bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composition and Abundance of Drifting Fish Eggs on the Upper Reaches of Xijiang River, China, after the Formation of the Cascade Reservoirs
Authors: Minghui Gao , Zhiqiang Wu , Xichang Tan , Liangliang Huang , Haibo Huang , Hao Liu 
Published: January 2020

AbstractTo develop effective management actions of riverine fisheries, it is important to monitor how fish resources (i.e., eggs) are recruited in the upper reaches of natural rivers, particularly where dams have been constructed, which potentially hinder life-history strategies. Here, we aimed to determine the State of drifting fish eggs resources, and the underlying environmental factors regulating the presence of fish eggs in the upper reaches of a river (Laibin section of Xijiang River, China). Based on surveys conducted over one spawning period (2016), we set out to: (1) describe the composition and abundance of drifting fish eggs in the 150 km Lainbin section under a dam control, and (2) analyze how the composition and distribution of fish eggs was correlated with environmental factors. A total of 15157 eggs belonging to two orders, four families, and 18 species were collected. Comparison of these data with historical records in the same area showed that the community structure of drifting eggs has changed considerably. Previously, the community was dominated by larger-bodied species, rather than the smaller species documented in 2016. Eggs were primarily detected between May and August. In the natural channel, the greatest abundance of eggs occurred during May and June. In comparison, the greatest abundance of eggs downstream of the dam was detected in July. The results of this study provide important information for water conservancy institutions towards managing regions containing dams to maintain the ecology of rivers and protect important fish resources.
De novolearning versus adaptation of continuous control in a manual tracking task
Authors: Yang Christopher S , Cowan Noah J , Haith Adrian M 
Published: January 2020

AbstractHow do people learn to perform tasks that require continuous adjustments of motor output, like riding a bicycle? People rely heavily on cognitive strategies when learning discrete movement tasks, but such time-consuming strategies are infeasible in continuous control tasks that demand rapid responses to ongoing sensory feedback. To understand how people can learn to perform such tasks without the benefit of cognitive strategies, we imposed a rotation/mirror reversal of visual feedback while participants performed a continuous tracking task. We analyzed behavior using a system identification approach which revealed two qualitatively different components of learning: adaptation of a baseline controller and formation of a new, task-specific continuous controller. These components exhibited different signatures in the frequency domain and were differentially engaged under the rotation/mirror reversal. Our results demonstrate that people can rapidly build a new continuous controllerde novoand can simultaneously deploy this process with adaptation of an existing controller.
Long weekend sleep is linked to stronger academic performance in male but not female pharmacy students
Authors: Leak Rehana Khan , Weiner Susan L. , Chandwani Manisha N. , Rhodes Diane C. 
Published: January 2020

AbstractIntroductionPoor sleep hygiene portends loss of physical and mental stamina. Therefore, maintaining a regular sleep/wake schedule on both weekdays and weekends is highly recommended. However, this advice runs contrary to the habits of university students, who may only experience recovery sleep if they sleep late on weekends. Pharmacy students at Duquesne University sit for frequent examinations, typically commencing at 7:30 AM, and they complain about fatigue. Here, we tested the central hypothesis that longer sleep durations on weekdays and weekends are linked to stronger academic performance in Pharmacy students.MethodsStudents in their first professional year were administered three surveys to collect data on sleep habits and factors that might influence sleep, such as roommates, long commute times, and sleep interruptions. GPAs were collected from the Dean’s office, with permission from the students.ResultsLonger weekend—but not weekday—sleep durations were significantly correlated with higher cumulative GPAs in men and not in women. Women achieved slightly higher cumulative GPAs than men. Students who fell asleep within 15 minutes of going to bed had higher professional-phase GPAs than those who fell asleep after an hour or more.ConclusionOur observations cannot establish causal links, but, given the body of prior evidence on the salutary properties of sleep, men in this cohort may reap benefit from recovery sleep on weekends. Rather than recommending that students force themselves awake early on weekends in an attempt to maintain a consistent sleep routine, the real-life habits of students should be given consideration.
ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
Authors: McKenzie Patrick F. , Eaton Deren A. R. 
Published: January 2020

