. 
Published: November 2018

ABSTRACTRibosomal frameshifting during the translation of RNA is implicated in both human disease and viral infection. While previous work has uncovered many mechanistic details about single RNA frameshifting kineticsin vitro, very little is known about how single RNA frameshift in living systems. To confront this problem, we have developed technology to quantify live-cell single RNA translation dynamics in frameshifted open reading frames. Applying this technology to RNA encoding the HIV-1 frameshift sequence reveals a small subset (~8%) of the translating pool robustly frameshift in living cells. Frameshifting RNA are preferentially in multi-RNA “translation factories,” are translated at about the same rate as non-frameshifting RNA (~2 aa/sec), and can continuously frameshift for more than four rounds of translation. Fits to a bursty model of frameshifting constrain frameshifting kinetic rates and demonstrate how ribosomal traffic jams contribute to the persistence of the frameshifting state. These data provide novel insight into retroviral frameshifting and could lead to new strategies to perturb the process in living cells.
Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA
Authors: Wan Nathan , Weinberg David , Liu Tzu-Yu , Niehaus Katherine , Delubac Daniel , Kannan Ajay , White Brandon , Ariazi Eric A. , Bailey Mitch , Bertin Marvin , Boley Nathan , Bowen Derek , Cregg James , Drake Adam M. , Ennis Riley , Fransen Signe , Gafni Erik , Hansen Loren , Liu Yaping , Otte Gabriel L , Pecson Jennifer , Rice Brandon , Sanderson Gabriel E. , Sharma Aarushi , John John St. , Tang Catherina , Tzou Abraham , Young Leilani , Putcha Girish , Haque Imran S. 
Published: November 2018

AbstractBackgroundBlood-based methods using cell-free DNA (cfDNA) are under development as an alternative to existing screening tests. However, early-stage detection of cancer using tumor-derived cfDNA has proven challenging because of the small proportion of cfDNA derived from tumor tissue in early-stage disease. A machine learning approach to discover signatures in cfDNA, potentially reflective of both tumor and non-tumor contributions, may represent a promising direction for the early detection of cancer.MethodsWhole-genome sequencing was performed on cfDNA extracted from plasma samples (N=546 colorectal cancer and 271 non-cancer controls). Reads aligning to protein-coding gene bodies were extracted, and read counts were normalized. cfDNA tumor fraction was estimated using IchorCNA. Machine learning models were trained using k-fold cross-validation and confounder-based cross-validation to assess generalization performance.ResultsIn a colorectal cancer cohort heavily weighted towards early-stage cancer (80% stage I/II), we achieved a mean AUC of 0.92 (95% CI 0.91-0.93) with a mean sensitivity of 85% (95% CI 83-86%) at 85% specificity. Sensitivity generally increased with tumor stage and increasing tumor fraction. Stratification by age, sequencing batch, and institution demonstrated the impact of these confounders and provided a more accurate assessment of generalization performance.ConclusionsA machine learning approach using cfDNA achieved high sensitivity and specificity in a large, predominantly early-stage, colorectal cancer cohort. The possibility of systematic technical and institution-specific biases warrants similar confounder analyses in other studies. Prospective validation of this machine learning method and evaluation of a multi-analyte approach are underway.
Dissociable Neural Correlates of Uncertainty Underlie Different Exploration Strategies
Authors: Tomov Momchil S. , Truong Van Q. , Hundia Rohan A. , Gershman Samuel J. 
Published: November 2018

SummaryMost real-world decisions involve a delicate balance between exploring unfamiliar alternatives and committing to the best known option. Uncertainty lies at the core of this “explore-exploit” dilemma, for if all options were perfectly known, there would be no need to explore. Yet despite the prominent role of uncertainty-guided exploration in decision making, evidence for its neural implementation is still sparse. We investigated this question with model-based fMRI (n = 31) using a two-armed bandit task that independently manipulates two forms of uncertainty underlying different exploration strategies. The relative uncertainty between the two options was correlated with BOLD activity in right rostrolateral prefrontal cortex and drove directed exploration, a strategy that adds an uncertainty bonus to each option. The total uncertainty across the two options was correlated with activity in left dorsolateral prefrontal cortex and drove random exploration, a strategy that increases choice stochasticity in proportion to total uncertainty. The subjective estimates of uncertainty from both regions were predictive of subject choices. These results are consistent with a hybrid computational architecture in which different uncertainty computations are performed separately and then combined by downstream decision circuits to compute choice.
Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
Authors: Daetwyler Stephan , Günther Ulrik , Modes Carl D. , Harrington Kyle , Huisken Jan 
Published: November 2018

