bluuebunny/crossref_metadata_2025_split huggingface dataset:
recount-brain: a curated repository of human brain RNA-seq datasets metadata
Authors: Razmara Ashkaun , Ellis Shannon E. , Sokolowski Dustin J. , Davis Sean , Wilson Michael D. , Leek Jeffrey T. , Jaffe Andrew E. , Collado-Torres Leonardo 
Published: April 2019

AbstractThe usability of publicly-available gene expression data is often limited by the availability of high-quality, standardized biological phenotype and experimental condition information (“metadata”). We released the recount2 project, which involved re-processing ∼70,000 samples in the Sequencing Read Archive (SRA), Genotype-Tissue Expression (GTEx), and The Cancer Genome Atlas (TCGA) projects. While samples from the latter two projects are well-characterized with extensive metadata, the ∼50,000 RNA-seq samples from SRA in recount2 are inconsistently annotated with metadata. Tissue type, sex, and library type can be estimated from the RNA sequencing (RNA-seq) data itself. However, more detailed and harder to predict metadata, like age and diagnosis, must ideally be provided by labs that deposit the data.To facilitate more analyses within human brain tissue data, we have complemented phenotype predictions by manually constructing a uniformly-curated database of public RNA-seq samples present in SRA and recount2. We describe the reproducible curation process for constructing recount-brain that involves systematic review of the primary manuscript, which can serve as a guide to annotate other studies and tissues. We further expanded recount-brain by merging it with GTEx and TCGA brain samples as well as linking to controlled vocabulary terms for tissue, Brodmann area and disease. Furthermore, we illustrate how to integrate the sample metadata in recount-brain with the gene expression data in recount2 to perform differential expression analysis. We then provide three analysis examples involving modeling postmortem interval, glioblastoma, and meta-analyses across GTEx and TCGA. Overall, recount-brain facilitates expression analyses and improves their reproducibility as individual researchers do not have to manually curate the sample metadata. recount-brain is available via the add_metadata() function from the recount Bioconductor package at bioconductor.org/packages/recount.
Cell fate determination by Lamarckian molecule-inheritance and chance
Authors: Bruggeman Frank J. , Schouten Jaap , de Groot Daan H. , Planqué Robert 
Published: April 2019

AbstractSingle, isogenic cells can differ in their survival and adaptation capacity. This phenotypic diversity is generally due to stochastic molecular events. Since mother cells on average pass half of their molecular content on to their daughters, the states of progeny cells strongly correlate with that of mother cells (Lamarckian inheritance). Why a particular cell deviates qualitatively from others therefore requires consideration of chance events along its ancestral lineage. Here we develop theory to understand cellular heterogeneity in terms of stochastic ancestral events of molecule synthesis, molecule degradation and cell divisions. We find that cell growth stochasticity has profound consequences for molecular heterogeneity in isogenic populations of cells, especially for long-lived molecules such as proteins. For instance, the lower bound on noise in molecule copy numbers that has often been observed experimentally is shown to be solely determined by the probability distribution for the generation times of cells. Thus, copy-number noise is unavoidable, even in high-copy number circuits. Stochastic cell-fate and cell-differentiation decisions are therefore not necessarily due to noise in genetic circuits. We conclude that consideration of past chance events along cell lineages improves our understanding of how adaptive and mal-adaptive phenotypic heterogeneity arises in populations of isogenic cells.
Plasmodium secretion induces hepatocyte lysosome exocytosis and promotes parasite entry
Authors: Vijayan Kamalakannan , Cestari Igor , Mast Fred D. , Glennon Elizabeth K.K. , McDermott Suzanne M , Kain Heather S. , Brokaw Alyssa M. , Aitchison John D. , Stuart Kenneth , Kaushansky Alexis 
Published: April 2019