AbstractSummaryipcoalis a free and open source Python package for simulating and analyzing genealogies and sequences. It automates the task of describing complex demographic models (e.g., with divergence times, effective population sizes, migration events) to themsprimecoalescent simulator by parsing a user-supplied species tree or network. Genealogies, sequences, and metadata are returned in tabular format allowing for easy downstream analyses.ipcoalincludes phylogenetic inference tools to automate gene tree inference from simulated sequence data, and visualization tools for analyzing results and verifying model accuracy. Theipcoalpackage is a powerful tool for posterior predictive data analysis, for methods validation, and for teaching coalescent methods in an interactive and visual environment.Availability and implementationSource code is available from the GitHub repository (https://github.com/pmckenz1/ipcoal/) and is distributed for packaged installation with conda. Complete documentation and interactive notebooks prepared for teaching purposes are available athttps://ipcoal.readthedocs.io/.
New complexities of SOS-induced “untargeted” mutagenesis inEscherichia colias revealed by mutation accumulation and whole-genome sequencing
Authors: Niccum Brittany A. , Coplen Christopher P. , Lee Heewook , Ismail Wazim Mohammed , Tang Haixu , Foster Patricia L. 
Published: January 2020

AbstractWhen its DNA is damaged,Escherichia coliinduces the SOS response, which consists of about 40 genes that encode activities to repair or tolerate the damage. Certain alleles of the major SOS-control genes,recAandlexA, cause constitutive expression of the response, resulting in an increase in spontaneous mutations. These mutations, historically called “untargeted”, have been the subject of many previous studies. Here we re-examine SOS-induced mutagenesis using mutation accumulation followed by whole-genome sequencing (MA/WGS), which allows a detailed picture of the types of mutations induced as well as their sequence-specificity. Our results confirm previous findings that SOS expression specifically induces transversion base-pair substitutions, with rates averaging about 60-fold above wild-type levels. Surprisingly, the rates of G:C to C:G transversions, normally an extremely rare mutation, were induced an average of 160-fold above wild-type levels. The SOS-induced transversion showed strong sequence specificity, the most extreme of which was the G:C to C:G transversions, 60% of which occurred at the middle base of 5′GGC3′+5′GCC3′ sites although these sites represent only 8% of the G:C base pairs in the genome. SOS-induced transversions were also DNA strand biased, occurring, on average, 2- to 4- times more often when the purine was on the leading strand template and the pyrimidine on the lagging strand template than in the opposite orientation. However, the strand bias was also sequence specific, and even of reverse orientation at some sites. By eliminating constraints on the mutations that can be recovered, the MA/WGS protocol revealed new complexities to the nature of SOS “untargeted” mutations.HighlightsThe SOS response to DNA damage induces “untargeted” mutationsSOS-mutations are revealed by mutation accumulation and whole genome sequencingSOS-mutations are both sequence and DNA-strand biasedG:C to C:G transversions are particularly highly induced by SOSG:C to C:G transversions are extremely sequence and DNA-strand biased
One-stop Microfluidic Assembly of Human Brain Organoids to Model Prenatal Cannabis Exposure
Authors: Ao Zheng , Cai Hongwei , Havert Daniel J , Wu Zhuhao , Gong Zhiyi , Beggs John M. , Mackie Ken , Guo Feng 
Published: January 2020

