bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolomics analysis of dandelions from different geographical regions in China
Authors: Zhang Songbao , Li Chao , Gu Wei , Qiu Rongli , Chao Jianguo , Pei Lingfeng , Ma Lijie , Guo Yangfang , Tian Rong
Published: February 2021

Introduction

Dandelion (Taraxacum mongolicum Hand.‐Mazz.) is a perennial herb with diverse pharmacological effects. The development and utilization of dandelion have attracted much attention.

Objectives

Our aims were to provide a reference basis for the identification of the origin of dandelions and to study the influence of their origin on their quality.

Methods

High‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry was used to analyze metabolites from dandelions from four different geographical regions in China, namely Gansu, Henan, Shanxi, and Jiangsu. Metabolite analysis was performed using orthogonal partial least‐squares discriminant analysis, and to identify potential metabolic pathways, MBRole was used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.

Results

Principal component analysis revealed that the chemical components of dandelions sampled from the four regions showed noticeable differences. Twenty‐six, six, six, eight, eight, and fifteen differentially produced metabolites were identified upon comparison between Gansu and Jiangsu, Gansu and Shanxi, Gansu and Henan, Henan and Shanxi, Henan and Jiangsu, and Shanxi and Jiangsu, respectively. These differentially produced metabolites were mainly phenolic compounds. Further, KEGG pathway enrichment analysis showed that the main metabolic pathways involved were biosynthesis of phenylpropanoids and flavonoids.

Conclusion

The methods reported herein can be used to identify the origin of dandelions; moreover, our results can serve as a reference basis for future studies.
Ex vivo glucocorticoid‐induced secreted proteome approach for discovery of glucocorticoid‐responsive proteins in human serum
Authors: Inder Warrick J. , Mohamed Ahmed , Keshvari Sahar , Barclay Johanna L. , Ruelcke Jayde E. , Stoll Thomas , Nolan Brendan J. , Cesana‐Nigro Nicole , Hill Michelle M.
Published: February 2021

Purpose

To identify glucocorticoid‐responsive proteins measurable in human serum that may have clinical utility in therapeutic drug monitoring and the diagnosis of cortisol excess or deficiency.

Experimental Design

A phased biomarker discovery strategy was conducted in two cohorts. Secretome from peripheral blood mononuclear cells (PBMC) isolated from six volunteers after ex vivo incubation ± dexamethasone (DEX) 100 ng/mL for 4 h and 24 h was used for candidate discovery and qualification using untargeted proteomics and a custom multiple reaction monitoring mass spectrometry (MRM‐MS) assay, respectively. For validation, five candidates were measured by immunoassay in serum from an independent cohort (n = 20), sampled at 1200 h before and after 4 mg oral DEX.

Results

The discovery secretome proteomics data generated a shortlist of 45 candidates, with 43 measured in the final MRM‐MS assay. Differential analysis revealed 16 proteins that were significant in at least one of two time points. In the validation cohort, 3/5 serum proteins were DEX‐responsive, two significantly decreased: lysozyme C (p < 0.0001) and nucleophosmin‐1 (p < 0.01), while high mobility group box 2 significantly increased (p < 0.01).

Conclusions and Clinical Relevance

Using an ex vivo proteomic approach in PBMC, we have identified circulating glucocorticoid‐responsive proteins which may have potential as serum biomarkers of glucocorticoid activity.
DbStRiPs: Database of structural repeats in proteins
Authors: Chakrabarty Broto , Parekh Nita
Published: February 2021

Recent interest in repeat proteins has arisen due to stable structural folds, high evolutionary conservation and repertoire of functions provided by these proteins. However, repeat proteins are poorly characterized because of high sequence variation between repeating units and structure‐based identification and classification of repeats is desirable. Using a robust network‐based pipeline, manual curation and Kajava's structure‐based classification schema, we have developed a database of tandem structural repeats, Database of Structural Repeats in Proteins (DbStRiPs). A unique feature of this database is that available knowledge on sequence repeat families is incorporated by mapping Pfam classification scheme onto structural classification. Integration of sequence and structure‐based classifications help in identifying different functional groups within the same structural subclass, leading to refinement in the annotation of repeat proteins. Analysis of complete Protein Data Bank revealed 16,472 repeat annotations in 15,141 protein chains, one previously uncharacterized novel protein repeat family (PRF), named left‐handed beta helix, and 33 protein repeat clusters (PRCs). Based on their unique structural motif, ~79% of these repeat proteins are classified in one of the 14 PRFs or 33 PRCs, and the remaining are grouped as unclassified repeat proteins. Each repeat protein is provided with a detailed annotation in DbStRiPs that includes start and end boundaries of repeating units, copy number, secondary and tertiary structure view, repeat class/subclass, disease association, MSA of repeating units and cross‐references to various protein pattern databases, human protein atlas and interaction resources. DbStRiPs provides easy search and download options to high‐quality annotations of structural repeat proteins (URL: http://bioinf.iiit.ac.in/dbstrips/).
Intervention by clinical pharmacists can improve blood glucose fluctuation in patients with diabetes and acute myocardial infarction: A propensity score‐matched analysis
Authors: Shi Fang‐Hong , Shen Long , Yue Jiang , Ma Jing , Gu Zhi‐Chun , Li Hao , Lin Hou‐Wen
Published: February 2021