AbstractThe invasion of a suitable host hepatocyte by Plasmodium sporozoites is an essential step in malaria infection. We demonstrate that in infected hepatocytes, lysosomes are redistributed away from the nucleus, and surface exposure of lysosomal-associated membrane protein (LAMP1) is increased. Lysosome exocytosis in infected cells occurs independently of sporozoite traversal. Instead, a sporozoite-secreted factor is sufficient for the process. Knockdown of the SNARE proteins involved in lysosome-plasma membrane fusion reduces lysosome exocytosis and Plasmodium infection. In contrast, promoting fusion between the lysosome and plasma membrane dramatically increases infection. Our work demonstrates new parallels between Plasmodium sporozoite entry of hepatocytes and infection by the excavate pathogen, Trypanosoma cruzi and raises the question of whether convergent evolution has shaped host cell invasion by divergent pathogens.
Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FOmotor
Authors: Kubo Shintaroh , Niina Toru , Takada Shoji 
Published: April 2019

AbstractThe FOmotor in FOF1ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FOrotary dynamics at structural details. Here, developing a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36°-stepwise rotations of FOper one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FOmotor reaches ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments.
Human 28s rRNA 5’ terminal derived small RNA inhibits ribosomal protein mRNA levels
Authors: Li Shuai 
Published: April 2019

AbstractRecent small RNA (sRNA) high-throughput sequencing studies reveal ribosomal RNAs (rRNAs) as major resources of sRNA. By reanalyzing sRNA sequencing datasets from Gene Expression Omnibus (GEO), we identify 28s rRNA 5’ terminal derived sRNA (named 28s5-rtsRNA) as the most abundant rRNA-derived sRNAs. These 28s5-rtsRNAs show a length dynamics with identical 5’ end and different 3’ end. Through exploring sRNA sequencing datasets of different human tissues, 28s5-rtsRNA is found to be highly expressed in bladder, macrophage and skin. We also show 28s5-rtsRNA is independent of microRNA biogenesis pathway and not associated with Argonaut proteins. Overexpression of 28s5-rtsRNA could alter the 28s/18s rRNA ratio and decrease multiple ribosomal protein mRNA levels. Our results reveal that 28s5-rtsRNA serves as a key regulator in ribosomal protein expression.
Axonal Na+ channels detect and transmit levels of input synchrony in local brain circuits
Authors: Zbili Mickaёl , Rama Sylvain , Yger Pierre , Inglebert Yanis , Boumedine-Guignon Norah , Fronzaroli-Moliniere Laure , Brette Romain , Russier Michaёl , Debanne Dominique 
Published: April 2019

AbstractSensory processing requires mechanisms of fast coincidence-detection to discriminate synchronous from asynchronous inputs. Spike-threshold adaptation enables such a discrimination but is ineffective in transmitting this information to the network. We show here that presynaptic axonal sodium channels read and transmit precise levels of input synchrony to the postsynaptic cell by modulating the presynaptic action potential (AP) amplitude. As a consequence, synaptic transmission is facilitated at cortical synapses when the presynaptic spike is produced by synchronous inputs. Using dual soma-axon recordings, imaging, and modeling, we show that this facilitation results from enhanced AP amplitude in the axon due to minimized inactivation of axonal sodium-channels. Quantifying local circuit activity and using network modeling, we found that spikes induced by synchronous inputs produced a larger effect on network activity than spikes induced by asynchronous inputs. Therefore, this input-synchrony dependent facilitation (ISF) may constitute a powerful mechanism regulating spike transmission.
Water storage and irrigation practices associated with cannabis production drive seasonal patterns of water extraction and use in Northern California watersheds
Authors: Dillis Christopher , McIntee Connor , Grantham Ted , Butsic Van , Le Lance , Grady Kason 
Published: April 2019

