bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus
Authors: Scarsbrook Lachie , Verry Alexander J. F. , Walton Kerry , Hitchmough Rodney A. , Rawlence Nicolas J. 
Published: March 2022

AbstractMethodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator‐free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898–2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post‐extraction micro‐computed tomography reconstructions. All “large gecko” specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea‐level change. Recent mainland extinction obscured these signals from the modern tissue‐derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.
Climate drives patterns of seed traits in Quercus species across China
Authors: Xia Ke , Daws Matthew I. , Peng Lin‐Lin 
Published: March 2022

Summary

Traits enabling seeds to survive post‐dispersal desiccation and subsequently germinate are important aspects of plant regeneration for species with desiccation‐sensitive seeds. However, how desiccation and germination‐related traits co‐vary and relate to patterns of climate variation are unknown.

We investigated physiological traits related to desiccation and germination of desiccation‐sensitive seeds from 19 Quercus species, which typically dominate subalpine, subtropical and temperate forests in China.

The results demonstrate a strong relationship between climate and seed traits consistent with a hypothesis of minimizing seed death from desiccation. Seeds of subalpine species were most desiccation sensitive and died fastest when dried. These species avoided drought and cold by germinating rapidly. Subtropical and temperate oaks had more variable strategies to minimize the risk of mortality reflecting a continuum between traits that facilitate rapid germination (with the risk of rapid desiccation) and slow germination (and slow desiccation).

Across the Quercus species, the relative level of seed desiccation sensitivity, which we predicted to be important for reducing the risk of drying related mortality, was independent of climate. For desiccation‐sensitive seeds this suggests a more diverse range of strategies for minimizing desiccation risk than reported previously.
Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6‐phosphate synthase1 (tps1) mutant
Authors: Zacharaki Vasiliki , Ponnu Jathish , Crepin Nathalie , Langenecker Tobias , Hagmann Jörg , Skorzinski Noemi , Musialak‐Lange Magdalena , Wahl Vanessa , Rolland Filip , Schmid Markus 
Published: March 2022

Summary

Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6‐PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6‐phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo‐lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON‐FERMENTING1 RELATED KINASE1 (SnRK1).

Here, we explored the role of SnRK1 in T6P‐mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches.

We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10.

Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss‐of‐function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.
A Focused review on the pathophysiology of post‐inflammatory hyperpigmentation
Authors: Maghfour Jalal , Olayinka Jadesola , Hamzavi Iltefat H. , Mohammad Tasneem F. 
Published: March 2022

AbstractPost‐inflammatory hyperpigmentation (PIH) is one of the most common disorders of acquired hyperpigmentation. It often develops following cutaneous inflammation and is triggered by various stimuli, from inflammatory and autoimmune conditions to iatrogenic causes and mechanical injuries. While it is well established that an increase in melanin production and distribution within the epidermis and dermis is a hallmark feature of this condition, the exact mechanisms underlying PIH are not completely understood. This article aims to review the current evidence on the pathophysiology of PIH as the cellular and molecular mechanism of PIH represents a promising avenue for the development of novel, targeted therapies.
Volume flexibility at responsive suppliers in reshoring decisions: Analysis of a dual sourcing inventory model
Authors: Gijsbrechts Joren , Boute Robert N. , Disney Stephen M. , Van Mieghem Jan A. 
Published: March 2022

AbstractWe investigate how volume flexibility, defined by a sourcing cost premium beyond a base capacity, at a local responsive supplier impacts the decision to reshore supply. The buyer also has access to a remote supplier that is cheaper with no restrictions on volume flexibility. We show that with unit lead time difference between both suppliers, the optimal dual sourcing policy is a modified dual base‐stock policy with three base‐stock levels , , and . The replenishment orders are generated by first placing a base order from the fast supplier of at most units to raise the inventory position to , if that is possible. After this base order, if the adjusted inventory position is still below , additional units are ordered from the fast supplier at an overtime premium to reach . Finally, if the adjusted inventory position is below , an order from the slow supplier is placed to bring the final inventory position to . Surprisingly, in contrast to single sourcing with limited volume flexibility, a more complex dual sourcing model often results in a “simpler” policy that replaces demand in each period. The latter allows analytical insights into the sourcing split between the responsive and the remote supplier. Our analysis shows how increased volume flexibility at the responsive supplier promotes the decision to reshore operations and effectively serves as a cost benefit. It also shows how investing in base capacity or additional volume flexibility act as strategic substitutes.
A model for wind farm management with option interactions
Authors: Bensoussan Alain , Chevalier‐Roignant Benoît , Rivera Alejandro 
Published: March 2022