AbstractTo quantitatively understand biological processes that occur over many hours or days, it is desirable to image multiple samples simultaneously and automatically process and analyze the resulting datasets. Here, we present a complete multi-sample preparation, imaging, processing, and analysis workflow to determine the development of the vascular volume in zebrafish. Up to five live embryos were mounted and imaged simultaneously over several days using selective plane illumination microscopy (SPIM). The resulting large imagery dataset of several terabytes was processed in an automated manner on a high-performance computer cluster and segmented with a novel segmentation approach that uses images of red blood cells as training data. This analysis yielded a precise quantification of growth characteristics of the whole vascular network, head vasculature, and tail vasculature over development. Our multi-sample platform demonstrates effective upgrades to conventional single-sample imaging platforms and paves the way for diverse quantitative long-term imaging studies.Summary statementWe present a dedicated multi-sample light sheet imaging, processing and analysis platform and demonstrate its value for studies of vascular growth in zebrafish.
Coverage, Opportunity and Challenges of expanded Program on Immunization among 12-23 Months old Children in Woldia Town, Northeast, Ethiopia, 2018: Mixed cross sectional study
Authors: Abebe Ayele Mamo , Kassaw Mesfin Wudu , Birara Alemu 
Published: November 2018

AbstractObjectiveThe purpose of this is to assess coverage, opportunity and challenges of EPI among children age 12-23 month in Woldia town, Amhara region, Ethiopia.ResultA total of 389 mothers/caretakers were interviewed. Based on vaccination card and mothers/caretakers’ recall, 385 (99%) of the children took at least a single dose of vaccine. About 343 (87.7%) children were fully immunized. Dropout rate was 9% for BCG to measles. Qualitative study revealed that workload, shortage of vaccine and non-compliance of mother/care taker for next schedule date was the major challenge faced by health professionals. In this study, vaccination coverage was low compared to the Millennium Development Goals target. Thus the town health office and concerned stakeholders need to work more to improve performance of the expanded program on immunization in this area.
Thermopneumatic suction integrated microfluidic blood analysis system
Authors: Yang Chiao-Hsun , Hsieh Yu-Ling , Tsou Ping-Hsien , Li Bor-Ran 
Published: November 2018

AbstractBlood tests provide crucial diagnostic information regarding several diseases. A key factor that affects the precision and accuracy of blood tests is the interference of red blood cells; however, the conventional methods of blood separation are often complicated and time consuming. In this study, we devised a simple but high-efficiency blood separation system on a self-strained microfluidic device that separates 99.7% of the plasma in only 6 min. Parameters, such as flow rate, design of the filter trench, and the relative positions of the filter trench and channel, were optimized through microscopic monitoring. Moreover, this air-difference-driven device uses a cost-effective and easy-to-use heater strip that creates a low-pressure environment in the microchannel within minutes. With the aforementioned advantages, this blood separation device could be another platform choice for point-of-care testing.
Temporal and spatial selectivity of hippocampal connectivity with sensorimotor cortex during individual finger movements
Authors: Miller Michael J. , Burman Douglas D. 
Published: November 2018

AbstractCognitive control refers to brain processes involved in regulating behavior according to internal goals or plans. This study examines whether hippocampal connectivity with sensorimotor cortex during paced movements shows a pattern of spatial and temporal selectivity required for cognitive control. Functional magnetic resonance imaging activity was recorded from thirteen right-handed subjects during a paced, non-mnemonic (repetitive tapping) motor task. Direct and inverse connectivity in sensorimotor cortex were examined from psychophysiological interactions (PPI) from hippocampal seed activity during two sets of analyses: the first identified motor interactions relative to rest, whereas the second identified interactions in motor activity between fingers. Finger representations identified in a previous study were used to evaluate patterns of temporal and spatial selectivity in hippocampal connectivity. Changes in the magnitude of connectivity were identified within the sensorimotor representations of the first (index) through third (ring) fingers across time periods when each finger moved; at each finger representation, hippocampal connectivity was greatest when the represented finger was moving, reflecting temporal selectivity for the timing of finger movements. Similarly, the seeds associated with each finger representation differed in their magnitude of connectivity for adjacent finger representations, reflecting spatial selectivity for the moving finger. The patterns of spatial and temporal selectivity of connectivity during volitional movements in this study meets the criteria for cognitive control adapted from oculomotor studies.
Whole Body Periodic Acceleration Improves Survival and Microvascular Leak in a Murine Endotoxin Model
Authors: Adams Jose A. , Uryash Arkady , Lopez Jose R. , Sackner Marvin A. 
Published: November 2018