AbstractPrenatal cannabis exposure (PCE) influences human brain development, but it is challenging to model PCE using animals and current cell culture techniques. Here, we developed a one-stop microfluidic platform to assemble and culture human cerebral organoids from human embryonic stem cells (hESC) to investigate the effect of PCE on early human brain development. By incorporating perfusable culture chambers, air-liquid interface, and one-stop protocol, this microfluidic platform can simplify the fabrication procedure, and produce a large number of organoids (169 organoids per 3.5 cm x 3.5 cm device area) without fusion, as compared with conventional fabrication methods. These one-stop microfluidic assembled cerebral organoids not only recapitulate early human brain structure, biology, and electrophysiology but also have minimal size variation and hypoxia. Under on-chip exposure to the psychoactive cannabinoid, delta-9-tetrahydrocannabinol (THC), cerebral organoids exhibited reduced neuronal maturation, downregulation of cannabinoid receptor type 1 (CB1) receptors, and impaired neurite outgrowth. Moreover, transient on-chip THC treatment also decreased spontaneous firing in microfluidic assembled brain organoids. This one-stop microfluidic technique enables a simple, scalable, and repeatable organoid culture method that can be used not only for human brain organoids, but also for many other human organoids including liver, kidney, retina, and tumor organoids. This technology could be widely used in modeling brain and other organ development, developmental disorders, developmental pharmacology and toxicology, and drug screening.
Invitro-Propagation of Threatened African Sandalwood (Osyris lanceolata Hochst. & Steud.) via Using IBA hormone
Authors: Admas Adugnaw , Melese Semegnwe , Genetu Amare , Kidane Berhane , Yilma Zewdu , Admasu Melaku , Misiga Tesaka 
Published: January 2020

AbstractThe African Sandalwood plant (Osyris lanceolata) is a threatened shrub or a small hemi-parasitic tree endemic to East Africa and South African regions, which is being severely affected by fungus, uproot-ing for oil extraction, poor natural regeneration, phenological structures (dioecious), medicinal values, lack of sexual recruitment, habitat loss, anthropogenic and climate factors and life span of its seed is short. It has been found a chllange through application of in situ conservation of natural trees like osyris lanceoleta since rapid human population growth and dramatically change the demands of fuel wood and agriculture investement, the available natural strands of valuable plants of African sandalwood have not been able to meet the demands of the people in world specifically developing countries. How ever, this study via using the advances of plant propagation method it provide new options for conserving and multiplication of Osyris lanceolata species using in vitro culture techniques of using IBA hormone by taking plant material of the targated plant.Propagation of African sandalwood (Osyris lanceolata) by rooting hormone of IBA in non-mist poly-propagator was investigated by taking young stem of osyris lanceoleta from Bazawit Hill and we provide an alternative propagation technique to the use of seeds. This Hill is near to Bahrdar town, Ethiopia.New leaf were initiated on the young stems of the osyris after six weeks of the experment.The influence of IBA as rooting promoter at three concentrations (50, 100 and 150 ppm) were recorded.Un expectedly, from the data collected it was observed that the success 83.3% can be achieved from young stem of un treatead cuting gave a new leaf and 50% were achived in the treatead plant, this propagation technique is a viable alternative to seed. The success may influenced by application orgin of a stem cutting with a type of soil.
Experimental Evolutionin vivoto Identify Selective Pressures During Pneumococcal Colonization
Authors: Cooper Vaughn S. , Honsa Erin , Rowe Hannah , Deitrick Christopher , Iverson Amy R. , Whittall Jonathan J. , Neville Stephanie L. , McDevitt Christopher A. , Kietzman Colin , Rosch Jason W. 
Published: January 2020

AbstractExperimental evolution is a powerful technique to understand how populations evolve from selective pressures imparted by the surrounding environment. With the advancement of whole-population genomic sequencing it is possible to identify and track multiple contending genotypes associated with adaptations to specific selective pressures. This approach has been used repeatedly with model speciesin vitro, but only rarelyin vivo. Herein we report results of replicate experimentally evolved populations ofStreptococcus pneumoniaepropagated by repeated murine nasal colonization with the aim of identifying gene products under strong selection as well as the population-genetic dynamics of infection cycles. Frameshift mutations in one gene,dltB, responsible for incorporation of D-alanine into teichoic acids on the bacterial surface, evolved repeatedly and swept to high frequency. Targeted deletions ofdltBproduced a fitness advantage during initial nasal colonization coupled with a corresponding fitness disadvantage in the lungs during pulmonary infection. The underlying mechanism behind the fitness tradeoff between these two niches was found to be enhanced adherence to respiratory cells balanced by increased sensitivity to host-derived antimicrobial peptides, a finding recapitulated in the murine model. Additional mutations were also selected that are predicted to affect trace metal transport, central metabolism and regulation of biofilm production and competence. These data indicate that experimental evolution can be applied to murine models of pathogenesis to gain insight into organism-specific tissue tropisms.ImportanceEvolution is a powerful force that can be experimentally harnessed to gain insight into how populations evolve in response to selective pressures. Herein we tested the applicability of experimental evolutionary approaches to gain insight into how the major human pathogenStreptococcus pneumoniaeresponds to repeated colonization events using a murine model. These studies revealed the population dynamics of repeated colonization events and demonstrated thatin vivoexperimental evolution resulted in highly reproducible trajectories that reflect the environmental niche encountered during nasal colonization. Mutations impacting the surface charge of the bacteria were repeatedly selected during colonization and provided a fitness benefit in this niche that was counterbalanced by a corresponding fitness defect during lung infection. These data indicate that experimental evolution can be applied to models of pathogenesis to gain insight into organism-specific tissue tropisms.
Gatekeeper helix activates Golgi SM protein Sly1 and directly mediates close-range vesicle tethering
Authors: Duan M. , Plemel R.L. , Takenaka T. , Lin A. , Delgado B.M. , Nattermann U. , Nickerson D.P. , Mima J. , Miller E.A. , Merz A.J. 
Published: January 2020