Acute phase hyperglycemia and exaggerated glucose fluctuation may be associated with poor outcomes in diabetic patients after acute myocardial infarction (AMI). This study aimed to determine whether intervention by clinical pharmacists can mitigate blood glucose and glucose fluctuations in these fragile patients. This retrospective study enrolled patients with diabetes and AMI, from 1 January 2019 to 30 June 2020 in our institution. Blood glucose and glucose fluctuations were calculated before and after the pharmacist's intervention and between patients who underwent intervention and those who did not. Propensity score matching (PSM) was used to reduce the impact of patient characteristics on the results. A total of 170 patients were included in our primary analysis, including 29 patients who received the pharmacist intervention and 141 patients who did not. After the pharmacist's intervention, blood glucose (fasting blood glucose‐FBG, from 11.9 to 9.8; postprandial blood glucose‐PBG, from 15.3 to 13.2; mean blood glucose‐BG, 14.5 to 12.3 mmol/L; p < .001), and glucose fluctuations (standard deviation of blood glucose‐SDBG, from 3.8 to 3.0, mmol/L, p = .005) were significantly improved. Before PSM, no clear effects were found in intervention versus nonintervention patients, in terms of blood glucose and glucose fluctuation indicators, except for FBG (9.3 vs. 8.0. mmol/L, p = .005). Further analysis indicated a high incidence of FBG <7.8 mmol/L in nonintervention versus intervention patients (51.5% vs. 27.6%, p = .003). After PSM, a significant reduction in blood glucose fluctuation (SDBG, 3.0 vs. 4.1, p = .031; PBGE, 2.1 vs. 4.1, p = .017; LAGE, 4.7 vs. 7.2, mmol/L, p = .004), and PBG (11.1 vs. 13.0, mmol/L, p = .048) was observed in the intervention group than in the nonintervention group. The clinical pharmacist intervention contributed to improved outcomes, specifically, in reducing blood glucose fluctuations and potential hypoglycemia risk.
Lp‐norm regularization approaches in variational data assimilation
Authors: Bernigaud Antoine , Gratton Serge , Lenti Flavia , Simon Ehouarn , Sohab Oumaima
Published: February 2021

This article presents a formulation of the 4D‐Var objective function using as a penalty term a Lp‐norm with 1 < p < 2. This approach is motivated by the nature of the problems encountered in data assimilation, for which such a norm may be more suited to tackle the generalized Gaussian distribution of the variables. It also aims at making a compromise between the L2‐norm that tends to oversmooth the solution, and the L1‐norm that tends to ‘oversparsify’ it, in addition to making the problem non‐smooth. We show the benefits of using this strategy on different set‐ups through numerical experiments where the background and measurement noise covariances are known and a sharp solution is expected.
The making of AI society: AI futures frames in German political and media discourses
Authors: Köstler Lea , Ossewaarde Ringo
Published: February 2021

In this article, we shed light on the emergence, diffusion, and use of socio-technological future visions. The artificial intelligence (AI) future vision of the German federal government is examined and juxtaposed with the respective news media coverage of the German media. By means of a content analysis of frames, it is demonstrated how the German government strategically uses its AI future vision to uphold the status quo. The German media largely adapt the government´s frames and do not integrate alternative future narratives into the public debate. These findings are substantiated in the framing of AI futures in policy documents of the German government and articles of four different German newspapers. It is shown how the German past is mirrored in the German AI future envisioned by the government, safeguarding the present power constellation that is marked by a close unity of politics and industry. The German media partly expose the government´s frames and call for future visions that include fundamentally different political designs less influenced by the power structures of the past and present.
On quantitative stability in infinite-dimensional optimization under uncertainty
Authors: Hoffhues M. , Römisch W. , Surowiec T. M.
Published: February 2021

The vast majority of stochastic optimization problems require the approximation of the underlying probability measure, e.g., by sampling or using observations. It is therefore crucial to understand the dependence of the optimal value and optimal solutions on these approximations as the sample size increases or more data becomes available. Due to the weak convergence properties of sequences of probability measures, there is no guarantee that these quantities will exhibit favorable asymptotic properties. We consider a class of infinite-dimensional stochastic optimization problems inspired by recent work on PDE-constrained optimization as well as functional data analysis. For this class of problems, we provide both qualitative and quantitative stability results on the optimal value and optimal solutions. In both cases, we make use of the method of probability metrics. The optimal values are shown to be Lipschitz continuous with respect to a minimal information metric and consequently, under further regularity assumptions, with respect to certain Fortet-Mourier and Wasserstein metrics. We prove that even in the most favorable setting, the solutions are at best Hölder continuous with respect to changes in the underlying measure. The theoretical results are tested in the context of Monte Carlo approximation for a numerical example involving PDE-constrained optimization under uncertainty.
Ferromagnetism and optical properties of SnS2 doped with two impurities: first-principles calculations
Authors: Lin Long , Chen Yujin , Tao Hualong , Yao Linwei , Huang Jingtao , Zhu Linghao , Lou Mengsi , Chen Ruixin , Yan Longbin , Zhang Zhanying
Published: February 2021

