bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Extreme Precipitation and Landslides Over High Mountain Asia
Authors: Kirschbaum D. , Kapnick S. B. , Stanley T. , Pascale S. 
Published: February 2020

AbstractHigh Mountain Asia is impacted by extreme monsoonal rainfall that triggers landslides in large proportions relative to global distributions, resulting in substantial human impacts and damage to infrastructure each year. Previous landslide research has qualitatively estimated how patterns in landslide activity may change based on climate change scenarios. We present the first quantitative view of potential modulation in future landslide activity over the High Mountain Asia region leveraging a new landslide hazard model and precipitation data from satellite and Global Climate Model sources. In doing so, we find that the rate of increase in landslide activity at the end of the century is expected to be greatest over areas covered by current glaciers and glacial lakes, potentially exacerbating the impacts of cascading hazards on populations downstream. This work demonstrates the potential of Global Climate Models and satellite‐based precipitation estimates to characterize landslide hazards at time scales affected by climate change.
Evaporative Resistance is of Equal Importance as Surface Albedo in High‐Latitude Surface Temperatures Due to Cloud Feedbacks
Authors: Kim Jinhyuk E. , Laguë Marysa M. , Pennypacker Sam , Dawson Eliza , Swann Abigail L. S. 
Published: February 2020

AbstractArctic vegetation is known to influence Arctic surface temperatures through albedo. However, it is less clear how plant evaporative resistance and albedo independently influence surface climate at high latitudes. We use surface properties derived from two common Arctic tree types to simulate the climate response to a change in land surface albedo and evaporative resistance in factorial combinations. We find that lower evaporative resistances lead to an increase of low clouds. The reflection of light due to the difference in albedos between vegetation types is similar to the loss of incident sunlight due to increased cloud cover resulting from lower evaporative resistance from vegetation change. Our results demonstrate that realistic changes in evaporative resistance can have an equal impact on surface temperature to changes in albedo and that cloud feedbacks play a first‐order role in determining the surface climate response to changes in Arctic land cover.
Simulation of Plasmaspheric Plume Impact on Dayside Magnetic Reconnection
Authors: Dargent J. , Aunai N. , Lavraud B. , Toledo‐Redondo S. , Califano F. 
Published: February 2020

AbstractDuring periods of strong magnetic activity, cold dense plasma from the plasmasphere typically forms a plume extending toward the dayside magnetopause, eventually reaching it. In this work, we present a large‐scale two‐dimensional fully kinetic particle‐in‐cell simulation of a reconnecting magnetopause hit by a propagating plasmaspheric plume. The simulation is designed so that it undergoes four distinct phases: initial unsteady state, steady state prior to plume arrival at the magnetospause, plume interaction, and steady state once the plume is well engulfed in the reconnection site. We show the evolution of the magnetopause's dynamics subjected to the modification of the inflowing plasma. Our main result is that the change in the plasma temperature (cold protons in the plume) has no effects on the magnetic reconnection rate, which on average depends only on the inflowing magnetic field and total ion density, before, during, and after the impact.
RASSF10 is frequently epigenetically inactivated in kidney cancer and its knockout promotes neoplasia in cancer prone mice
Authors: Richter Antje M. , Woods Michelle L. , Küster Miriam M. , Walesch Sara K. , Braun Thomas , Boettger Thomas , Dammann Reinhard H. 
Published: February 2020

