bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population
Authors: Ravelombola Waltram , Shi Ainong , Huynh Bao-Lam 
Published: February 2021

AbstractCowpea is a nutrient-dense legume that significantly contributes to the population’s diet in sub-Saharan Africa and other regions of the world. Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance. The use of a multi-parent advanced generation intercross (MAGIC) population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits. In addition, drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions. Therefore, the objectives of this study were to evaluate the drought tolerance index for plant growth habit, plant maturity, flowering time, 100-seed weight, and grain yield in a MAGIC cowpea population, to conduct genome-wide association study (GWAS) and identify single nucleotide polymorphism (SNP) markers associated with the drought tolerance indices, to investigate the potential relationship existing between the significant loci associated with the drought tolerance indices, and to conduct genomic selection (GS). These analyses were performed using the existing phenotypic and genotypic data published for the MAGIC population which consisted of 305 F8 recombinant inbred lines (RILs) developed at University of California, Riverside. The results indicated that: (1) large variation in drought tolerance indices existed among the cowpea genotypes, (2) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, and drought tolerance indices for maturity, flowering time, 100-seed weight, and grain yield, respectively, (3) the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and (4) the GS accuracy varied from low to moderate. These results could be applied to improve drought tolerance in cowpea through marker-assisted selection (MAS) and genomic selection (GS). To the best of our knowledge, this is the first report on marker loci associated with drought tolerance indices in cowpea.
Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
Authors: Garrido-Martín Diego , Borsari Beatrice , Calvo Miquel , Reverter Ferran , Guigó Roderic 
Published: February 2021

AbstractAlternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it to analyze the GTEx dataset, generating a comprehensive catalog of sQTLs in the human genome. Downstream analysis of this catalog provides insight into the mechanisms underlying splicing regulation. We report that a core set of sQTLs is shared across multiple tissues. sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many also affect the expression of the same or other genes, uncovering regulatory loci that act through different mechanisms. sQTLs tend to be located in post-transcriptionally spliced introns, which would function as hotspots for splicing regulation. While many variants affect splicing patterns by altering the sequence of splice sites, many more modify the binding sites of RNA-binding proteins. Genetic variants affecting splicing can have a stronger phenotypic impact than those affecting gene expression.
Pretreatment neutrophil-to-lymphocyte ratio and mutational burden as biomarkers of tumor response to immune checkpoint inhibitors
Authors: Valero Cristina , Lee Mark , Hoen Douglas , Weiss Kate , Kelly Daniel W. , Adusumilli Prasad S. , Paik Paul K. , Plitas George , Ladanyi Marc , Postow Michael A. , Ariyan Charlotte E. , Shoushtari Alexander N. , Balachandran Vinod P. , Hakimi A. Ari , Crago Aimee M. , Long Roche Kara C. , Smith J. Joshua , Ganly Ian , Wong Richard J. , Patel Snehal G. , Shah Jatin P. , Lee Nancy Y. , Riaz Nadeem , Wang Jingming , Zehir Ahmet , Berger Michael F. , Chan Timothy A. , Seshan Venkatraman E. , Morris Luc G. T. 
Published: February 2021

AbstractTreatment with immune checkpoint inhibitors (ICI) has demonstrated clinical benefit for a wide range of cancer types. Because only a subset of patients experience clinical benefit, there is a strong need for biomarkers that are easily accessible across diverse practice settings. Here, in a retrospective cohort study of 1714 patients with 16 different cancer types treated with ICI, we show that higher neutrophil-to-lymphocyte ratio (NLR) is significantly associated with poorer overall and progression-free survival, and lower rates of response and clinical benefit, after ICI therapy across multiple cancer types. Combining NLR with tumor mutational burden (TMB), the probability of benefit from ICI is significantly higher (OR = 3.22; 95% CI, 2.26-4.58; P < 0.001) in the NLR low/TMB high group compared to the NLR high/TMB low group. NLR is a suitable candidate for a cost-effective and widely accessible biomarker, and can be combined with TMB for additional predictive capacity.
Mesenchymal stem cell-derived interleukin-28 drives the selection of apoptosis resistant bone metastatic prostate cancer
Authors: McGuire Jeremy J. , Frieling Jeremy S. , Lo Chen Hao , Li Tao , Muhammad Ayaz , Lawrence Harshani R. , Lawrence Nicholas J. , Cook Leah M. , Lynch Conor C. 
Published: February 2021