The contribution of Fe and Cr to the magnetic properties in (0, 1) doped SnS2 configurations can be seen intuitively.
The configuration and failed eruption of a complex magnetic flux rope above aδsunspot region
Authors: Liu Lijuan , Liu Jiajia , Chen Jun , Wang Yuming , Wang Guoqiang , Zhou Zhenjun , Cui Jun
Published: February 2021

Aims.We aim to investigate the configuration of a complex flux rope above theδsunspot region in the National Oceanic and Atmospheric Administration AR 11515 and its eruptive expansion during a confined M5.3-class flare.

Methods.We studied the formation of theδsunspot using the continuum intensity images and photospheric vector magnetograms provided by the Helioseismic and Magnetic Imager on-board the Solar Dynamics Observatory (SDO). We employed the extreme-ultraviolet and ultraviolet images provided by the Atmospheric Imaging Assembly on-board SDO and the hard X-ray emission recorded by theReuven RamatyHigh-Energy Solar Spectroscopic Imager to investigate the eruptive details. The coronal magnetic field is extrapolated from the photospheric field using a nonlinear force free field (NLFFF) method, based on which the flux rope is identified through calculating the twist numberTwand squashing factorQ. We searched the null point via a modified Powell hybrid method.

Results.The collision between two newly emerged spot groups form theδsunspot. A bald patch (BP) configuration forms at the collision location between one umbra and the penumbra, above which a complex flux rope structure is identified. The flux rope has a multilayer configuration, with one compact end and the other end bifurcating into different branches. It has a non-uniformTwprofile, which decreases from the core to the boundary. The outmost layer is merely sheared. A null point is located above the flux rope. The eruptive process consists of precursor flarings at av-shaped coronal structure, rise of the filament, and brightening below the filament, corresponding well with the topological structures deduced from the NLFFF, including a higher null point, a flux rope, and a BP and a hyperbolic flux tube (HFT) below the flux rope. Two sets of post-flare loops and three flare ribbons in theδsunspot region further support the bifurcation configuration of the flux rope.

Conclusions.Combining the observations and magnetic field extrapolation, we conclude that the precursor reconnection, which occurs at the null point, weakens the overlying confinement to allow the flux rope to rise, fitting the breakout model. The main phase reconnection, which may occur at the BP or HFT, facilitates the flux rope rising. The results suggest that theδspot configuration presents an environment prone to the formation of complex magnetic configurations that work together to produce activities.
Surgical Treatment for Asymptomatic Congenital Pulmonary Airway Malformations in Children: Waiting or Not?
Authors: Zeng Jiahang , Liang Jianhua , Li Le , Liu Wei , Tang Jue , Yin Xiaoli , Yin Guocai
Published: February 2021

Introduction Infection is undoubtedly the most important factor in influencing the timing and surgical strategy of congenital pulmonary airway malformation (CPAM) surgery. However, there have been no studies on the optimal timing of surgery for patients based on the probability of infection. The aim of this study was performed to explore the optimal timing of surgery of CPAM in children from the risk of infection.

Materials and Methods The correlation of age distribution and pulmonary infection of 237 children diagnosed by pathology from January 2012 to January 2020 in Guangzhou Women and Children's Medical Center were analyzed retrospectively. We defined the cases with preoperative computed tomographic findings of infection, pathological findings of large number of neutrophils, tissue cells, and abscess formation as the infection group.

Results The rate of infection in patients less than 2 years old was significantly lower than in patients over 2 years old (11.4% vs. 45.7%, p < 0.001). And the pulmonary lobectomy rate of patients with infection (29.0%) was significantly higher than in noninfected patients (17.2%) and whole patients (36.3%), p = 0.033. Patients with infection lose more blood during surgery (noninfected patients: 81.76 ± 13.14 mL, infected patients: 145.10 ± 25.39 mL, p = 0.027). The univariate analysis revealed that the infection rate of patients over 2 years old was 3.084 times that of patients ≤2 years old (odds ratio [OR]: 3.084, 95% confidence interval [CI]: 1.196–7.954; p = 0.020). The infection rate of CPAM types III and IV patients is lower than types I and II (OR: 0.531, 95% CI: 0.307–0.920; p = 0.024).