ABSTRACTSepsis is a life threatening condition which produces multi-organ dysfunction with profound circulatory and cellular derangements. Administration of E.Coli endotoxin (LPS) produces systemic inflammatory effects of sepsis including disruption of endothelial barrier, and if severe enough death. Whole body periodic acceleration (pGz) is the headward-footward motion of the body. pGz has been shown to induce pulsatile shear stress to the endothelium, thereby releasing vascular and cardio protective mediators. The purpose of this study was to determine whether or not pGz performed as a pre-treatment or post-treatment strategy improves survival in a lethal murine endotoxin model.This study was designed as a prospective randomized controlled study in mice. pGz was performed in mice as pre-treatment (pGz-LPS, 3 days prior to LPS), post-treatment (LPS-pGz, 30 min after LPS) strategies or Control (LPS-CONT), in a lethal murine model of endotoxemia. Endotoxemia was induced with intraperitoneal injection of E.Coli (40mg/kg). In a separate group of mice, a nonspecific nitric oxide synthase inhibitor (L-NAME) was provided in their drinking water and pGz-LPS and LPS-pGz performed to determine the effect of nitric oxide (NO) inhibition on survival. In another subset of mice, micro vascular leakage was determined. Behavioral scoring around the clock was performed in all mice at 30 min intervals after LPS administration, until 48 hrs. survival or death. LPS induced 100% mortality in LPS-CONT animals by 30 hrs. In contrast, survival to 48 hrs. occurred in 60% of pGz-LPS and 80% of LPS-pGz. L-NAME abolished the survival effects of pGz. Microvascular leakage was markedly reduced in both pre and post pGz treated animals and was associated with increased TIE2 and p-TIE2. In a murine model of lethal endotoxemia, pGz performed as a pre or post treatment strategy significantly improved survival, and markedly reduced microvascular leakage. The effect was modulated, in part, by NO since a non-selective inhibitor of NO abolished the pGz survival effect.
Categorical encoding of decision variables in orbitofrontal cortex
Authors: Onken Arno , Xie Jue , Panzeri Stefano , Padoa-Schioppa Camillo 
Published: November 2018

AbstractA fundamental and recurrent question in systems neuroscience is that of assessing what variables are encoded by a given population of neurons. Such assessments are often challenging because neurons in one brain area may encode multiple variables, and because neuronal representations might be categorical (different neurons encoding different variables) or mixed (individual neurons encoding a combination of variables). These issues are particularly pertinent to the representation of decision variables in the orbitofrontal cortex (OFC) – an area implicated in economic choices. Here we present a new algorithm to assess whether a neuronal representation is categorical or mixed, and to identify the encoded variables if the representation is indeed categorical. The algorithm is based on two clustering procedures, one variable-independent and the other variable-based. The two partitions are then compared through adjusted mutual information. The present algorithm overcomes limitations of previous approaches and is widely applicable. We tested the algorithm on synthetic data and then used it to examine neuronal data recorded in the primate OFC during economic decisions. Confirming previous assessments, we found the neuronal representation in OFC to be categorical in nature. We also found that neurons in this area encode the value of individual offers, the binary choice outcome and the chosen value. In other words, during economic choice, neurons in the primate OFC encode decision variables in a categorical way.Author SummaryMental functions such as sensory perception or decision making ultimately rely on the activity of neuronal populations in different brain regions. Much research in neuroscience is devoted to understanding how different groups of neurons support specific brain functions by representing behaviorally relevant variables. In this respect, one important question is whether individual neurons represent single variables, or linear combination of variables. Here we developed a new algorithm to assess this general issue. We then used the algorithm to examine neurons in the orbitofrontal cortex (OFC) recorded while non-human primates performed economic decisions. We found that different neurons represent different variables (categorical encoding). Specifically, neurons in the OFC encoded the value of individual offers, the binary choice outcome, and the chosen value. The present results support the hypothesis that economic decisions are formed within the OFC.
Research on comment target extracting in Chinese online shopping platform
Authors: Liu Zhishuo , Shen Qianhui , Ma Jingmiao , Dong Ziqi 
Published: November 2018

Purpose
This paper aims to extract the comment targets in Chinese online shopping platform.

Design/methodology/approach
The authors first collect the comment texts, word segmentation, part-of-speech (POS) tagging and extracted feature words twice. Then they cluster the evaluation sentence and find the association rules between the evaluation words and the evaluation object. At the same time, they establish the association rule table. Finally, the authors can mine the evaluation object of comment sentence according to the evaluation word and the association rule table. At last, they obtain comment data from Taobao and demonstrate that the method proposed in this paper is effective by experiment.

Findings
The extracting comment target method the authors proposed in this paper is effective.

Research limitations/implications
First, the study object of extracting implicit features is review clauses, and not considering the context information, which may affect the accuracy of the feature excavation to a certain degree. Second, when extracting feature words, the low-frequency feature words are not considered, but some low-frequency feature words also contain effective information.