AbstractBone metastatic prostate cancer (PCa) promotes mesenchymal stem cell (MSC) recruitment and their differentiation into osteoblasts. However, the effects of bone-marrow derived MSCs on PCa cells are less explored. Here, we report MSC-derived interleukin-28 (IL-28) triggers prostate cancer cell apoptosis via IL-28 receptor alpha (IL-28Rα)-STAT1 signaling. However, chronic exposure to MSCs drives the selection of prostate cancer cells that are resistant to IL-28-induced apoptosis and therapeutics such as docetaxel. Further, MSC-selected/IL-28-resistant prostate cancer cells grow at accelerated rates in bone. Acquired resistance to apoptosis is PCa cell intrinsic, and is associated with a shift in IL-28Rα signaling via STAT1 to STAT3. Notably, STAT3 ablation or inhibition impairs MSC-selected prostate cancer cell growth and survival. Thus, bone marrow MSCs drive the emergence of therapy-resistant bone metastatic prostate cancer yet this can be disabled by targeting STAT3.
Calcium channel ITPR2 and mitochondria–ER contacts promote cellular senescence and aging
Authors: Ziegler Dorian V. , Vindrieux David , Goehrig Delphine , Jaber Sara , Collin Guillaume , Griveau Audrey , Wiel Clotilde , Bendridi Nadia , Djebali Sophia , Farfariello Valerio , Prevarskaya Natacha , Payen Léa , Marvel Jacqueline , Aubert Sébastien , Flaman Jean-Michel , Rieusset Jennifer , Martin Nadine , Bernard David 
Published: February 2021

AbstractCellular senescence is induced by stresses and results in a stable proliferation arrest accompanied by a pro-inflammatory secretome. Senescent cells accumulate during aging, promoting various age-related pathologies and limiting lifespan. The endoplasmic reticulum (ER) inositol 1,4,5-trisphosphate receptor, type 2 (ITPR2) calcium-release channel and calcium fluxes from the ER to the mitochondria are drivers of senescence in human cells. Here we show that Itpr2 knockout (KO) mice display improved aging such as increased lifespan, a better response to metabolic stress, less immunosenescence, as well as less liver steatosis and fibrosis. Cellular senescence, which is known to promote these alterations, is decreased in Itpr2 KO mice and Itpr2 KO embryo-derived cells. Interestingly, ablation of ITPR2 in vivo and in vitro decreases the number of contacts between the mitochondria and the ER and their forced contacts induce premature senescence. These findings shed light on the role of contacts and facilitated exchanges between the ER and the mitochondria through ITPR2 in regulating senescence and aging.
Asymmetric thinning of the cerebral cortex across the adult lifespan is accelerated in Alzheimer’s disease
Authors: Roe James M. , Vidal-Piñeiro Didac , Sørensen Øystein , Brandmaier Andreas M. , Düzel Sandra , Gonzalez Hector A. , Kievit Rogier A. , Knights Ethan , Kühn Simone , Lindenberger Ulman , Mowinckel Athanasia M. , Nyberg Lars , Park Denise C. , Pudas Sara , Rundle Melissa M. , Walhovd Kristine B. , Fjell Anders M. , Westerhausen René ,   The Australian Imaging Biomarkers and Lifestyle Flagship Study of Ageing, Masters Colin L. , Bush Ashley I. , Fowler Christopher , Darby David , Pertile Kelly , Restrepo Carolina , Roberts Blaine , Robertson Jo , Rumble Rebecca , Ryan Tim , Collins Steven , Thai Christine , Trounson Brett , Lennon Kate , Li Qiao-Xin , Ugarte Fernanda Yevenes , Volitakis Irene , Vovos Michael , Williams Rob , Baker Jenalle , Russell Alyce , Peretti Madeline , Milicic Lidija , Lim Lucy , Rodrigues Mark , Taddei Kevin , Taddei Tania , Hone Eugene , Lim Florence , Fernandez Shane , Rainey-Smith Stephanie , Pedrini Steve , Martins Ralph , Doecke James , Bourgeat Pierrick , Fripp Jurgen , Gibson Simon , Leroux Hugo , Hanson David , Dore Vincent , Zhang Ping , Burnham Samantha , Rowe Christopher C. , Villemagne Victor L. , Yates Paul , Pejoska Sveltana Bozin , Jones Gareth , Ames David , Cyarto Elizabeth , Lautenschlager Nicola , Barnham Kevin , Cheng Lesley , Hill Andy , Killeen Neil , Maruff Paul , Silbert Brendan , Brown Belinda , Sohrabi Harmid , Savage Greg , Vacher Michael 
Published: February 2021