Conclusion In consideration of the high risk of infection, lower minimally invasive surgery rate, an increased rate of pulmonary lobectomy, and more blood loss in patients over 2 years old, our study also supports early surgical treatment. Therefore, we suggest that for asymptomatic patients with CPAM I and CPAM II, surgical treatment should be performed when they are less than 2 years old, providing more options for surgical strategies and monitoring of CPAM patients.
Temporal effect of feeding on the body temperature and behaviour of captive koalas (
Authors: Adam D. , Johnston S. D. , Beard L. , Nicolson V. , Lisle A. T. , Gaughan J. B. , Larkin R. , Theilemann P. , Ellis W.
Published: February 2021

Free-ranging koalas generally feed at night; however, captive koalas are usually fed during the day in order to encourage activity for display purposes. We studied the temporal effect of feeding on body temperature of captive koalas in Queensland, to determine whether nocturnal feeding may be beneficial for koalas in warmer climates. Six adult koalas were implanted with thermal transmitters and data loggers, waxed together as a single package, to record internal body temperature. Koalas were exposed to two treatments: koalas were fed in the morning (between 0730 and 0830 hours) during the AM treatment or late afternoon (between 1700 and 1800 hours) for the PM treatment. The body temperature of koalas fed in the mornings was on average 0.5°C higher at its peak (P ≤ 0.01) when compared to koalas fed in the evening. Furthermore, the body temperature maxima of morning-fed koalas was reached ~2 h earlier in the afternoon, compared with those fed in the evening. There was no significant difference between behaviours associated with the two feeding regimes: inactivity (P = 0.840), feeding (P = 0.472) and activity (P = 0.634). We postulate that nocturnal feeding by koalas may be an adaptive mechanism that reduces diurnal heat load during times of high environmental temperatures.
Hormone-induced ovulation and artificial fertilisation in four terrestrial-breeding anurans
Authors: Silla Aimee J. , Byrne Phillip G.
Published: February 2021

The development and application of reproductive technologies has great potential to enhance the conservation management of threatened amphibians globally. The present study quantified the efficacy of protocols previously developed for Pseudophryne guentheri for hormonally inducing egg release and artificial fertilisation in three additional terrestrial-breeding species of Australian ground frog; namely Pseudophryne bibronii, Pseudophryne coriacea and Heleioporus eyrei. Females of each species were administered a priming dose of 0.4 µg g−1 of gonadotropin-releasing hormone analogue (GnRHa), followed by an ovulatory dose of 2 µg g−1 GnRHa. Egg release was achieved in all species (response 94.7–100%), but early embryo survival differed significantly, ranging from 23.8% to 89.3%. Overall, the protocols were considered effective in P. guentheri, P. bibronii and P. coriacea, but further protocol refinement is required for H. eyrei.
Gastrointestinal cancers in China, the USA, and Europe
Authors: Xie Yumo , Shi Lishuo , He Xiaosheng , Luo Yanxin
Published: February 2021

Gastrointestinal (GI) cancers, including colorectal cancer, gastric cancer, and esophageal cancer, are a major medical and economic burden worldwide and have the largest number of new cancer cases and cancer deaths each year. Esophageal and gastric cancers are most common in developing countries, while colorectal cancer forms the major GI malignancy in Western countries. However, a great shift in the predominant GI-cancer type is happening in countries under economically transitioning and, at the same time, esophageal and gastric cancers are reigniting in Western countries due to the higher exposure to certain risk factors. The development of all GI cancers is highly associated with lifestyle habits and all can be detected by identified precancerous diseases. Thus, they are all suitable for cancer screening. Here, we review the epidemiological status of GI cancers in China, the USA, and Europe; the major risk factors and their distribution in these regions; and the current screening strategies.
Neighborhood Built Environment and Late-Life Depression: A Multilevel Path Analysis in a Chinese Society
Authors: Lu Shiyu , Liu Yuqi , Guo Yingqi , Ho Hung Chak , Song Yimeng , Cheng Wei , Chui Cheryl , Chan On Fung , Webster Chris , Chiu Rebecca L H , Lum Terry Y
Published: February 2021

Objectives

Neighborhood built environments (BEs) are increasingly recognized as being associated with late-life depression. However, their pathways are still understudied. This study investigates the mediating effects of physical and social activities (PA and SA) and functional ability (FA) in the relationships between BEs and late-life depression.

Methods

We conducted a cross-sectional analysis with data from 2,081 community-dwellers aged 65 years and older in Hong Kong in 2014. Two road-network-based service area buffers (200- and 500-m buffers) adjusted by terrain and slope from participants’ residences were created to define the scope of neighborhoods. BEs comprised population density in District Council Constituency Areas, urban greenness, land-use diversity, and neighborhood facilities within 200- and 500-m buffers. Multilevel path analysis models were used.

Results

More urban greenness within both buffers and more commercial facilities within a 500-m buffer were directly associated with fewer depressive symptoms. SA mediated the relationship between the number of community facilities and depressive symptoms within a 200-m buffer. Neighborhood urban greenness and the number of commercial facilities had indirect associations on depressive symptoms within a 500-m buffer, which were mediated by FA.