A renewable energy site can expand its power generation capacity by an endogenous amount but may also want to shut down to save on fixed operating costs and interest payments if the market prospects deteriorate. We model such circumstances and derive managerial implications that help us explain real‐world conundrums, illustrating the intricate interactions between the operational decision to build up capacity and the financial decision to exit an industry. Shutting down may be delayed in the hope of expanding capacity upon recovery; an expansion may also be delayed in the presence of a valuable exit option. Numerical extensions provide further managerial insights. In particular, the presence of fixed or proportional financing costs may lead the firm to delay its expansion decision, but the scale of investment will only be affected by proportional costs. If herding behavior causes equipment prices to increase (respectively, decrease) when electricity prices are high (respectively, low), managers should invest earlier (respectively, later) and more (respectively, less) while equipment prices are low (respectively, high). Furthermore, although volume swings (due to capacity decommissionings and expansions) are marked in a homogeneous industry (when the default and expansion thresholds are reached), heterogeneity in the population of wind farms smooths out such effects.
Genome‐wide identification of invertases in Fabaceae, focusing on transcriptional regulation of Pisum sativum invertases in seed subjected to drought
Authors: Morin Amélie , Kadi Fadia , Porcheron Benoit , Vriet Cécile , Maurousset Laurence , Lemoine Rémi , Pourtau Nathalie , Doidy Joan 
Published: March 2022

AbstractInvertases are key enzymes for carbon metabolism, cleaving sucrose into energy‐rich and signaling metabolites, glucose and fructose. Invertases play pivotal roles in development and stress response, determining yield and quality of seed production. In this context, the repertoire of invertase gene families is critically scarce in legumes. Here, we performed a systematic search for invertase families in 16 Fabaceae genomes. For instance, we identified 19 invertase genes in the model plant Medicago and 17 accessions in the agronomic crop Pisum sativum. Our comprehensive phylogenetic analysis sets a milestone for the scientific community as we propose a new nomenclature to correctly name plant invertases. Thus, neutral invertases were classified into four clades of cytosolic invertase (CINV). Acid invertases were classified into two cell wall invertase clades (CWINV) and two vacuolar invertase clades (VINV). Then, we explored transcriptional regulation of the pea invertase family, focusing on seed development and water stress. Invertase expression decreased sharply from embryogenesis to seed‐filling stages, consistent with higher sucrose and lower monosaccharide contents. The vacuolar invertase PsVINV1.1 clearly marked the transition between both developmental stages. We hypothesize that the predominantly expressed cell wall invertase, PsCWINV1.2, may drive sucrose unloading towards developing seeds. The same candidates, PsVINV1.1 and PsCWINV1.2, were also regulated by water deficit during embryonic stage. We suggest that PsVINV1.1 along with vacuolar sugar transporters maintain cellular osmotic pressure and PsCWINV1.2 control hexose provision, thereby ensuring embryo survival in drought conditions. Altogether, our findings provide novel insights into the regulation of plant carbon metabolism in a challenging environment.
Soil organic matter storage in temperate lowland arable, grassland and woodland topsoil and subsoil
Authors: Antony Dedy , Collins Chris D. , Clark Joanna M. , Sizmur Tom 
Published: March 2022