AbstractAging and Alzheimer’s disease (AD) are associated with progressive brain disorganization. Although structural asymmetry is an organizing feature of the cerebral cortex it is unknown whether continuous age- and AD-related cortical degradation alters cortical asymmetry. Here, in multiple longitudinal adult lifespan cohorts we show that higher-order cortical regions exhibiting pronounced asymmetry at age ~20 also show progressive asymmetry-loss across the adult lifespan. Hence, accelerated thinning of the (previously) thicker homotopic hemisphere is a feature of aging. This organizational principle showed high consistency across cohorts in the Lifebrain consortium, and both the topological patterns and temporal dynamics of asymmetry-loss were markedly similar across replicating samples. Asymmetry-change was further accelerated in AD. Results suggest a system-wide dedifferentiation of the adaptive asymmetric organization of heteromodal cortex in aging and AD.
Unusual solute segregation phenomenon in coherent twin boundaries
Authors: He Cong , Li Zhiqiao , Chen Houwen , Wilson Nick , Nie Jian-Feng 
Published: February 2021

AbstractInterface segregation of solute atoms has a profound effect on properties of engineering alloys. The occurrence of solute segregation in coherent twin boundaries (CTBs) in Mg alloys is commonly considered to be induced by atomic size effect where solute atoms larger than Mg take extension sites and those smaller ones take compression sites in CTBs. Here we report an unusual solute segregation phenomenon in a group of Mg alloys—solute atoms larger than Mg unexpectedly segregate to compression sites of {10$$\overline 1$$1¯1} fully coherent twin boundary and do not segregate to the extension or compression site of {10$$\overline 1$$1¯2} fully coherent twin boundary. We propose that such segregation is dominated by chemical bonding (coordination and solute electronic configuration) rather than elastic strain minimization. We further demonstrate that the chemical bonding factor can also predict the solute segregation phenomena reported previously. Our findings advance the atomic-level understanding of the role of electronic structure in solute segregation in fully coherent twin boundaries, and more broadly grain boundaries, in Mg alloys. They are likely to provide insights into interface boundaries in other metals and alloys of different structures.
Hypnotic suggestions of safety reduce neuronal signals of delay discounting
Authors: Schmidt Barbara , Holroyd Clay B. 
Published: February 2021

AbstractWaiting for delayed rewards is important to reach long-term goals, yet most people prefer immediate rewards. This tendency is called delay discounting. Evidence shows that people are more willing to wait for delayed rewards when they believe that the delayed reward is certain. We hypothesized that feeling safe makes delayed outcomes subjectively more certain, which should in turn reduce neuronal signals of delay discounting. We hypnotized 24 highly suggestible participants and gave them a suggestion to feel safe. We then used EEG to measure their brain responses to immediate and delayed rewards while they played a delayed gratification game. As compared to a control condition without hypnosis, participants that were suggested to feel safe under hypnosis reported feeling significantly safer. Further, their reward-related brain activity differentiated less between immediate and delayed rewards. We conclude that feeling safe makes delayed outcomes subjectively more certain and therefore reduces neuronal signals of delay discounting.
Enhanced fatty acid methyl esters recovery through a simple and rapid direct transesterification of freshly harvested biomass of Chlorella vulgaris and Messastrum gracile
Authors: Loh Saw Hong , Chen Mee Kee , Fauzi Nur Syazana , Aziz Ahmad , Cha Thye San 
Published: February 2021