Discussion

Our findings have implications for the ecological model of aging. The mediating effects of SA and FA underscore the importance of promoting active social lifestyles and maintaining FA for older adults’ mental health in high-density cities. Policy implications on how to build age-friendly communities are discussed.
Effect of supplementation with different fatty acid profile to the dam in early gestation and to the offspring on the finishing diet on offspring growth and hypothalamus mRNA expression in sheep
Authors: Oviedo-Ojeda Mario Francisco , Roque-Jiménez José Alejandro , Whalin Megan , Lee-Rangel Héctor Aarón , Relling Alejandro Enrique
Published: February 2021

Supplementation with omega-3 and omega-9 fatty acids (FA) during late gestation regulates offspring development; however, their effect in the first third of gestation is unknown in sheep. The objective of this experiment was to evaluate the effects of the maternal supplementation with an enriched source of monounsaturated FA (MUFA) or an enriched source of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) during the first third of gestation on productive performance on ewes and offspring, and hypothalamic neuropeptides on offspring. Seventy-nine post-weaning lambs, born of sheep supplemented in the first third of gestation with 1.61% Ca salts rich with MUFA or EPA+DHA (dam supplementation, DS), were distributed in a 2×2 factorial arrangement of treatments to finishing diets containing 1.48% of Ca salts of MUFA or EPA+DHA (lamb supplementation, LS). The finishing period of the offspring lasted for 56 d. During the finishing period dry matter intake (DMI, daily) and body weight (BW) were recorded. Plasma was collected for metabolites analysis. Twenty-four lambs were slaughtered, and hypothalamus was collected for mRNA expression of hormone receptors, neuropeptides, and lipid transport genes. The data were analyzed with a mixed model in SAS (9.4) using repeated measurements, when needed. There was a DS×LS interaction for BW (P = 0.10) where LS with EPA+DHA born from DS with MUFA were heavier than the other 3 treatments. Lambs born from DS with MUFA have a greater DMI (P < 0.01) than the offspring born from DS with EPA+DHA. Lambs born from MUFA supplemented dams had a greater (P ≤ 0.05) hypothalamus mRNA expression for cocaine and amphetamine regulated transcript, growth hormone receptor, metastasis suppressor 1, leptin receptor, pro-opiomelanocortin, and Neuropeptide Y. These results indicate that growth depends not on the type of FA during the finishing phase but the interaction of different sources of FA ad different stages. Also, supplementation with FA during early pregnancy changes productive performance and neuropeptides’ mRNA expression of lambs independently of the finishing diet.
Interaural place-of-stimulation mismatch estimates using CT scans and binaural perception, but not pitch, are consistent in cochlear-implant users
Authors: Bernstein Joshua G. W. , Jensen Kenneth K. , Stakhovskaya Olga A. , Noble Jack H. , Hoa Michael , Jeffery Kim H. , Shih Robert , Kolberg Elizabeth , Cleary Miranda , Goupell Matthew J.
Published: February 2021

ABSTRACT

Bilateral cochlear implants (BI-CIs) or a CI for single-sided deafness (SSD; one normally functioning acoustic ear) can partially restore spatial-hearing abilities including sound localization and speech understanding when there are competing sounds. However for these populations, frequency information is not explicitly aligned across the ears, resulting in interaural place-of-stimulation mismatch. This diminishes spatial-hearing abilities because binaural encoding occurs in interaurally frequency-matched neurons. This study examined whether plasticity – the reorganization of central neural pathways over time – can compensate for peripheral interaural place mismatch. We hypothesized differential plasticity across two systems: none for binaural processing but adaptation toward the frequencies delivered by the specific electrodes for sequential pitch perception. Interaural place mismatch was evaluated in 43 human subjects (20 BI-CI and 23 SSD-CI, both sexes) using interaural-time-difference (ITD) discrimination (simultaneous bilateral stimulation), place-pitch ranking (sequential bilateral stimulation), and physical electrode- location estimates from computed-tomography (CT) scans. On average, CT scans revealed relatively little BI-CI interaural place mismatch (26° insertion-angle mismatch), but relatively large SSD-CI mismatch, particularly at the apical end of the array (166° for an electrode tuned to 300 Hz, decreasing to 14° at 7000 Hz). ITD and CT measurements were in agreement, suggesting little binaural-system plasticity to mismatch. The pitch measurements did not agree with the binaural and CT measurements, suggesting plasticity for pitch encoding or procedural biases. The combined results show that binaural processing may be optimized by using CT-scan information, but not pitch measurements, to program the CI frequency allocation to reduce interaural place mismatch.

SIGNIFICANCE STATEMENT

Placement of electrode arrays in users of cochlear implants (CIs; bionic auditory prostheses that partially restore hearing) does not align the frequency information to acoustic neural encoding across the ears. This interaural place-of-stimulation mismatch diminishes spatial hearing abilities. This study shows that for experienced adult CI users with two CIs or with one CI and one normal-hearing ear, the best possible binaural sensitivity occurs when the same cochlear location is stimulated in both ears. This means that binaural brainstem pathways do not experience “plasticity” to compensate for interaural place mismatch – i.e., they do not reorganize to respond to input from different cochlear places. Therefore, explicit correction of interaural place mismatch by a clinician is necessary to derive maximum spatial-hearing benefits.
The Role of Sociodemographic and Psychosocial Variables in Early Childhood Development: A Secondary Data Analysis of the 2014 Multiple Indicator Cluster Survey in the Dominican Republic
Authors: Sánchez-Vincitore Laura V. , Castro Arachu
Published: February 2021

Introduction

The association between sociodemographic factors, such as poverty, lack of maternal schooling, and being male at birth, and childhood developmental delay and poor educational outcomes has been established in the Dominican Republic. However, moderating factors present or introduced in families to buffer the effects of such factors on childhood development are still unknown.

