bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shortleaf Pine (Pinus echinata) Site Index Equation for the Cumberland Plateau, USA
Authors: Zobel John M , Schubert Martin R , Granger Joshua J 
Published: May 2022

Abstract
Shortleaf pine site index on the Cumberland Plateau is one of the least studied silvics of the species. To obtain site index information, practitioners must use site index curves from outside the region. This research proposes a novel approach to using USDA Forest Service, Forest Inventory and Analysis data to develop a shortleaf pine site index equation specific to the Plateau. Shortleaf pine site trees (n = 410) were grown forward or backward until base age of 50 years, using site specific, mixed-model parameters. Over thirty height models were then fit using traditional methods and the algebraic difference approach (ADA). Fit and cross-validation statistics, along with examinations of model behavior, showed that a derivation of the Lundqvist-Korf model provided the best estimates. The model was rearranged to directly estimate site index, and a traditional site index graph is provided. Site index estimates had average validation results nearly four times better than the currently recommended site index curve developed off the Plateau. Forest practitioners now have access to improved site index estimation for restoring and managing shortleaf pine on the Cumberland Plateau.
Estimated Erosion from Clearcut Timber Harvests in the Southeastern United States
Authors: Fielding Jonah A H , Hawks Brent S , Aust W Michael , Bolding M Chad , Barrett Scott M 
Published: May 2022

Abstract
Timber harvests with inadequate forestry best management practices (BMPs) can accelerate soil erosion, which has been associated with reductions in water quality and site productivity. Previous studies affirm positive water quality effects accrued by harvesting with BMPs. However, few studies document erosion rates and masses associated with harvest and access network features (e.g., decks, roads, skid trails, stream crossings) across different southeastern regions. This research evaluated 109 recent harvests across eleven southeastern states and three topographically different regions (Coastal Plain, Piedmont, and Mountains). Descriptive statistics of erosion for harvests and access features were developed from USLE-Forest model estimates. Harvests and access network areas were used in conjunction with erosion averages to calculate total erosion masses. Across the southeast, combined network features averaged nearly 12% of total harvest area yet produced approximately 48% of total site erosion due to disproportionately higher erosion rates. Regional differences indicated that the Mountain region had an average overall erosion rate of 6.8 t/ac/yr, whereas the Piedmont and Coastal Plain sites had lower average erosion rates of 2.7 and 2.2 t/ac/yr, respectively. Results suggest that additional BMP implementation strategies may be beneficial for erosion control from roads, skid trails, and stream crossings, particularly in erosive landscapes.
Effects of 21 Years of Simulated Acidic Deposition on Tree Growth and Species Composition in an Aggrading Appalachian Hardwood Forest
Authors: Storm Alexander , Adams Mary Beth , Fowler Zachariah , Schuler Jamie L 
Published: May 2022

Abstract
The long-term effects of soil acidification on the development of a young aggrading Appalachian forest were examined after 21 years of continuous treatment. Beginning with a clearcut harvest in 1997, annual ammonium sulfate (N+S) and ammonium sulfate with lime (N+S+LIME) treatments were aerially applied to a developing forest. The lime treatment was designed to counteract the acidification of the nitrogen and sulfur amendments. After 21 years, the N+S and N+S+LIME treatments had little impact on total woody biomass accumulation relative to the control. There were significant differences among species and treatment responses with respect to woody biomass accumulation, however. Biomass of Prunus pensylvanica was about twice as much as any other species in N+S and N+S+LIME treatments but was similar to Liriodendron tulipifera and Betula lenta on control areas. Treatment effects were not significant for average tree diameter or stem density, although both varied among the six tree species with the highest importance values. The importance value of P. pensylvanica decreased by almost half in the last 6 years due to mortality, but this was not associated with either the N+S or N+S+LIME treatments. The dynamic nature of this short-lived tree species is potentially masking any effects of the N+S or N+S+LIME treatments to date.
Study Implications: We examined the long-term impact of nitrogen and sulfur additions with and without lime on forest stand development. After 21 years, the forest showed little change in aboveground woody biomass, although the distribution of biomass among species was affected by the treatments. Prunus pensylvanica (pin cherry) accumulated the greatest biomass on N+S and N+S+LIME treatments relative to the untreated areas. However, P. pensylvanica is a short-lived species, and our data show it is declining. It is unclear whether the treatments are having minimal impacts or they are being masked by the early dominance and subsequent mortality of P. pensylvanica.
Dynamic Interactions Between Mega Symbiosis ICEs and Bacterial Chromosomes Maintain Genome Architecture
Authors: Weisberg Alexandra J. , Sachs Joel L. , Chang Jeff H. 
Published: May 2022