ABSTRACTThe essential Golgi protein Sly1 is a member of the SM (Sec1/mammalian Unc-18) family of SNARE chaperones. Sly1 was originally identified through gain-of-function alleles that bypass requirements for diverse vesicle tethering factors. Employing genetic analyses and chemically defined reconstitutions of ER-Golgi fusion, we discovered that a loop conserved among Sly1 family members is not only autoinhibitory, but also acts as a positive effector. An amphipathic helix within the loop directly binds high-curvature membranes; membrane binding is required for relief of Sly1 autoinhibition and allows Sly1 to directly tether incoming vesicles to the Qa-SNARE on the target organelle. TheSLY1-20allele bypasses requirements for diverse tethering factors but loses this functionality if Sly1 membrane binding is impaired. We propose that long-range tethers, including Golgins and multisubunit tethering complexes, hand off vesicles to Sly1, which then tethers at close range to activate SNARE assembly and fusion in the early secretory pathway.
Modular lipid nanoparticle platform technology for siRNA and lipophilic prodrug delivery
Authors: van der Meel Roy , Chen Sam , Zaifman Josh , Kulkarni Jayesh A. , Zhang Xu Ran S. , Tam Ying K. , Bally Marcel B. , Schiffelers Raymond M. , Ciufolini Marco A. , Cullis Pieter R. , Tam Yuen Yi C. 
Published: January 2020

ABSTRACTSuccessfully employing therapeutic nucleic acids, such as small interfering RNA (siRNA), requires chemical modifications or the use of nanocarrier technology to prevent their degradation in the circulation and to facilitate intracellular delivery. Lipid nanoparticles (LNP) are among the most advanced nanocarriers culminating in the first siRNA therapeutic’s clinical translation and approval. At the same time, their applicability as modular platform technology due to the interchangeable building blocks and siRNA payload hallmarks one of LNPs’ major advantages. In addition, drug derivatization approaches to synthesize lipophilic small molecule prodrugs enable stable incorporation in LNPs. This provides ample opportunities to develop combination therapies by co-encapsulating multiple therapeutic agents in a single formulation. Here, we describe how the modular LNP platform can be applied for combined gene silencing and chemotherapy to induce additive anti-cancer effects. We show that various lipophilic taxane prodrug derivatives and siRNA against the androgen receptor, a prostate cancer driver, can be efficiently and stably co-encapsulated in LNPs. In addition, we demonstrate that prodrug incorporation does not affect LNPs’ gene silencing ability and that the combination therapy induces additive therapeutic effectsin vitro. Using a double-radiolabeling approach, we quantitively determined the LNPs’ and prodrugs’ pharmacokinetic properties and biodistribution following systemic administration in tumor-bearing mice. Our results indicate that co-encapsulation of siRNA and lipophilic prodrugs into LNPs is an attractive and straightforward approach for combination therapy development.GRAPHICAL ABSTRACT
The regulation of mammalian maternal-to-embryonic transition by Eukaryotic translation initiation factor 4E
Authors: Li Yan , Huang Xuefeng , Tang Jianan , Ji Xu , Liu Miao , Chang Lu , Liu Jing , Gu Yihua , Shi Changgen , Ni Wuhua , Shi Hui-juan , O’Neill Chris , Jin Xingliang 
Published: January 2020