AbstractKidney cancer incidences are rising globally, thereby fueling the demand for targeted therapies and precision medicine. In our previous work, we have identified and characterized the Ras-Association Domain Family encoding ten members that are often aberrantly expressed in human cancers. In this study, we created and analyzed theRassf10knockout mice. Here we show thatRassf10haploinsufficiency promotes neoplasia formation in two established mouse cancer models (Rassf1A−/−and p53−/−). HaploinsufficientRassf10knockout mice were significantly prone to various diseases including lymphoma (Rassf1A−/−background) and thymoma (p53−/−background). Especially Rassf10−/−and p53-deficient mice exhibited threefold increased rates of kidney cysts compared with p53−/−controls. Moreover, we observed that in human kidney cancer,RASSF10is frequently epigenetically inactivated by its CpG island promoter hypermethylation. Primary tumors of renal clear cell and papillary cell carcinoma confirmed thatRASSF10methylation is associated with decreased expression in comparison to normal kidney tissue. In independent data sets, we could validate thatRASSF10inactivation clinically correlated with decreased survival and with progressed disease state of kidney cancer patients and polycystic kidney size. Functionally, we revealed that the loss ofRassf10was significantly associated with upregulation of KRAS signaling andMYCexpression. In summary, we could show thatRassf10functions as a haploinsufficient tumor suppressor. In combination with other markers,RASSF10silencing can serve as diagnostic and prognostic cancer biomarker in kidney diseases.
Lysosome biology in autophagy
Authors: Yim Willa Wen-You , Mizushima Noboru 
Published: February 2020

AbstractAutophagy is a major intracellular degradation system that derives its degradative abilities from the lysosome. The most well-studied form of autophagy is macroautophagy, which delivers cytoplasmic material to lysosomes via the double-membraned autophagosome. Other forms of autophagy, namely chaperone-mediated autophagy and microautophagy, occur directly on the lysosome. Besides providing the means for degradation, lysosomes are also involved in autophagy regulation and can become substrates of autophagy when damaged. During autophagy, they exhibit notable changes, including increased acidification, enhanced enzymatic activity, and perinuclear localization. Despite their importance to autophagy, details on autophagy-specific regulation of lysosomes remain relatively scarce. This review aims to provide a summary of current understanding on the behaviour of lysosomes during autophagy and outline unexplored areas of autophagy-specific lysosome research.
Cryo-EM structures of PAC1 receptor reveal ligand binding mechanism
Authors: Wang Jia , Song Xianqiang , Zhang Dandan , Chen Xiaoqing , Li Xun , Sun Yaping , Li Cui , Song Yunpeng , Ding Yao , Ren Ruobing , Harrington Essa Hu , Hu Liaoyuan A. , Zhong Wenge , Xu Cen , Huang Xin , Wang Hong-Wei , Ma Yingli 
Published: February 2020

AbstractThe pituitary adenylate cyclase-activating polypeptide type I receptor (PAC1R) belongs to the secretin receptor family and is widely distributed in the central neural system and peripheral organs. Abnormal activation of the receptor mediates trigeminovascular activation and sensitization, which is highly related to migraine, making PAC1R a potential therapeutic target. Elucidation of PAC1R activation mechanism would benefit discovery of therapeutic drugs for neuronal disorders. PAC1R activity is governed by pituitary adenylate cyclase-activating polypeptide (PACAP), known as a major vasodilator neuropeptide, and maxadilan, a native peptide from the sand fly, which is also capable of activating the receptor with similar potency. These peptide ligands have divergent sequences yet initiate convergent PAC1R activity. It is of interest to understand the mechanism of PAC1R ligand recognition and receptor activity regulation through structural biology. Here we report two near-atomic resolution cryo-EM structures of PAC1R activated by PACAP38 or maxadilan, providing structural insights into two distinct ligand binding modes. The structures illustrate flexibility of the extracellular domain (ECD) for ligands with distinct conformations, where ECD accommodates ligands in different orientations while extracellular loop 1 (ECL1) protrudes to further anchor the ligand bound in the orthosteric site. By structure-guided molecular modeling and mutagenesis, we tested residues in the ligand-binding pockets and identified clusters of residues that are critical for receptor activity. The structures reported here for the first time elucidate the mechanism of specificity and flexibility of ligand recognition and binding for PAC1R, and provide insights toward the design of therapeutic molecules targeting PAC1R.
Designing minimal genomes using whole-cell models
Authors: Rees-Garbutt Joshua , Chalkley Oliver , Landon Sophie , Purcell Oliver , Marucci Lucia , Grierson Claire 
Published: February 2020