Abstract
Acquisition of mobile genetic elements can confer novel traits to bacteria. Some integrative and conjugative elements confer upon members of Bradyrhizobium the capacity to fix nitrogen in symbiosis with legumes. These so-called symbiosis integrative conjugative elements (symICEs) can be extremely large and vary as monopartite and polypartite configurations within chromosomes of related strains. These features are predicted to impose fitness costs and have defied explanation. Here, we show that chromosome architecture is largely conserved despite diversity in genome composition, variations in locations of attachment sites recognized by integrases of symICEs, and differences in large-scale chromosomal changes that occur upon integration. Conversely, many simulated nonnative chromosome–symICE combinations are predicted to result in lethal deletions or disruptions to architecture. Findings suggest that there is compatibility between chromosomes and symICEs. We hypothesize that the size and structural flexibility of symICEs are important for generating combinations that maintain chromosome architecture across a genus of nitrogen-fixing bacteria with diverse and dynamic genomes.
Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus
Authors: Surendranadh Parvathy , Arathoon Louise , Baskett Carina A , Field David L , Pickup Melinda , Barton Nicholas H 
Published: May 2022

Abstract
Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.
The Effects of Graded Levels of Calorie Restriction: XVIII.Tissue-Specific Changes in Cell Size and Number in Response to Calorie Restriction
Authors: Phillips Daniel , Mathers Hayleigh , Mitchell Sharon E , Speakman John R 
Published: May 2022

Abstract
Calorie restriction (CR) without malnutrition increases the health and life span of diverse taxa. The mechanism(s) behind CR are debated but may be directly linked to body composition changes that maintain energy balance. During a deficit, energy is primarily obtained from white adipose tissue (WAT; utilized) while other tissues remain unchanged (protected) or grow (invested) relative to body mass. The changes in mass of 6 tissues from 48 male C57BL/6 mice following 3-month graded (10%, 20%, 30%, or 40%) CR or fed ad libitum for 12 or 24 hours a day were related to cell size (hypo/hypertrophy) and/or number (hypo/hyperplasia). Tissues studied were retroperitoneal and subcutaneous WAT, brown adipose tissue (BAT; utilized), lungs (protected), and stomach and cecum (invested). Methodology was based on number of nuclei/tissue equaling the number of cells. Extracted DNA was quantified and used to estimate cell numbers (total DNA/DNA per diploid nucleus) and size (tissue mass/nuclei number). WAT utilization was caused solely by hypotrophy whereas BAT utilization resulted from reduced cell number and size. WAT cell size positively correlated with circulating hormones related to energy balance, and BAT cell number and size positively correlated with body temperature. No changes were found in the lungs, consistent with their protected status, whereas hyperplasia appeared to be the dominant mechanism for invested alimentary-tract tissues. These findings indicate the pattern of change of cell size and number across increasing levels of short-term CR is tissue-specific.
Volunteer Engagement and Systemic Inflammation: Does Helping Others Benefit Oneself?
Authors: Bell Mallory J , Ferraro Kenneth F , Sauerteig-Rolston Madison R 
Published: May 2022

Abstract

Background and Objectives
Although research on the health benefits of volunteering has proliferated, most studies are cross-sectional and rely on self-reported measures of health. Drawing from role theory, the objectives of this study are to examine if (a) volunteering engagement is related to systemic inflammation in later life, as measured by C-reactive protein (CRP); (b) the effect of volunteering varies by age; and (c) volunteering is related to change in CRP over time.

Research Design and Methods
This study uses 4 waves of data from the Health and Retirement Study, a nationally representative survey of adults 50 years or older. Nested linear regression models were used to examine the relationship between volunteer engagement and CRP concentration in later life. Residualized regression models were used to examine the effects of volunteer engagement on change in CRP.

Results
Results revealed that volunteering is modestly associated with lower CRP concentration, but only for respondents 65+. Highly engaged volunteers had lower CRP than both mid-level and nonvolunteers. Longitudinal analyses revealed a leveling of the beneficial effect of volunteering by age, indicative of reduced returns among the oldest respondents in our sample.

Discussion and Implications
These results support previous studies that volunteering, and doing so at a high engagement level, is associated with slightly lower levels of CRP. Leaders in medicine, public health, and social services should consider implementing volunteering programs for older adults.
Chromosome-level genome assembly of the black widow spider Latrodectus elegans illuminates composition and evolution of venom and silk proteins
Authors: Wang Zhongkai , Zhu Kesen , Li Haorong , Gao Lei , Huang Huanying , Ren Yandong , Xiang Hui 
Published: May 2022

Abstract

Background
The black widow spider has both extraordinarily neurotoxic venom and three-dimensional cobwebs composed of diverse types of silk. However, a high-quality reference genome for the black widow spider was still unavailable, which hindered deep understanding and application of the valuable biomass.