AbstractSoils are the largest terrestrial pool of organic carbon, with up to 50% of soil organic carbon (SOC) stored below 30 cm. Knowledge of the impact of land use on the mechanisms by which SOC is stored in subsoils is critical to developing and delivering strategies to mitigate climate change. We characterized SOC under arable, grassland, and deciduous woodland land uses in lowland England to determine how land use affects the mechanisms by which topsoil and subsoil SOC are protected. Soil organic matter (SOM) physical fractionation and ammonium oxalate extractable Al, Fe and Mn were analysed to elucidate protection mechanisms. Results revealed that the mineral‐free particulate organic matter (fPOM) fraction was significantly greater in both the topsoil and subsoil under woodland than under grassland or arable. The mineral‐associated organic carbon (MinOC) fraction was proportionally greater in the subsoil compared with topsoil under all land uses, with arable >grassland > woodland. These findings indicate that land use affects the extent to which SOC is protected, with woodlands containing a higher proportion of carbon that has less protection from decomposition. Subsoil SOC is protected from decomposition by organo‐mineral interactions with amorphous Al, Fe and Mn, and may be susceptible to future pH shifts as a result of land use change. This study highlights the need to consider the impact of land use change on SOC, given policy and public interest in woodland planting for climate change mitigation.
Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility
Authors: Gong Wenfang , Xiao Shixin , Wang Linkai , Liao Zhenyang , Chang Yihong , Mo Wenjuan , Hu Guanxing , Li Wenying , Zhao Guang , Zhu Huaguo , Hu Xiaoming , Ji Ke , Xiang Xiaofeng , Song Qiling , Yuan Deyi , Jin Shuangxia , Zhang Lin 
Published: March 2022

SUMMARYThe section Oleifera (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome‐scale genome of the sect. Oleifera using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. Camellia lanceoleosa underwent a whole‐genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of C. lanceoleosa and Camellia sinensis (approx. 6–7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in C. lanceoleosa were significantly enriched in oil biosynthesis, and the expansion of homomeric acetyl‐coenzyme A carboxylase (ACCase) genes and the seed‐biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde‐3‐phosphate dehydrogenase and stearoyl‐ACP desaturase could be of primary importance for the high oil and oleic acid content found in C. lanceoleosa. Theanine and catechins were present in the leaves of C. lanceoleosa. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM‐dependent N‐methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late‐acting self‐incompatibility of C. lanceoleosa is likely to have favoured a novel mechanism co‐occurring with gametophytic self‐incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. Oleifera.
Functional divergence of a pair of Arabidopsis phospho‐base methyltransferases, PMT1 and PMT3, conferred by distinct N‐terminal sequences
Authors: Liu Yu‐chi , Tan Yue‐Rong , Chang Chin‐Wen , Nguyen Van C. , Kanehara Kazue , Kobayashi Koichi , Nakamura Yuki 
Published: March 2022

SUMMARYIn seed plants, phospho‐base N‐methyltransferase (PMT) catalyzes a key step in the biosynthesis pathway of phosphatidylcholine (PC), the most abundant phospholipid class. Arabidopsis thaliana possesses three copies of PMT, with PMT1 and PMT3 play a primary role because the pmt1 pmt3 double mutant shows considerably reduced PC content with a pale seedling phenotype. Although the function of PMT1 and PMT3 may be redundant because neither of the parental single mutants showed a similar mutant phenotype, major developmental defects and possible functional divergence of these PMTs underlying the pale pmt1 pmt3 seedling phenotype are unknown. Here, we show the major developmental defect of the pale seedlings in xylem of the hypocotyl with partial impairments in chloroplast development and photosynthetic activity in leaves. Although PMT1 and PMT3 are localized at the endoplasmic reticulum, their tissue‐specific expression pattern was distinct in hypocotyls and roots. Intriguingly, the function of PMT3 but not PMT1 requires its characteristic N‐terminal sequence in addition to the promoter because truncation of the N‐terminal sequence of PMT3 or substitution with PMT1 driven by the PMT3 promoter failed to rescue the pale pmt1 pmt3 seedling phenotype. Thus, PMT3 function requires the N‐terminal sequence in addition to its promoter, whereas the PMT1 function is defined by the promoter.
Digitising SU(2) gauge fields and the freezing transition
Authors: Hartung Tobias , Jakobs Timo , Jansen Karl , Ostmeyer Johann , Urbach Carsten 
Published: March 2022

AbstractEfficient discretisations of gauge groups are crucial with the long term perspective of using tensor networks or quantum computers for lattice gauge theory simulations. For any Lie group other than U(1), however, there is no class of asymptotically dense discrete subgroups. Therefore, discretisations limited to subgroups are bound to lead to a freezing of Monte Carlo simulations at weak couplings, necessitating alternative partitionings without a group structure. In this work we provide a comprehensive analysis of this freezing for all discrete subgroups of SU(2) and different classes of asymptotically dense subsets. We find that an appropriate choice of the subset allows unfrozen simulations for arbitrary couplings, though one has to be careful with varying weights of unevenly distributed points. A generalised version of the Fibonacci spiral appears to be particularly efficient and close to optimal.
Evaluation of Wide Corneal Epithelial Remodeling after Small Incision Lenticule Extraction (SMILE) with Wide-Field Optical Coherence Tomography
Authors: Ye Yiming , Chen Pei , Yu Na , Wan Linxi , Lan Min , Zheng Hua , Yu Keming 
Published: March 2022