Methods

We conducted a secondary analysis of the 2014 Multiple Indicator Cluster Survey for the Dominican Republic, a national household survey focused on maternal and child health and development. The first aim of our study was to determine if a sociodemographic model predicted early childhood development. The second aim was to determine if a psychosocial model (including family childrearing practices, discipline, and early childhood stimulation) predicted early childhood development above and beyond the sociodemographic model.

Results

We found that both models predicted childhood development significantly, but that the psychosocial model explained 5% more variance than the sociodemographic model. The most relevant sociodemographic predictors were socioeconomic position and mother’s education, which uniquely explained 21% and 17% of the early childhood development variance, respectively. The most salient psychosocial predictors of early childhood development were: 1) attendance to an early childhood education program, which uniquely explained 15.0% of the variance; 2) negative discipline, which uniquely explained 12.4% (negative impact); 3) the number of children’s books at home, which uniquely explained 12.0%; and 4) stimulating activities at home, which uniquely explained 5%.

Conclusion

These results have multiple implications for social programs that aim to improve children’s developmental potential in contexts of poverty. Although the results show a protective effect of psychosocial factors, sustainable and large-scale intervention should not be limited to just buffering effects, but to actually solve the underlying problem which is that poverty prevents children from reaching their developmental potential.
Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq
Authors: Massarat Arya R. , Sen Arko , Jaureguy Jeff , Tyndale Sélène T. , Fu Yi , Erikson Galina , McVicker Graham
Published: February 2021

Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost ‘capture’ method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.
Structural basis of phosphorylation kinetics in the transcriptional activation domain (TAD) of c-Jun and insight of two new phosphorylation sites Ser58 and Thr62
Authors: Kumar Arnit , Bharti Shikha , Jatav Anuj , Singh Viraj
Published: February 2021

This manuscript has been removed due to unethical behavior by the authors that includes violation of copyright.
Identification of a chromosomally-encoded sucrose operon-like gene cluster in Vibrio parahaemolyticus strain PH05 isolated from Negros Island, Philippines
Authors: De Mesa Czarina Anne E. , Mendoza Remilyn M. , Amar Edgar C. , de la Peña Leobert D. , Saloma Cynthia P.
Published: February 2021

The ability of bacteria to metabolize a wide variety of carbon sources has been known to aid in their ability for efficient colonization. Vibrio parahaemolyticus, a known aquatic pathogen has been reported to have the ability to metabolize a number of carbohydrates including D-glucose, D-galactose, L-arabinose, D-mannose, and D-ribose to name a few. Classical isolation of V. parahaemolyticus from other members of the family Vibrionaceae relies on its carbon utilization pattern. Conventionally, V. parahaemolyticus lacks the ability to utilize sucrose and this has been the basis for its isolation using the Thiosulfate-citrate-bile salts-sucrose (TCBS) agar. Reports of V. parahaemolyticus having the ability to utilize sucrose have been presented yet there is paucity of information and detailed study on this phenotype. In this study, we report the V. parahaemolyticus strain PH05 that has the ability to metabolize sucrose. Phenotypic and genotypic characterization of this V. parahaemolyticus strain isolated from Negros Island, Philippines, revealed that V. parahaemolyticus strain PH05 is atypical appearing yellow on TCBS agar plates. It is capable of utilizing sucrose, unlike the majority of V. parahaemolyticus isolates. Genome analyses of this strain revealed the presence of a chromosomally encoded sucrose operon-like gene cluster encoded in chromosome 2 with the following sucrose-utilization associated genes: scrY, ccpA, treP, scrK, and scrB genes coding for sucrose porin, catabolite control protein A, PTS System sucrose-specific EIIBC component, fructokinase, and sucrose-6-phosphate hydrolase. The mode of transmission of these genes to V. parahaemolyticus strain PH05 is still unknown. However, the presence of insertion sequences (IS) and phage elements in the same chromosome suggests horizontal gene transfer events. Taken together, our results point to the possibility that acquired sucrose utilization genes may contribute to the fitness of V. parahaemolyticus strain PH05 in the environment.
Cascading indirect genetic effects in a clonal vertebrate
Authors: Makowicz Amber M. , Bierbach David , Richardson Christian , Hughes Kimberly A.
Published: February 2021