AbstractConcerns have been raised over the impacts of cannabis farms on the environment and water resources in particular, yet data on cultivation practices and water use patterns and have been limited. Estimates of water use for cannabis cultivation have previously relied on extrapolated values of plant water demand, which are unable to account for differences in cultivation practices, variation across the growing season, or the role of water storage in altering seasonal extraction patterns. The current study uses data reported by enrollees in California’s North Coast Regional Water Quality Control Board (Regional Water Board) Cannabis Program to model how variation in cultivation practices and the use of stored water affect the timing and amount of water extracted from the environment. We found that the supplemental use of stored water resulted in a seasonal pattern of water extraction (i.e. water withdrawals from the environment) that was distinct from water demand (i.e. water applied to plants). Although water input to storage in the off-season months (November through March) reduced water extraction in the growing season (April through October), farms generally did not have sufficient storage to completely forbear from surface water extraction during the growing season. Beginning in 2019, forbearance will be required during this period for those in the regulated cannabis industry. The two most important predictors of storage sufficiency (type of storage infrastructure and seasonality of water source) also had reliable effects on seasonal extraction patterns, further emphasizing the link between water storage and extraction profiles. These findings suggest that resource managers and policy makers should consider the ways in which cultivation practices drive water extraction patterns and how these practices may be influenced by participation in the regulated cannabis industry.
Long-Term Outcomes of Pediatric Graves Disease Patients Treated with Anti-Thyroid Drugs: Experience from a Taiwan Medical Center
Authors: Chiang Ya-Ting , Ting Wei-Hsin , Huang Chi-Yu , Huang Shih-Kang , Chan Chon-In , Cheng Bi-Wen , Lin Chao-Hsu , Wu Yi-Lei , Hung Chen-Mei , Li Hsin-Jung , Chan Chia-Jung , Lee Yann-Jinn 
Published: April 2019

AbstractGraves disease (GD) is the most common cause of thyrotoxicosis in children and adolescents, accounting for 15% of all thyroid diseases during childhood. Anti-thyroid drugs (ATD) are recommended as the first-line treatment in children and adolescents. However, the remission rate is lower in children than in adults, and the optimal treatment duration and favorite factors associated with remission remain unknown. We aimed to investigate long-term outcomes of pediatric GD patients receiving ATD. We retrospectively reviewed medical charts of 300 pediatric GD subjects, who were initially treated with ATD and followed up for more than one year, from 1985 to 2017 at MacKay Children’s Hospital. The 300 patients comprised 257 (85.7%) females and 43 (14.3%) males, median age at diagnosis was 11.6 (range 2.7-17.8) years, and median follow-up period was 4.7 (range 1.1-23.9) years. Overall, 122 patients achieved the criteria for discontinuing ATD treatment, seventy-nine (39.9%) patients achieved remission, with a median follow-up period of 5.3 (range 1.5-20.1) years. Patients in the remission group were more likely to be aged < 5 years (remission vs. relapse vs. ongoing ATD; 11.4 vs. 0 vs. 2.6%, P=0.02), less likely to have a family history of thyroid disease (24.1 vs. 42.1 vs. 52.6 %, P=0.001), and had lower TRAb levels (42.8 vs. 53.6 vs. 65.1 %, P=0.02).ConclusionLong-term ATD remains an effective treatment option for GD in children and adolescents. Pediatric GD patients aged < 5 years, having no family history of thyroid disease and having lower TRAb levels were more likely to achieve remission.
Exogenous Melatonin accelerates seed germination in cotton(Gossypium hirsutum L.)
Authors: Xiao Shuang , Liu Liantao , Wang Hao , Li Dongxiao , Bai Zhiying , Zhang Yongjiang , Sun Hongchun , Zhang Ke , Li Cundong 
Published: April 2019