Practical implications
Because of the mass online reviews data, reading every comment one by one is impossible. Therefore, it is important that research on handling product comments and present useful or interest comments for clients.

Originality/value
The extracting comment target method the authors proposed in this paper is effective.
Food away from home in Brazil: the role of sociodemographic factors and family structure
Authors: Queiroz Pedro , Coelho Alexandre B. 
Published: November 2018

Purpose
The purpose of this paper is to estimate the determinants of per capita expenditures with disaggregate food away from home (FAFH) including variables such as family structure.

Design/methodology/approach
The authors estimated a system of expenditure equations (SUR method) with data from the latest Consumer Expenditure Survey of 2008–2009 – (or Pesquisa de Orçamentos Familiares – POF), considering the complex sample design in estimation procedures.

Findings
The authors found a positive relationship between woman’s opportunity cost of time and FAFH spending only when the authors considered the effects of wife’s education in higher income class. Hiring domestic help diminishes FAFH spending, mostly for lunch and dinner time meals. The presence of children in the household decreases the consumption of most FAFH categories.

Social implications
Even though, Brazilian FAFH consumption has been increasing, the presence of women in the labor market seems to play a small role in the determining this type of food consumption. Family structure plays an important role in determining FAFH.

Originality/value
The contribution of the paper is to estimate FAFH expenditures at the disaggregate level and by income class for Brazil. The authors also included alternative family structure specifications as determinants in the model. The authors considered the sample design characteristics in estimation.
Influence of hard rolling and the cooling lubricant on the material properties and the rolling strength of PM gears
Authors: Klocke Fritz , Bergs Thomas , Löpenhaus Christoph , Scholzen Philipp , Frech Tim 
Published: November 2018

Purpose
The lower density of powder metallurgical (PM) gears compared to solid steel gears leads to not only a lower weight but also a lower load-carrying capacity. Therefore, PM gears are cold rolled before hardening to increase the density in the highly stressed surface zone and, thus, the flank load-carrying capacity. A further approach to increase the flank load-carrying capacity is the reduction of friction and wear in the tooth contact. The purpose of this paper is to analyze the hard rolling process as a new manufacturing step in the PM process chain to influence the boundary layer.

Design/methodology/approach
The investigation includes the new process of hard rolling, the variation of the cooling lubricant in the hard rolling process and the evaluation of its influence on the material properties and the flank load-carrying capacity. Therefore, the additives of the cooling lubricant are varied regarding the sulfur and phosphorous content. The load-carrying capacity is evaluated on disk-on-disk test rig and the material properties are evaluated by metallographic tests and boundary layer.

Findings
The results of the specimen characteristics in the micro and nano range show a significant influence of hard rolling on the residual stresses and the chemical surface composition. Because of hard rolling, residual compressive stresses as well as roughness are reduced and the flank load-carrying capacity is increased by high phosphorous content of the cooling lubricant.

Originality/value
This paper investigates a new manufacturing step to increase resource efficiency by increasing the flank load-carrying capacity of spur gears.
Women’s experiences and acceptability of medical termination of pregnancy
Authors: Saejeng Kittipong , Jaisamrarn Unnop , Naravage Wanapa 
Published: November 2018

Purpose
The purpose of this paper is to understand women’s experiences, acceptability and outcomes of using the medical termination of pregnancy (MTP). The study is conducted at nine reproductive health and family planning clinics at university hospitals as well as regional and provincial hospitals located in Bangkok and the locations within Thailand.

Design/methodology/approach
This is a descriptive research recruiting healthy women with pregnancy up to 63 days since the last menstrual period (LMP) who opted for MTP during 2012–2014.

Findings
A total of 443 women who were referred from the reproductive health networks voluntarily participated in the study. Overall, 92.6 percent of participants had a complete abortion. No serious adverse events were found for cases using misoprostol at home or at clinic. More than 98.3 percent of the women felt satisfied or very satisfied with the method. More than 80 percent of participants thought that the side-effects of the method were as expected or less than expected. More than 95 percent of the women recommended having MTP available in Thailand.

Originality/value
The introduction of MTP that uses a mifepristone and misoprostol regimen (Medabon®) in pregnancies up to 63 days, since LMP demonstrates that misoprostol can be safely used by women at home or at clinic. The administration of misoprostol at home reduces the number of hospital visits, which saves time and costs for traveling from home to the facility. In addition, women have more privacy and control over their bodies by self-administering misoprostol. The MTP’s introductory results also show that MTP service provision is well integrated into reproductive health and family planning services. It is useful for stakeholders who would be involved in design and planning of health system services before the MTP is made broadly available throughout the country.