Understanding how individual differences among organisms arise and how their effects propagate through groups of interacting individuals are fundamental questions in biology.Individual differences can arise from genetically-based variation in the conspecifics with which an individual interacts, and these effects might then be propagated to other individuals. Using a clonal species, the Amazon molly (Poecilia formosa), we test the hypothesis that such indirect genetic effects (IGE) propagate beyond individuals that experience them firsthand. We tested this hypothesis by exposing genetically identical Amazon mollies to social partners of different genotypes, and then moving these individuals to new social groups in which they were the only member to have experienced the IGE. We found that genetically different social environments induced different levels of aggression experienced by the focal animals, and that these genetically-based social effects carried over into new social groups to influence the behavior of individuals that did not directly experience the previous social environments. Our data reveal that IGE can cascade beyond the individuals that directly experience them to influence phenotypes even when there is no genetically-based variation present within interacting groups. Theoretical and empirical expansion of the quantitative genetic framework developed for IGE to include cascading and other types of carry-over effects will improve understanding of social behavior and its evolution.
Circumpolar peoples and their languages: lexical and genomic data suggest ancient Chukotko-Kamchatkan–Nivkh and Yukaghir-Samoyedic connections
Authors: Starostin George , Altınışık N. Ezgi , Zhivlov Mikhail , Changmai Piya , Flegontova Olga , Spirin Sergey A. , Zavgorodnii Andrei , Flegontov Pavel , Kassian Alexei S.
Published: February 2021

Relationships between universally recognized language families represent a hotly debated topic in historical linguistics, and the same is true for correlation between signals of genetic and linguistic relatedness. We developed a weighted permutation test and applied it on basic vocabularies for 31 pairs of languages and reconstructed proto-languages to show that three groups of circumpolar language families in the Northern Hemisphere show evidence of relationship though borrowing in the basic vocabulary or common descent: [Chukotko-Kamchatkan and Nivkh]; [Yukaghir and Samoyedic]; [Yeniseian, Na-Dene, and Burushaski]. The former two pairs showed the most significant signals of language relationship, and the same pairs demonstrated parallel signals of genetic relationship implying common descent or substantial gene flows. For finding the genetic signals we used genome-wide genetic data for present-day groups and a bootstrapping model comparison approach for admixture graphs or, alternatively, haplotype sharing statistics. Our findings further support some hypotheses on long-distance language relationship put forward based on the linguistic methods but lacking universal acceptance.

Significance statement

Indigenous people inhabiting polar and sub-polar regions in the Northern Hemisphere speak diverse languages belonging to at least seven language families which are traditionally thought of as unrelated entities. We developed a weighted permutation test and applied it to basic vocabularies of a number of languages and reconstructed proto-languages to show that at least three groups of circumpolar language families show evidence of relationship though either borrowing in the basic vocabulary or common descent: Chukotko-Kamchatkan and Nivkh; Yukaghir and Samoyedic; Yeniseian, Na-Dene, and Burushaski. The former two pairs showed the most significant signals of language relationship, and the same pairs demonstrated parallel signals of genetic relationship implying common descent or substantial gene flows.
Mapping yeast mitotic 5’ resection at base resolution reveals the sequence and positional dependence of nucleasesin vivo
Authors: Bazzano Dominic , Lomonaco Stephanie , Wilson Thomas E.
Published: February 2021

Resection of the 5’-terminated strand at DNA double strand breaks (DSBs) is the critical regulated step in the transition to homologous recombination. Biochemical and genetic studies have led to a multi-step model of DSB resection in which endonucleolytic cleavage mediated by Mre11 in partnership with Sae2 is coupled with exonucleolytic cleavage mediated by redundant pathways catalyzed by Exo1 and Sgs1/Dna2. These models have not been well tested at mitotic DSBsin vivobecause most methods used to monitor resection cannot precisely map early cleavage events. Here we report resection monitoring with high-throughput sequencing in which molecular identifiers allow exact counting of cleaved 5’ ends at base pair resolution. Mutant strains, includingexo1Δ,mre11-H125N,exo1Δ andexo1Δsgs1Δ, revealed a major Mre11-dependent cleavage position 60 to 70 bp from the DSB end whose exact position depended on local sequence and tracked a possible motif. They further revealed an Exo1-dependent pause point approximately 200 bp from the DSB. Suppressing resection extension inexo1Δsgs1Δ yeast exposed a footprint of regions where cleavage was restricted within 119 bp of the DSB. These results provide detailedin vivosupport of prevailing models of DSB resection and extend them to show the combined influence of sequence specificity and access restrictions on Mre11 and Exo1 nucleases.
Allelic and Genotypic Frequencies of NAT2, CYP2E1 and AADAC genes in a cohort of Peruvian Tuberculosis Patients
Authors: Levano Kelly S. , Jaramillo-Valverde Luis , Tarazona David D. , Sanchez Cesar , Capristano Silvia , Solari Lely , Mendoza-Ticona Alberto , Soto Alonso , Rojas Christian , Zegarra-Chapoñan Roberto , Guio Heinner
Published: February 2021

Background

We determined the frequency of genetic polymorphisms in three anti-TB drug metabolic proteins previously reported: N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1) and arylacetamide deacetylase (AADAC) within a Peruvian population in a cohort of TB patients. We included 395 participants completed their anti-tuberculosis treatment.

Results

∼74% of the participants are carriers of slow metabolizer genotypes: NAT2*5, NAT2*6 and NAT2*7, which increase the sensitivity of INH at low doses and increase the risk of drug-induced liver injuries. ∼ 64% are homozygous for the wild-type CYP2E1*1A allele, which could increase the risk of hepatotoxicity. However, 16% had a NAT2 fast metabolizer phenotype which could increase the risk of acquiring resistance to INH, thereby increasing the risk of multidrug-resistant (MDR) or treatment failure. The frequency of rs1803155 (AADAC*2 allele) was higher (99.9%) in Peruvians than in in European American, African American, Japanese, and Korean populations.