AbstractIn the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay whether the cell replicates or not. We used the first (and currently only published) whole-cell model for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in silico minimal genomes which, if biologically correct, predict in vivo genomes smaller than JCVI-Syn3.0; a bacterium with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essential genes and produced evidence for at least two Mycoplasma genitalium in silico minimal genomes. This work brings combined computational and laboratory genome engineering a step closer.
Genome-wide gene expression profiling of the melon fly, Zeugodacus cucurbitae, during thirteen life stages
Authors: Wei Dong , Xu Hui-Qian , Chen Dong , Zhang Su-Yun , Li Wei-Jun , Smagghe Guy , Wang Jin-Jun 
Published: February 2020

AbstractThe melon fly,Zeugodacus cucurbitae(Coquillett), is an important destructive pest worldwide. Functional studies of the genes associated with development and reproduction during different life stages are limited inZ. cucurbitae. There have yet to be comprehensive transcriptomic resources for genetic and functional genomic studies to identify the molecular mechanisms related to its development and reproduction. In this study, we comprehensively sequenced the transcriptomes of four different developmental stages: egg, larva, pupa, and adults. Using the Illumina RNA-Seq technology, we constructed 52 libraries from 13 stages with four biological replicates in each and generated 435.61 Gb clean reads. We comprehensively characterized the transcriptomes with high-coverage mapping to the reference genome. A total of 13,760 genes were mapped to the reference genome, and another 4481 genes were characterized as new genes. Finally, 14,931 genes (81.85%) were functionally annotated against six annotation databases. This study provides the first comprehensive transcriptome data of all developmental stages ofZ. cucurbitae, and will serve as a valuable resource for future genetic and functional studies.
Interactions between worker ants may influence the growth of ant cemeteries
Authors: Sakiyama Tomoko 
Published: February 2020

AbstractWhen an ant dies within a nest, a worker ant carries its corpse away from the nest and drops it onto a pile known as an ant cemetery. These ant cemeteries form cluster patterns, and the dynamics of the corpse piles have been studied experimentally. The aim of the present study was to investigate how sensitivity to the presence of nest-mates would influence the corpse-carrying behaviour of ants, and how this would impact the dynamics of corpse pile clustering. This was achieved by developing an agent-based computational model in which simulated ‘ants’ (the agents) carry and drop ‘corpses’, resulting in the growth of the corpse pile. In the model, the probability of an ant dropping a corpse was tuned according to the presence or absence of nest-mates. The pile dynamics of the resulting model showed a partial match with the time series evolution of corpse piles observed with real ants in previous experimental studies. Although the switch of probabilities is a thought experiment, our results suggest that the corpse-carrying behaviour of worker ants might be influenced by interactions with their nest-mates because there is evidence that ant behaviour can be influenced by encounter rates.
Nucleosome destabilization by nuclear non-coding RNAs
Authors: Fujita Risa , Yamamoto Tatsuro , Arimura Yasuhiro , Fujiwara Saori , Tachiwana Hiroaki , Ichikawa Yuichi , Sakata Yuka , Yang Liying , Maruyama Reo , Hamada Michiaki , Nakao Mitsuyoshi , Saitoh Noriko , Kurumizaka Hitoshi 
Published: February 2020

AbstractIn the nucleus, genomic DNA is wrapped around histone octamers to form nucleosomes. In principle, nucleosomes are substantial barriers to transcriptional activities. Nuclear non-coding RNAs (ncRNAs) are proposed to function in chromatin conformation modulation and transcriptional regulation. However, it remains unclear how ncRNAs affect the nucleosome structure. Eleanors are clusters of ncRNAs that accumulate around the estrogen receptor-α (ESR1) gene locus in long-term estrogen deprivation (LTED) breast cancer cells, and markedly enhance the transcription of the ESR1 gene. Here we detected nucleosome depletion around the transcription site of Eleanor2, the most highly expressed Eleanor in the LTED cells. We found that the purified Eleanor2 RNA fragment drastically destabilized the nucleosome in vitro. This activity was also exerted by other ncRNAs, but not by poly(U) RNA or DNA. The RNA-mediated nucleosome destabilization may be a common feature among natural nuclear RNAs, and may function in transcription regulation in chromatin.
Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning
Authors: Mahmoud Amr H. , Masters Matthew R. , Yang Ying , Lill Markus A. 
Published: February 2020

