bluuebunny/crossref_metadata_2025_split huggingface dataset:
The will to consensus
Authors: Kwesi Richmond 
Published: April 2024

AbstractIn a democracy, when a group of deliberators have a set of differing (and contrary) views and beliefs about a particular policy or action, p, a recommended course of action is for them to pursue, and ultimately reach, a consensus on p. The pursuit of consensus allows deliberators to ‘reach over the aisle’ in accommodating dissenting views through rational dialogue until a consensual agreement is reached by all the deliberators. What fuels this pursuit of consensus is the ‘will to consensus’—a ‘frame of mind’ or a ‘disposition’ to resolve disagreements into a consensus. In this paper, I will raise some conceptual problems with positing a ‘will to consensus’ that is prior to, and supervenes on, the rational discussion of deliberators. Instead of a ‘will to consensus’, democratic theorists should be content with the minimal claim of a ‘will to dialogue’.
Transcriptional dynamics in source‐sink tissues identifies molecular factors regulating the corm development process in saffron (Crocus sativus L.)
Authors: Jose‐Santhi Joel , Sheikh Firdous Rasool , Kalia Diksha , Sood Riya , Kumar Ravi , Acharya Vishal , Singh Rajesh Kumar 
Published: April 2024

AbstractAimsGeophytic plants have evolved to develop underground storage organs (USO) in the active growing season to withstand harsh environments as well as to coordinate growth and reproduction when conditions are favourable. Saffron is an autumn flowering geophyte and an expensive spice crop restricted to certain geographical locations in the world. Saffron, being sterile, does not produce seeds and thus propagates only through corms, the quality of which determines its yield. Corm development in saffron is unexplored and the underlying molecular mechanism is still elusive. In this study, we performed an extensive characterisation of the transcriptional dynamics in the source (leaf) and sink (corm) tissues during corm development in saffron.Key resultsVia morphological and transcriptome studies, we identified molecular factors regulating corm development process in saffron, which defined corm development into three stages: the initiation stage demonstrates enhanced vegetative growth aboveground and swelling of shoot base belowground due to active cell division & carbohydrate storage; the bulking stage comprises of increased source and sink strength, active photosynthesis, circadian gating and starch accumulation; the maturation stage represents reduced source and sink strength, lowered photosynthesis, sugar transport, starch synthesis and cell cycle arrest.UtilityThe global view of transcriptional changes in source and sink identifies similar and new molecular factors involved in the saffron corm development process compared to USO formation in other geophytes and provides a valuable resource for dissecting the molecular network underlying the corm development. We propose a hypothetical model based on data analysis, of how molecular factors via environmental cues can regulate the corm development process in saffron.
Transcriptome analysis reveals molecular mechanisms underlying chloroplast biogenesis in albino Agave angustifolia plantlets
Authors: Andrade‐Marcial Mauricio , Pacheco‐Arjona Ramón , Hernández‐Castellano Sara , Che‐Aguilar Ligia , De‐la‐Peña Clelia 
Published: April 2024

AbstractAlbino plants display partial or complete loss of photosynthetic pigments and defective thylakoid membrane development, consequently impairing plastid function and development. These distinctive attributes render albino plants excellent models for investigating chloroplast biogenesis. Despite their potential, limited exploration has been conducted regarding the molecular alterations underlying these phenotypes, extending beyond photosynthetic metabolism. In this study, we present a novel de novo transcriptome assembly of an albino somaclonal variant of Agave angustifolia Haw., which spontaneously emerged during the micropropagation of green plantlets. Additionally, RT‐qPCR analysis was employed to validate the expression of genes associated with chloroplast biogenesis, and plastome copy numbers were quantified. This research aims to gain insight into the molecular disruptions affecting chloroplast development and ascertain whether the expression of critical genes involved in plastid development and differentiation is compromised in albino tissues of A. angustifolia. Our transcriptomic findings suggest that albino Agave plastids exhibit high proliferation, activation of the protein import machinery, altered transcription directed by PEP and NEP, dysregulation of plastome expression genes, reduced expression of photosynthesis‐associated nuclear genes, disruption in the tetrapyrrole and carotenoid biosynthesis pathway, alterations in the plastid ribosome, and an increased number of plastome copies, among other alterations.
Patient experiences using public and private insurance coverage for abortion in Illinois: Implementation successes and remaining gaps
Authors: Quasebarth Madeline , Boesche Madeleine , Turner Tecora , Moore Amy , Young Danielle , Stulberg Debra , Hasselbacher Lee 
Published: April 2024

AbstractContextInsurance coverage for abortion in states where care remains legal can alleviate financial burdens for patients and increase access. Recent policy changes in Illinois required Medicaid and some private insurance plans to cover abortion care. This study explores policy implementation from the perspectives of patients using their insurance to obtain early abortion care.MethodologyBetween July 2021 and February 2022, we interviewed Illinois residents who recently sought abortion care at ≤11 weeks of pregnancy. We also interviewed nine key informants with experience providing or billing for abortion or supporting insurance policy implementation in Illinois. We coded interview transcripts in Dedoose and developed code summaries to identify salient themes across interviews.ResultsMost participants insured by Illinois Medicaid or eligible for enrollment received full coverage for their abortions; most with private insurance did not and faced challenges learning about coverage status. Some opted not to use insurance, often citing privacy concerns. Participants who benefited from abortion coverage expressed relief, gave examples of other financial challenges they could prioritize, and described feeling in control of their abortion experience. Those without coverage described feeling stressed, uncertain, and constrained in their decision‐making.ConclusionWhen abortion was fully covered by insurance, it reduced financial burdens and enhanced reproductive autonomy. Illinois Medicaid policy—with seamless enrollment options and appropriate reimbursement rates—offers a model for improving abortion access in other states. Further investigation is needed to determine compliance among private insurance companies and increase transparency.
Low rate of surgical site infections after liver transplantation: A 5‐year retrospective cohort study
Authors: Tun Taryar , Marinelli Tina , Liu Ken , Strasser Simone I , Crawford Michael , Patanwala Asad E. 
Published: April 2024