Findings
We assembled the Latrodectus elegans genome, including a genome size of 1.57 Gb with contig N50 of 4.34 Mb and scaffold N50 of 114.31 Mb. Hi-C scaffolding assigned 98.08% of the genome to 14 pseudo-chromosomes, and with BUSCO, completeness analysis revealed that 98.4% of the core eukaryotic genes were completely present in this genome. Annotation of this genome identified that repetitive sequences account for 506.09 Mb (32.30%) and 20,167 protein-coding genes, and specifically, we identified 55 toxin genes and 26 spidroins and provide preliminary analysis of their composition and evolution.

Conclusions
We present the first chromosome-level genome assembly of a black widow spider and provide substantial toxin and spidroin gene resources. These high-qualified genomic data add valuable resources from a representative spider group and contribute to deep exploration of spider genome evolution, especially in terms of the important issues on the diversification of venom and web-weaving pattern. The sequence data are also firsthand templates for further application of the spider biomass.
Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4)
Authors: Jefri Malvin , Zhang Xin , Stumpf Patrick S , Zhang Li , Peng Huashan , Hettige Nuwan , Theroux Jean-Francois , Aouabed Zahia , Wilson Khadija , Deshmukh Shriya , Antonyan Lilit , Ni Anjie , Alsuwaidi Shaima , Zhang Ying , Jabado Nada , Garcia Benjamin A , Schuppert Andreas , Bjornsson Hans T , Ernst Carl 
Published: May 2022

Abstract
Kabuki syndrome is frequently caused by loss-of-function mutations in one allele of histone 3 lysine 4 (H3K4) methyltransferase KMT2D and is associated with problems in neurological, immunological and skeletal system development. We generated heterozygous KMT2D knockout and Kabuki patient-derived cell models to investigate the role of reduced dosage of KMT2D in stem cells. We discovered chromosomal locus-specific alterations in gene expression, specifically a 110 Kb region containing Synaptotagmin 3 (SYT3), C-Type Lectin Domain Containing 11A (CLEC11A), Chromosome 19 Open Reading Frame 81 (C19ORF81) and SH3 And Multiple Ankyrin Repeat Domains 1 (SHANK1), suggesting locus-specific targeting of KMT2D. Using whole genome histone methylation mapping, we confirmed locus-specific changes in H3K4 methylation patterning coincident with regional decreases in gene expression in Kabuki cell models. Significantly reduced H3K4 peaks aligned with regions of stem cell maps of H3K27 and H3K4 methylation suggesting KMT2D haploinsufficiency impact bivalent enhancers in stem cells. Preparing the genome for subsequent differentiation cues may be of significant importance for Kabuki-related genes. This work provides a new insight into the mechanism of action of an important gene in bone and brain development and may increase our understanding of a specific function of a human disease-relevant H3K4 methyltransferase family member.
Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock
Authors: Jiang Lijuan , Shen Wenyun , Liu Chen , Tahir Muhammad Mobeen , Li Xuewei , Zhou Shuangxi , Ma Fengwang , Guan Qingmei 
Published: May 2022

Abstract
Drought poses a major threat to apple fruit production and quality. Because of the apple’s long juvenile phase, developing varieties with improved drought tolerance using biotechnology approaches is needed. Here, we used the RNAi approach to knock down six GH3 genes in the apple. Under prolonged drought stress, the MdGH3 RNAi plants performed better than wild-type plants and had stronger root systems, higher root-to-shoot ratio, greater hydraulic conductivity, increased photosynthetic capacity, and increased water use efficiency. Moreover, MdGH3 RNAi plants promoted the drought tolerance of the scion when they were used as rootstock, compared with wild-type and M9-T337 rootstocks. Scions grafted onto MdGH3 RNAi plants showed increased plant height, stem diameter, photosynthetic capacity, specific leaf weight, and water use efficiency. The use of MdGH3 RNAi plants as rootstocks can also increase the C/N ratio of the scion and achieve the same effect as the M9-T337 rootstock in promoting the flowering and fruiting of the scion. Notably, using MdGH3 RNAi plants as rootstocks did not reduce fruit weight and scion quality compared with using M9-T337 rootstock. Our research provides candidate genes and demonstrates a general approach that could be used to improve the drought tolerance of fruit trees without sacrificing the yield and quality of scion fruits.
Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond
Authors: de Tomás Carlos , Bardil Amélie , Castanera Raúl , Casacuberta Josep M , Vicient Carlos M 
Published: May 2022

AbstractHybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (Prunus persica). The merging of two different genomes in a hybrid often triggers a so-called “genomic shock” with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in an F1 hybrid using high-throughput sequencing technologies. Contrary to the “genomic shock” expectations, we found that the overall levels of DNA methylation in the transposable elements in the hybrid are not significantly altered compared with those of the parental genomes. We also observed that the levels of transcription of the transposable elements in the hybrid are in most cases intermediate as compared with that of the parental species and we have not detected cases of higher transcription in the hybrid. We also found that the proportion of genes whose expression is altered in the hybrid compared with the parental species is low. The expression of genes potentially involved in the regulation of the activity of the transposable elements is not altered. We can conclude that the merging of the two parental genomes in this Prunus persica x Prunus dulcis hybrid does not result in a “genomic shock” with significant changes in the DNA methylation or in the transcription. The absence of major changes may facilitate using interspecific peach x almond crosses for peach improvement.
Pro: Fresh versus frozen embryo transfer. Is frozen embryo transfer the future?
Authors: Venetis Christos A 
Published: May 2022

Abstract
Embryo cryopreservation has been an integral part of ART for close to 40 years and vitrification has boosted overall ART efficacy and safety. Recently, there has been a vivid scientific discussion on whether elective cryopreservation of all embryos (freeze-all) should be pursued for most patients, with a fresh embryo transfer taking place only in selected cases. In terms of efficacy, the available evidence suggests that the freeze-all strategy leads to higher live birth rates after the first embryo transfer compared to the conventional strategy in high responders, while there is no difference in normal responders. There is no evidence to suggest that the freeze-all strategy is inferior to the conventional strategy of fresh transfer when comparing cumulative live birth rates using data from all available randomized controlled trials. The incidence of ovarian hyperstimulation syndrome is significantly reduced in the freeze-all policy. However, regarding obstetric complications and neonatal outcomes, the evidence suggests that each strategy is associated with certain risks and, therefore, there is no approach that could be unequivocally accepted as safer. Similarly, limited evidence does not support the notion that patients would be universally against freeze-all owing to the inevitable delay in pregnancy achievement. Finally, the cost-effectiveness of freeze-all is likely to vary in different settings and there have been studies supporting that this policy can be, under certain conditions, cost-effective. Adoption of the freeze-all policy can also allow for more flexible treatment strategies that have the potential to increase efficacy, reduce cost and make treatment easier for patients and clinics. Importantly, freeze-all does not require the use of any experimental technologies, further training of personnel or the costly acquisition of new equipment. For these reasons, transitioning to the freeze-all policy for most patients appears to be the next logical step in ART.
Inflammatory Bowel Disease and Long-term Risk of Cancer: A Prospective Cohort Study Among Half a Million Adults in UK Biobank
Authors: Wu Shanshan , Xie Sian , Yuan Changzheng , Yang Zhirong , Liu Si , Zhang Qian , Sun Feng , Wu Jing , Zhan Siyan , Zhu Shengtao , Zhang Shutian 
Published: May 2022

AbstractBackgroundThis study aims to examine the prospective association of inflammatory bowel disease (IBD) with long-term risk of overall, site-specific cancer and cancer-specific mortality in middle-aged and older people.MethodsThe study included participants free of any cancer at baseline from the UK Biobank, with IBD patients as an exposure group and non-IBD patients as a reference group. Primary outcome was the incidence of overall cancer and cancer-specific mortality. Secondary outcomes included site-specific cancers and types of digestive cancers. Cox proportional hazard model was used to investigate the associated risk of incident malignancies and related mortality.ResultsAmong 455 927 participants, 5142 were diagnosed with IBD (3258 ulcerative colitis [UC]; 1449 Crohn’s disease [CD]; others unspecified). During a median of 12.2-year follow-up, 890 cases of incident cancer were identified in IBD patients (15.74 per 1000 person years) compared with 63 675 cases in reference individuals (12.46 per 1000 person years). Of these cases, 220 and 12 838 cancer-specific deaths occurred in IBD and non-IBD groups. Compared with non-IBD participants, the adjusted hazard ratio (AHR) for overall cancer and cancer-specific mortality was 1.17 (95% CI, 1.09-1.25) and 1.26 (95% CI, 1.18-1.35) among IBD patients, with an AHR of 1.15 (95% CI, 1.02-1.31) and 1.38 (95% CI, 1.08-1.75) in UC and 1.15 (95% CI, 1.06-1.25) and 1.25 (95% CI, 1.06-1.49) in CD, respectively. Specifically, increased risk of digestive (1.33; 95% CI, 1.12-1.57), nonmelanoma (1.25; 95% CI, 1.11-1.41), and male genital (1.29; 95% CI, 1.09-1.52) cancers was observed in IBD patients.ConclusionsCompared with non-IBD, IBD may be associated with an increased risk of overall cancer and cancer-specific mortality, particularly digestive cancers, nonmelanoma and male genital cancers.