AbstractConventional microalgae oil extraction applies physicochemical destruction of dry cell biomass prior to transesterification process to produce fatty acid methyl esters (FAMEs). This report presents a simple and rapid direct transesterification (DT) method for FAMEs production and fatty acid profiling of microalgae using freshly harvested biomass. Results revealed that the FAMEs recovered from Chlorella vulgaris were 50.1 and 68.3 mg with conventional oil-extraction-transesterification (OET) and DT method, respectively. While for Messastrum gracile, the FAMEs recovered, were 49.9 and 76.3 mg, respectively with OET and DT methods. This demonstrated that the DT method increased FAMEs recovery by 36.4% and 53.0% from C. vulgaris and M. gracile, respectively, as compared to OET method. Additionally, the DT method recovered a significantly higher amount of palmitic (C16:0) and stearic (C18:0) acids from both species, which indicated the important role of these fatty acids in the membranes of cells and organelles. The DT method performed very well using a small volume (5 mL) of fresh biomass coupled with a shorter reaction time (~ 15 min), thus making real-time monitoring of FAMEs and fatty acid accumulation in microalgae culture feasible.
Dominance style predicts differences in food retrieval strategies
Authors: Gomez-Melara Jose Luis , Acosta-Naranjo Rufino , Castellano-Navarro Alba , Beltrán Francés Victor , Caicoya Alvaro Lopez , MacIntosh Andrew J. J. , Maulany Risma Illa , Ngakan Putu Oka , Amici Federica 
Published: February 2021

AbstractIn several species, rank predicts access to food, and subordinates may need specific behavioural strategies to get a share of resources. This may be especially important in despotic species, where resources are strongly biased in favour of dominants and subordinates may more strongly rely on specific tactics to maximize food intake. Here, we compared three macaque species with an experimental set-up reproducing feeding competition contest. Following our predictions, more tolerant species mostly retrieved food in the presence of others and were less dependent on specific tactics. Contrarily, subordinates in more despotic species more likely collected food (1) when dominants could not see food or (2) were attacking others, (3) while “dissimulating”, or (4) “storing food”. Our study reveals that dominance styles reliably predict the probability of using specific food retrieval tactics and provides important insights on the social conditions that might have led to the emergence of tactical deception.
Natural dimethyl sulfide gradients would lead marine predators to higher prey biomass
Authors: Owen Kylie , Saeki Kentaro , Warren Joseph D. , Bocconcelli Alessandro , Wiley David N. , Ohira Shin-Ichi , Bombosch Annette , Toda Kei , Zitterbart Daniel P. 
Published: February 2021

AbstractFinding prey is essential to survival, with marine predators hypothesised to track chemicals such as dimethyl sulfide (DMS) while foraging. Many predators are attracted to artificially released DMS, and laboratory experiments have shown that zooplankton grazing on phytoplankton accelerates DMS release. However, whether natural DMS concentrations are useful for predators and correlated to areas of high prey biomass remains a fundamental knowledge gap. Here, we used concurrent hydroacoustic surveys and in situ DMS measurements to present evidence that zooplankton biomass is spatially correlated to natural DMS concentration in air and seawater. Using agent simulations, we also show that following gradients of DMS would lead zooplankton predators to areas of higher prey biomass than swimming randomly. Further understanding of the conditions and scales over which these gradients occur, and how they are used by predators, is essential to predicting the impact of future changes in the ocean on predator foraging success.
Exploring the mechanism of (-)-Epicatechin on premature ovarian insufficiency based on network pharmacology and experimental evaluation
Authors: Yan Fei , Zhao Qi , Gao Huanpeng , Wang Xiaomei , Xu Ke , Wang Yishu , Han Fuguo , Liu Qingfei , Shi Yun 
Published: February 2021