AbstractAccurate and efficient prediction of protein-ligand interactions has been a long-lasting dream of practitioners in drug discovery. The insufficient treatment of hydration is widely recognized to be a major limitation for accurate protein-ligand scoring. Using an integration of molecular dynamics simulations on thousands of protein structures with novel big-data analytics based on convolutional neural networks and deep Taylor decomposition, we consistently identify here three different patterns of hydration to be essential for protein-ligand interactions. In addition to desolvation and water-mediated interactions, the formation of enthalpically favorable networks of first-shell water molecules around solvent-exposed ligand moieties is identified to be essential for protein-ligand binding. Despite being currently neglected in drug discovery, this hydration phenomenon could lead to new avenues in optimizing the free energy of ligand binding. Application of deep neural networks incorporating hydration to docking provides 89% accuracy in binding pose ranking, an essential step for rational structure-based drug design.
The Relationship Between the Onset of Canonical Syllables and Speech Perception Skills in Children With Cochlear Implants
Authors: Jung Jongmin , Houston Derek 
Published: February 2020

PurposeThe study sought to determine whether the onset of canonical vocalizations in children with cochlear implants (CIs) is related to speech perception skills and spoken vocabulary size at 24 months postactivation.MethodThe vocal development in 13 young CI recipients (implanted by their third birthdays; mean age at activation = 20.62 months,SD= 8.92 months) was examined at every 3-month interval during the first 2 years of CI use. All children were enrolled in auditory–oral intervention programs. Families of these children used spoken English only. To determine the onset of canonical syllables, the first 50 utterances from 20-min adult–child interactions were analyzed during each session. The onset timing was determined when at least 20% of utterances included canonical syllables. As children's outcomes, we examined their Lexical Neighborhood Test scores and vocabulary size at 24 months postactivation.ResultsPearson correlation analysis showed that the onset timing of canonical syllables is significantly correlated with phonemic recognition skills and spoken vocabulary size at 24 months postactivation. Regression analyses also indicated that the onset timing of canonical syllables predicted phonemic recognition skills and spoken vocabulary size at 24 months postactivation.ConclusionMonitoring vocal advancement during the earliest periods following cochlear implantation could be valuable as an early indicator of auditory-driven language development in young children with CIs. It remains to be studied which factors improve vocal development for young CI recipients.
Cross-species utility of microsatellite loci for the genetic characterisation ofAnisakis berlandi(Nematoda: Anisakidae)
Authors: Bello Eleonora , Paoletti Michela , Webb Stephen C. , Nascetti Giuseppe , Mattiucci Simonetta 
Published: February 2020

Eight microsatellite loci, recently developed in the speciesAnisakis pegreffii,were successfully amplified inAnisakis berlandi, sibling species of theA. simplex(s. l.) complex. They were validated on adult specimens (n = 46) of the parasite species, collected from two individuals of the definitive host, the long-finned pilot whaleGlobicephala melasfrom New Zealand waters. Among the eight loci scored, one,Anisl 07132,had null alleles inA. berlandiand was thus excluded from the subsequent genetic analysis. Two loci,Anisl 00314andAnisl 10535,were monomorphic. In addition, as also previously detected in the other species of theA. simplex(s. l.) complex, theAnisl 7locus was seen to be sex-linked, showing hemizygosity in male specimens. Differential allele frequency distributions ofA. berlandi,with respect to those previously observed inA. pegreffiiandA. simplex(s. s.), were found at some microsatellite loci. TheAnisl 7locus provided 100% diagnosis betweenA. berlandiandA. pegreffii,while others resulted in 99% diagnosis betweenA. berlandiand the other two species. Simple sequence repeat (SSR) loci also allowed us to estimate the genetic differentiation ofA. berlandifromA. pegreffii(Fst ≈ 0.45, Dc = 0.82) andA. simplex(s. s.) (Fst ≈ 0.57, Dc = 0.73). The results suggest that SSRs provide a set of candidate markers for population genetics analysis ofA. berlandi, as well as for the investigation, through a multi-locus genotyping approach, of possible patterns of hybridisation/introgression events betweenA. berlandiand the other twoAnisakisspecies in sympatric conditions.
Diagnostic Accuracy of Doppler Ultrasound in Predicting Perinatal Outcome in Appropriate for Gestational Age Fetuses: A Prospective Study
Authors: Buca Danilo , Rizzo Giuseppe , Gustapane Sarah , Mappa Ilenia , Leombroni Martina , Bascietto Francesca , Flacco Maria Elena , Acuti Martellucci Cecilia , Manzoli Lamberto , Nappi Luigi , Familiari Alessandra , Scambia Giovanni , Liberati Marco , D'Antonio Francesco 
Published: February 2020