Purpose. This study aims to assess the corneal epithelial remodeling within a 9 mm diameter zone induced by small incision lenticule extraction (SMILE) and evaluate its relationship with the refractive outcomes. Methods. A total of 64 eyes of 64 patients were included. Wide-field optical coherence tomography (OCT) was used to measure the epithelial thickness (ET) across a 9 mm diameter area, preoperatively, and after one day, one week, one month, three months, and six months postoperatively. The ET changes were compared among the different time points and analyzed zones. Results. The ET increases from one week to three months and stabilized from three months to six months. Compared to the preoperative values, the mean ET changes at six months in central (2 mm), paracentral (2–5 mm), mid-peripheral (5–7 mm), and peripheral (7–9 mm) zones were 4.37, 4.36, 1.61, and −1.59 μm, respectively. The correlation between the epithelial thickening and the amount of myopia correction was positive in central (

P

= 0.001) and paracentral zones (

P

< 0.001) and negative in peripheral zone (

P

= 0.006). The intended diameter of the optical zone was negatively related to epithelial hyperplasia in the central (

P

= 0.020) and paracentral zone (

P

= 0.006), and the correlation was positive in the mid-peripheral zone (

P

= 0.001). The epithelial thickening of central zone (

P

= 0.012) and the difference of mean ET between central and paracentral zone (

P

= 0.020) were negatively related to the spherical equivalent at six months. Conclusion. An asymmetric lenticule-like pattern of epithelial remodeling occurred in 9 mm diameter cornea at six months after myopic SMILE. The epithelial remodeling may affect the refractive outcomes of SMILE.
Abstract 175: Atrial Fibrillation in the USF Resident Clinics: Quality-Driven Medical Therapy
Authors: Sadic Edin 
Published: March 2022

Patients with atrial fibrillation (afib) have a high rate of serious complications including stroke and decompensated heart failure. While patients with afib are five times more likely to suffer a stroke in their lifetime than the general population, this risk can be reduced by 64% with appropriate anticoagulation using warfarin or approved novel oral anticoagulants (NOACs). Reducing the morbidity and mortality from excess strokes is a common interest nationwide due to unsustainable healthcare costs, increasing human resource gaps in medicine, and payment reforms that hold physicians and healthcare organizations financially accountable for having poor outcomes. Our project aims to investigate the success in achieving appropriate anticoagulation therapy for afib patients in the University of South Florida (USF) Internal Medicine resident clinics. Our goal is to achieve a 90% success rate for both linkage to follow-up and anticoagulation.
Our project identified all patients in the USF Internal Medicine clinics greater than 18 years of age who were discharged from Tampa General Hospital (TGH) between January 1, 2016 and December 31, 2016 and are diagnosed with atrial fibrillation. It investigated the percentage of eligible patients prescribed an anticoagulant (eligibility was determined by CHADSVASC criteria), as well as the percentage of patients who returned for follow-up at least once post-discharge.
Our query identified 49 patients with atrial fibrillation who met our search criteria. Of these, 28 (57%) were appropriately anticoagulated as per CHADSVASC criteria. Unfortunately, 21 patients (43%) who should have been on anticoagulation were not. Twelve patients (24%) were either lost to follow-up or were unavailable to contact. Eight (16%) were deceased since starting our project. Per chart review, zero deaths were related to afib or bleeding.
Our study revealed a significant gap in care for atrial fibrillation patients at USF resident clinics. With just over half being appropriately anticoagulated, we implemented a bundle of quality improvement methodologies. We reached out to our patients and scheduled 29 follow-up appointments in the coming months to discuss their anticoagulation. We created a best practices reminder in the electronic medical record to alert prescribers if a patient has afib in their problem list but does not have an anticoagulant in their medication list. We also plan to review the registry of afib patients yearly to schedule appointments for the patients who have no anticoagulation prescriptions. This way, we will catch patients who are newly diagnosed within the past year or those who have had a transition of care and may have had their medication inadvertently discontinued. We hope these interventions will move us closer to our goals of 90% linkage to care and anticoagulation.