AbstractSeed germination is considered as the beginning of the spermatophyte lifecycle, as it is a crucial stage in determining subsequent plant growth and development. Although many previous studies have found that melatonin can promote seed germination, the role of melatonin in cotton germination remains unexamined. The main objective of this study is the characterization of potential promotional effects of melatonin (at doses of 0, 10, 20, 50, 100 and 200 μM) on cotton seed germination. This experiment demonstrated that low concentrations of melatonin can promote germination, while high concentrations failed to promote germination and even inhibited germination. Together, these results indicate that a 20 μM melatonin treatment optimally promotes cotton seed germination. Compared with the control, germination potential (GP), germination rate (GR) and final fresh weight (FW) increased by 16.67%, 12.30% and 4.81% respectively. Although low concentrations of melatonin showed some improvement in vigor index (VI), germination index (GI) and mean germination time (MGT), these effects did not reach significant levels. Antioxidant enzyme activity during seed germination was most prominent under the 20 μM melatonin treatment. Superoxide dismutase (SOD) and peroxidase (POD) activities were significantly increased by 10.37–59.73% and 17.79–47.68% compared to the melatonin-free control. Malondialdehyde (MDA) content was reduced by 16.73–40.33%. Two important plant hormones in seed germination were also studied. As melatonin concentration increased, ABA content in seeds decreased first and then increased, and GA3 content showed a diametrically opposite trend, in which the 20 μM melatonin treatment was optimal. The 20 μM melatonin treatment reduced ABA content in seeds by 42.13–51.68%, while the 20 μM melatonin treatment increased GA3 content in seeds to about 1.7–2.5 times that of seeds germinated without melatonin. This study provides new evidence suggesting that low concentrations of melatonin can promote cotton seed germination by increasing the activity of antioxidant enzymes, thereby reducing the accumulation of MDA and regulating plant hormones. This has clear applications for improving the germination rate of cotton seeds using melatonin.
How can neuroscience inform our coaching practice -- six strategies to facilitate an optimal brain state in coachees
Authors: Bamber Rachel 
Published: April 2019

Purpose
How do you ensure that your coachees are getting the most value, support, and challenge from your coaching sessions? Before you even start asking questions and engaging in a coaching conversation, neuroscience can help you! The purpose of this paper is to outline six easy strategies that you can deploy to enable the best brain state to aid cognition, decisions, and creative thinking for your coachee and yourself.

Design/methodology/approach
A viewpoint based on the latest research from neuroscience and the author’s expertise as a coach for over 15 years.

Findings
Using the latest research from neuroscience to assist coachees to find their own solutions to the issues they face ensures they take ownership and are more motivated to take action.

Originality/value
The paper takes key elements from the latest evidence in neuroscience and applies them to the practice of coaching.
Care living labs’ effect on care organization and quality of working life
Authors: Vereycken Anselm Yennef , De Kort Leen , Vanhootegem Geert , Dessers Ezra 
Published: April 2019

PurposeThere is a growing interest in living labs (a research concept in which innovations are co-created with end-users and tested in practice) as a method to test and develop health and social care innovations. However, little is known about their effect on the care organization and care providers’ quality of working life. By using the Flanders Care Living Labs program (Belgium) as a case study, the purpose of this paper is to explore how innovations in a living lab context may affect those issues.Design/methodology/approachThis qualitative study combined data from document analysis, in-depth interviews and focus groups involving 23 care innovation projects. Deductive category application was used for analyzing data.FindingsOutcomes indicate that 22/23 care innovation projects resulted in organizational changes, and that 22 affected at least one care provider’s quality of working life. Surprisingly, no project deliberately intended to affect the care organization and quality of working life. Future care innovation projects should focus on actual innovation and its implications for specific end-users, and on the broader organizational consequences and the possible effect on the care providers’ work.Originality/valueThis is the first study that specifically focused on care innovation’s effect on the care organization and on the quality of working life within a living labs context.
Relationships between maternal characteristics and infant birth weight
Authors: Javadi Maryam , Rafiei Sima , Zahedifar Fariba , Barikani Ameneh 
Published: April 2019

Purpose
Nowadays, the importance of infant birth weight (IBW) as a key factor in determining the future of physical and mental development of children is a growing concern. The purpose of this paper is to investigate the relationship between maternal characteristics and IBW among pregnant women who were referred to health centers in Qazvin city in the year 2016.