Abstract
Objective To elucidate the role of Doppler ultrasound in predicting perinatal outcome in appropriate for gestational age (AGA) fetuses at term.
Material and Methods Prospective study carried out in a dedicated research ultrasound clinic. The inclusion criterion was AGA fetuses, defined as those with an estimated fetal weight between the 10th and 90th percentile, at 36 + 0–37 + 6 weeks of gestation. The primary outcome was a composite score of adverse perinatal outcome including either adverse intrapartum events or abnormal acid-base status at birth. Secondary outcomes were the individual components of the primary outcome. The Doppler parameters explored were umbilical artery (UA) PI, middle cerebral artery (MCA) PI, uterine arteries (UtA) PI and cerebroplacental ratio (CPR). Attending clinicians were blinded to Doppler findings. Logistic regression and ROC curve analyses were used to analyze the data.
Results 553 AGA fetuses were included. There was no difference in mean UA PI (p = 0.486), MCA PI (p = 0.621), CPR (p = 0.832) and UtA PI (p = 0.611) between pregnancies complicated by composite perinatal morbidity compared to those not complicated by composite perinatal morbidity. In pregnancies complicated by adverse intrapartum outcome, the mean MCA PI (1.47 ± 0.4 vs 1.61 ± 0.4, p = 0.0039) was lower compared to the control group, while there was no difference in UA PI (p = 0.758), CPR (p = 0.108), and UtA PI (p = 0.177). Finally, there was no difference in any of the Doppler parameters explored between AGA fetuses with abnormal acid-base status at birth compared to those without abnormal acid-base status at birth. In the logistic regression analysis, UA PI, MCA PI, CPR, UtA PI, EFW and AC percentiles were not independently associated with composite adverse outcome, adverse intrapartum outcome or abnormal acid-base status at birth in non-SGA fetuses. The diagnostic performance of all of these Doppler parameters for predicting composite adverse outcome, adverse intrapartum outcome and abnormal acid-base status was poor.
Conclusion Cerebroplacental and maternal Doppler is not associated with or predictive of adverse pregnancy outcome in AGA fetuses close to term.
Relationship between Trunk Muscularity and Club Head Speed in Male
Golfers
Authors: Izumoto Yoka , Kurihara Toshiyuki , Maeo Sumiaki , Sugiyama Takashi , Kanehisa Hiroaki , Isaka Tadao 
Published: February 2020

AbstractThis study examined how the volume of trunk muscles and its bilateral asymmetry
are related to club head speed in golfers. Fourteen right-handed male golfers
performed five driver shots, and the club head speed for each trial was
calculated from a three-dimensional reflective marker position of the club head
immediately before impact. The volume of each side of the rectus abdominis,
erector spinae, psoas major, quadratus lumborum, lateral abdominal wall muscle,
and multifidus was determined using magnetic resonance imaging. For each muscle,
the ratio of the larger to smaller side in muscle volume was calculated to
assess bilateral asymmetry. The club head speed correlated positively with the
volume of each side of the rectus abdominis and erector spinae, left quadratus
lumborum, and the asymmetric ratio of the psoas major
(r=0.595–0.747), but negatively with the asymmetric ratio of the
quadratus lumborum (r=−0.641). Multiple regression analysis
revealed that the right erector spinae volume and the asymmetric ratio of the
psoas major were significant contributors for the club head speed
(R2=0.797). These results indicate that the variation in the
club head speed can be strongly explained by the absolute volume and bilateral
asymmetry of specific trunk muscles.