AbstractGenetic and inhibitor studies show expression of eukaryotic translation initiation factor 4E (eIF4E) was required for the successful maternal-to-embryonic transition of mouse embryos. eIF4E was in both gametes and in the cytoplasm and pro-nuclei soon after fertilization, and at each stage of early development. Knockout (Eif4e−/−) byPiggyBac (PB) [Act-RFP]transposition caused peri-implantation embryonic lethality due to the failure of embryos to form a pluripotent epiblast. Maternal stores of eIF4E supported development up to the 2-4-cell stage after which new expression occurred from both alleles. Inhibition of the maternally acquired stores of eIF4E (4EGI-1 inhibitor) resulted in a developmental block at the 2-4-cell stage. 4E-BP1 is a hypophosphorylation-dependent negative regulator of eIF4E. mTOR activity was required for 4E-BP1 phosphorylation and inhibiting 4EGI-1 retarded embryo development. eIF4E expression and activity is regulated at key embryonic transitions in the mammalian embryo and is essential for successful transition to embryonic control of development.Significance StatementeIF4E is recognized as the rate-limiting factor for CAP-dependent translation. This work used a combination of a gene knockout model, selective pharmacological inhibition and expression analyses to investigate the expression and function of Eif4e in the early mouse embryo. It provides compelling evidence for the essential role of Eif4E in the normal processes of early mammalian embryo development, including the formation of the pluripotent epiblast and the maternal-embryonic transition. The unexpected evidence for a growth deficit in mice hypomorphic for Eif4e will be a key area of future investigation. It also provides for the first time a powerful demonstration of the utility of thePB [Act-RFP]transposon mouse model for analyzing the molecular regulation of early mammalian embryo development.
Regeneration in the adultDrosophilabrain
Authors: Crocker Kassi L. , Marischuk Khailee , Rimkus Stacey A. , Zhou Hong , Yin Jerry C.P. , Boekhoff-Falk Grace 
Published: January 2020

AbstractNeurodegenerative diseases such as Alzheimer’s and Parkinson’s currently affect ∼25 million people worldwide (Erkkinenet al. 2018). The global incidence of traumatic brain injury (TBI) is estimated at ∼70 million/year (Dewanet al. 2018). Both neurodegenerative diseases and TBI remain without effective treatments. We are utilizing adultDrosophila melanogasterto investigate the mechanisms of brain regeneration with the long term goal of identifying targets for neural regenerative therapies. Like mammals, Drosophila have few proliferating cells in the adult brain. Nonetheless, within 24 hours of a Penetrating Traumatic Brain Injury (PTBI) to the central brain, there is a significant increase in the number of proliferating cells. We subsequently detect both new glia and new neurons and the formation of new axon tracts that target appropriate brain regions. Glial cells divide rapidly upon injury to give rise to new glial cells. Other cells near the injury site upregulate neural progenitor genes includingasenseanddeadpanand later give rise to the new neurons. Locomotor abnormalities observed after PTBI are reversed within two weeks of injury, supporting the idea that there is functional recovery. Together, these data indicate that adultDrosophilabrains are capable of neuronal repair. We anticipate that this paradigm will facilitate the dissection of the mechanisms of neural regeneration and that these processes will be relevant to human brain repair.
Core Role of TRPC6 Channels in Regulating Airway Re-modelling in Chronic Obstructive Pulmonary Disease
Authors: Zhao Kun , Xie Raoying , Wei Jie , Gu Wenyue , Fei Zhenghua 
Published: January 2020

Withdrawal StatementThis manuscript has been withdrawn by the authors as they did not obtain patient consent for the tissue samples use in this study and were, therefore, not able to be approved by the Institute’s Ethics Committee of Wenzhou Medical University. The authors also declare that there are interest conflict about authorship. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.