Design/methodology/approach
A descriptive-analytical study was conducted among pregnant women in 28–36 weeks of gestation who referred to healthcare centers and facilities affiliated by the Qazvin University of Medical Sciences in April–June 2016. The associations between maternal physical activity, mothers’ socioeconomic status and birth weight were examined by SPSS Software Package version 16 through linear and logistic regression tests.

Findings
Linear regression modeling suggested that maternal weight (p=0.001), income (p=0.04), gestational age of delivery (p=0.00) and pre-pregnancy BMI (p=0.02) were positively associated with birth weight, while occupational and heavy physical activity (p=0.003 and 0.008, respectively) were negatively associated with IBW. In this study, low birth weight infants are compared to those with normal weight belonged to mothers who have spent more time in doing heavy physical activities (OR=1.11, 95% CI 1.01–1.23). Also infants with low birth weight compared to others in the normal weight category were born from mothers with lower pre-pregnancy BMI (OR=0.65, 95% CI 0.62–0.78), gestational age of delivery (OR=0.82, 95% CI 0.79–0.86), maternal weight (OR=0.86, 95% CI 0.84–0.88) and income (OR=0.79, 95% CI 0.69–0.83).

Practical implications
The study findings revealed that certain maternal characteristics could play a significant role in IBW. Despite the importance, in most of developing countries (particularly Iran), future mothers are not advised about an appropriate weight gain during pregnancy or the optimal level of physical activity in such a period of time. Therefore, counseling pregnant women and giving them proper information on appropriate perinatal care would be helpful in order to have pregnancies with optimal outcomes.

Originality/value
The authors applied several statistical methods to analyze IBW among mothers with different maternal characteristics and predict birth weight based on contributing factors.
Understanding causes of volatility in onion prices in India
Authors: Birthal Pratap , Negi Akanksha , Joshi P.K. 
Published: April 2019

Purpose
Post-2008 global food crisis the prices of perishable high-value food commodities, such as vegetables and fruits, in India have risen faster and become more volatile compared to that of cereals. The welfare consequences of price shocks though are well understood yet the policy responses to manage these remain blurred because of a lack of clarity on their causes. Focusing on onions that comprise an important constituent of the Indian diet, the purpose of this paper is to explore causes of high price volatility.

Design/methodology/approach
Using high-frequency time series data on wholesale prices and arrivals of onions in major markets and other relevant variables, this paper analyzes causes of price volatility from several angles, that is production shocks, seasonality in production and market arrivals, internal trade, export policies and market power of intermediaries on the supply chain.

Findings
Despite markets being integrated and no significant climatic shocks to production there exists a strong element of uncertainty in market arrivals of onions, pointing toward the market power immediate downstream the production or alternatively anti-competition trade practices in major markets as a cause of high price volatility. The measures to manage price volatility, such as an increase in minimum export prices and bans on exports, are also not found to have an immediate cooling effect on prices.

Research limitations/implications
The agricultural policy should provide for a system of market intelligence to monitor anti-competitive trade practices along the supply chain, and to take proactive trade control measures to prevent frequent ups and downs in domestic prices. In addition, it should provide for incentives for developing efficient supply chains and for the cultivation of onions in the regions that have agronomic potential but it has remained underexploited due to one or the other constraint.

Social implications
Excessive volatility in food prices impacts farmers, consumers, processors, and traders and even political system. It may distort production and investment decisions of farmers and intermediaries on the value chains, leading to inefficient allocation of resources. The poor consumers may be forced to reduce food and non-food productive expenditures. If persists for a longer period, it may lead to political instability too.

Originality/value
Several studies have analyzed volatility in food prices and causes thereof. However, rarely any of these has examined volatility in prices of perishable high-value food commodities. This paper is an attempt toward filling this gap.