Abstract
Methods: Relevant potential targets for EC were obtained based on Traditional Chinese Medicine System Pharmacology Database (TCMSP), a bioinformatics analysis tool for molecular mechanism of Traditional Chinese Medicine (BATMAN-TCM) and STITCH databases. The Online Mendelian Inheritance in Man (OMIM) and GeneCards databases were utilized to screen the known POI-related targets, while Cytoscape software was used for network construction and visualization. Then, the Gene Ontology (GO) and pathway enrichment analysis were carried out by the Database for Annotation, Visualization and Integrated Discovery (DAVID) database. Furthermore, KGN cells were performed to validate the predicted results in oxidative stress (OS) model, and antioxidant effect was examined.
Results: A total of 70 potential common targets for EC in the treatment of POI were obtained through network pharmacology. Metabolic process, response to stimulus and antioxidant activity occupied a leading position of Gene Ontology (GO) enrichment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that PI3K/protein kinase B (AKT), TNF, estrogen, VEGF and MAPK signaling pathways were significantly enriched. In addition, cell experiments showed that EC exhibited antioxidant effects in an H2O2-mediated OS model in ovarian granulosa cells by regulating the expression of PI3K/AKT/nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway and multiple downstream antioxidant enzymes.
Conclusion: EC could regulate multiple signaling pathways and several biological processes (BPs). EC had the ability to down-regulate elevated OS level through the PI3K/AKT/Nrf2 signaling pathway and represented a potential novel treatment for POI.
A Nonrandomized Trial for Student Teachers of an In-Person and Telepractice Global Voice Prevention and Therapy Model With Estill Voice Training Assessed by the VoiceEvalU8 App
Authors: Grillo Elizabeth U. 
Published: February 2021

PurposeThis study investigated the effects of the in-person and telepractice Global Voice Prevention and Therapy Model (GVPTM) treatment conditions and a control condition with vocally healthy student teachers.MethodIn this single-blinded, nonrandomized trial, 82 participants completed all aspects of the study. Estill Voice Training was used as the stimulability component of the GVPTM to train multiple new voices meeting all the vocal needs of the student teachers. Outcomes were assessed using acoustic, perceptual, and aerodynamic measures captured by the VoiceEvalU8 app at pre and post in fall and during student teaching in spring.ResultsSignificant improvements were achieved for several acoustic and perceptual measures in the treatment conditions, but not in the control condition. The in-person and telepractice conditions produced similar results. The all-voiced phrase and connected speech were more successful in demonstrating voice change for some of the perturbation measures as compared to sustained /a/.ConclusionsThe treatment conditions were successful in improving the participants' voices for fundamental frequency and some acoustic perturbation measures while maintaining the improvements during student teaching. In addition, the treatment conditions were successful in decreasing the negative impact of voice-related quality of life and vocal fatigue during student teaching. Future research should address the effectiveness of the various components of the GVPTM, the application of the GVPTM with patients with voice disorders, the relevance of defining auditory–perceptual terms by the anatomy and physiology of the voice production system (i.e., Estill Voice Training), and the continued use of the VoiceEvalU8 app for clinical voice investigations.Supplemental Materialhttps://doi.org/10.23641/asha.13626824
Deficits of Learning in Procedural Memory and Consolidation in Declarative Memory in Adults With Developmental Language Disorder
Authors: Earle F. Sayako , Ullman Michael T. 
Published: February 2021

Purpose
This study examined procedural and declarative learning and consolidation abilities in adults with developmental language disorder (DLD) relative to their typical language (TD) peers.

Method

A total of 100 young adults (age 18–24 years) with (
n
= 21) and without (
n
= 79) DLD participated across two sites. Performance measures on a recognition memory task and a serial reaction time task were used to assess declarative and procedural memory, respectively. Performance was measured shortly after learning (8 a.m.) and again after a 12-hr, overnight delay (8 a.m.).

Results
Linear mixed-effects modeling was used to examine the effects of time and group membership on task performance. For the serial reaction time task, there were significant effects of group (TD > DLD) and time (Day 1 > Day 2), but no interaction between them. For the recognition memory task, there was a significant interaction between group and time, driven by overnight gains in the TD group, combined with stable performance across days by those with DLD.

Conclusions
In procedural memory, adults with DLD demonstrate a learning deficit relative to adults without DLD, but appear to have comparable retention of learned information. In declarative memory, adults with DLD demonstrate a deficit in the overnight enhancement of memory retrieval, despite typical-like learning exhibited when tested shortly after encoding.

Supplemental Material

https://doi.org/10.23641/asha.13626485