bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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.
Gastrointestinal cancers in China, the USA, and Europe
Authors: Xie Yumo , Shi Lishuo , He Xiaosheng , Luo Yanxin 
Published: February 2021

Abstract
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

Abstract

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

Abstract
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 &lt; 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

ABSTRACTBilateral 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 STATEMENTPlacement 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

AbstractIntroductionThe 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.MethodsWe 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.ResultsWe 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%.ConclusionThese 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

ABSTRACTGenetic 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.
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

ABSTRACTThe 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

AbstractUnderstanding 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

AbstractRelationships 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 statementIndigenous 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

AbstractResection 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.