Conclusions

This high prevalence of slow metabolizers for Isoniazid in the Peruvian population should be further studied and considered to help individualize drug regimens, especially in countries with a great genetic diversity like Peru. These data will help the Peruvian National Tuberculosis Control Program develop new strategies for therapies.
De novopurine nucleotide biosynthesis mediated by amidophosphoribosyl transferase is required for conidiation and essential for the successful host colonization ofMagnaporthe oryzae
Authors: Aron Osakina , Wang Min , Guo Jiayuan , Otieno Jagero Frankline , Zuriegat Qussai , Lu Songmao , Wang Zonghua , Tang Wei
Published: February 2021

Amidophosphoribosyl transferase catalyzes the first step of the purine nucleotide biosynthesis by converting 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine. In this study, we identified and characterized the functions of MoAde4, an ortholog of yeast Ade4 in the rice blast fungus. MoAde4 is a 537-amino acid protein containing the GATase_6 and pribosyltran domains. Quantitative real-time PCR analysis showedMoADE4transcripts were highly expressed during conidiation, early-infection, and late-infection stages of the fungus. Disruption ofMoADE4gene resulted in ΔMoade4mutant exhibiting adenine, adenosine, and hypoxanthine auxotrophy on MM. Conidia quantification assays showed ΔMoade4mutant was significantly reduced in sporulation. The conidia of ΔMoade4mutant could still form appressoria but mostly failed to penetrate the rice cuticle. Pathogenicity test showed ΔMoade4was completely nonpathogenic on rice and barley leaves which was attributed by failure of its infectious hyphae to colonize the host cells. The ΔMoade4was defective in induction of strong host immunity and had its purine transporter genes repressed during in planta infection. Addition of exogenous adenine partially rescued conidiation and pathogenicity defects of the ΔMoade4mutant on the barley and rice leaves. Localization assays showed that MoAde4 is located in the cytoplasm. Taken together, our results demonstrate that purine biosynthesis orchestrated by MoAde4 is required for fungal development, conidiation, more importantly, we found it to be essential for fungal pathogenicity not because of the appressorial formation, but appressorium penetration and host colonization during the plant infection ofM. oryzae. Thus this findings suggests that purine biosynthesis could act as an important target for combating recalcitrant plant fungal pathogens.
Concurrent feature-specific reactivation within the hippocampus and neocortex facilitates episodic memory retrieval
Authors: Bone Michael B. , Buchsbaum Bradley R.
Published: February 2021

The hippocampus is a key brain region for the storage and retrieval of episodic memories, but how it performs this function is unresolved. According to the hippocampal indexing theory, the hippocampus stores an event-specific index of the pattern of neocortical activity that occurred during perception. During retrieval, reactivation of the index by a partial cue facilitates the reactivation of the associated neocortical pattern. Therefore, event-specific retrieval requires joint reactivation of the hippocampal index and the associated neocortical networks. To test this theory, we examine the relation between performance on a recognition memory task requiring retrieval of image-specific visual details and feature-specific reactivation within the hippocampus and neocortex. We show that trial-by-trial recognition accuracy correlates with neural reactivation of low-level features (e.g. luminosity and edges) within the posterior hippocampus and early visual cortex for participants with high recognition lure accuracy. As predicted, the two regions interact, such that recognition accuracy correlates with hippocampal reactivation only when reactivation co-occurs within the early visual cortex (and vice-versa). In addition to supporting the hippocampal indexing theory, our findings show large individual differences in the features underlying visual memory and suggest that the anterior and posterior hippocampus represents gist-like and detailed features, respectively.
Direct and indirect contributions of energy consumption structure to carbon emission intensity
Authors: Yin Jiuli , Ding Qing , Fan Xinghua
Published: February 2021

Purpose

Reductions in emissions intensity have been expressed in commitments of many countries’ intended nationally determined contribution. Energy structure adjustment is one of the main approaches to reduce carbon emissions. This paper aims to study the causal relationship between carbon emission intensity and energy consumption structure in China based on path analysis.

Design/methodology/approach

After data collection, this paper performs correlation analysis, regression and path analysis.

Findings

Correlation results display clear collinearity among energy structure variables. Regression finds that coal, oil, natural gas and technology can be used as indicators for carbon intensity while primary electricity has been excluded. Path analysis shows that coal had the largest direct and positive impact on emission intensity. Natural gas had a positive direct and negative indirect effect through its negative relationship with coal on emission intensity. Technology has the largest negative elasticity while all fossil energies are positive. Results indicate a negative effect of energy structure adjustment on China’s national carbon intensity.

Originality/value

Given the major role of China in global climate change mitigation, significant future reductions in China’s CO2 emissions will require transformation toward low-carbon energy systems. Considering the important role in mitigating global climate change, China needs to transition toward a low-carbon energy system to significantly reduce its carbon intensity in the future.