AbstractBackgroundSurgical site infection (SSI) after liver transplant (LT) is common, but no studies have been conducted in Australia. The purpose of this study was to determine the proportion of patients who developed an SSI post‐LT in Australia's largest LT unit.MethodsThis was a single‐center retrospective cohort study. We included all LT recipients who were aged 18 years or more and received their transplant between March 1, 2018 and April 1, 2023. The primary outcome was to determine the proportion of LT recipients who developed an SSI within 30 days of transplantation.ResultsThere were 404 LTs performed during the study period, and 375 met inclusion criteria. Of these, 8% (n = 31/375) developed an SSI and were classified as superficial (3%, n = 12/375) or deep/organ space (5%, n = 19/375). The most common antibiotics used for prophylaxis were amoxicillin/clavulanate (75%, n = 281/375), followed by piperacillin/tazobactam (17%, n = 62/375). Independent risk factors associated with the development of SSI were Roux‐en‐Y hepaticojejunostomy (aOR 3.16, 95% CI 1.17–8.28, p = .02), operative time (per 60‐min increment) (aOR 1.23, 95% CI 1.02–1.48), and re‐operation (aOR 4.16, 95% CI 1.81–9.58, p < .01). Type of antibiotic received perioperatively was not significantly associated with SSI.ConclusionSSI occurred in 8% of LT recipients and was predominantly related to operation‐related factors rather than patient‐ or antibiotic‐related factors.
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The BTB‐BACK‐TAZ domain protein MdBT2 reduces drought resistance by weakening the positive regulatory effect of MdHDZ27 on apple drought tolerance via ubiquitination
Authors: Zhang Quan‐Yan , Ma Chang‐Ning , Gu Kai‐Di , Wang Jia‐Hui , Yu Jian‐Qiang , Liu Bo , Wang Yun , He Jun‐Xia , Hu Da‐Gang , Sun Quan 
Published: April 2024

SUMMARYDrought stress is one of the dominating challenges to the growth and productivity in crop plants. Elucidating the molecular mechanisms of plants responses to drought stress is fundamental to improve fruit quality. However, such molecular mechanisms are poorly understood in apple (Malus domestica Borkh.). In this study, we explored that the BTB‐BACK‐TAZ protein, MdBT2, negatively modulates the drought tolerance of apple plantlets. Moreover, we identified a novel Homeodomain‐leucine zipper (HD‐Zip) transcription factor, MdHDZ27, using a yeast two‐hybrid (Y2H) screen with MdBT2 as the bait. Overexpression of MdHDZ27 in apple plantlets, calli, and tomato plantlets enhanced their drought tolerance by promoting the expression of drought tolerance‐related genes [responsive to dehydration 29A (MdRD29A) and MdRD29B]. Biochemical analyses demonstrated that MdHDZ27 directly binds to and activates the promoters of MdRD29A and MdRD29B. Furthermore, in vitro and in vivo assays indicate that MdBT2 interacts with and ubiquitinates MdHDZ27, via the ubiquitin/26S proteasome pathway. This ubiquitination results in the degradation of MdHDZ27 and weakens the transcriptional activation of MdHDZ27 on MdRD29A and MdRD29B. Finally, a series of transgenic analyses in apple plantlets further clarified the role of the relationship between MdBT2 and MdHDZ27, as well as the effect of their interaction on drought resistance in apple plantlets. Collectively, our findings reveal a novel mechanism by which the MdBT2‐MdHDZ27 regulatory module controls drought tolerance, which is of great significance for enhancing the drought resistance of apple and other plants.
Haplotype‐resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation
Authors: Li Fangping , Hou Zhuangwei , Xu Shiqiang , Han Danlu , Li Bin , Hu Haifei , Liu Jieying , Cai Shike , Gan Zhenpeng , Gu Yan , Zhang Xiufeng , Zhou Xiaofan , Wang Shaokui , Zhao Junliang , Mei Yu , Zhang Jisen , Wang Zefu , Wang Jihua 
Published: April 2024

SUMMARYThe Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome‐scale haplotype‐resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor‐AA and Ancestor‐BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high‐quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.
A 3‐step method for preparing cryopreserved samples of apheresis products for post‐thaw analysis yields a higher percentage of viable cells
Authors: Strasburg Dustin J. , Sterner Rosalie M. , Va Sildane , Jacob Eapen K. , DiGuardo Margaret A. 
Published: April 2024

AbstractBackgroundStandard flow cytometry protocols for CD34+ cell enumeration designed for fresh samples are not appropriate for cryopreserved products. Special protocols have been developed to remove the cryoprotectant by quickly washing a freshly thawed sample. Exposing cells to a large volume of hypotonic solution and subsequent washing process was hypothesized to cause lab‐induced cell death. Moreover, standard gating strategies must be altered to avoid reporting falsely high viabilities.Study Design and MethodsWe developed a novel method whereby thawed samples were diluted step‐wise to 1:2 by 3 additions of 1/3 sample volume using 1% Human Albumin in Dextran 40 (10% Low Molecular Weight Dextran in 0.9% NaCl) separated by 5 min between each addition. An additional 1:10 dilution was required to obtain a desired cell concentration for flow cytometry testing resulting in a 1:20 dilution.ResultsTwenty samples were tested simultaneously in a method comparison; the new method demonstrated significant increases in mean cell viabilities for white blood cells, hematopoietic progenitor cells, and T cells as well as reduced standard deviations for each parameter.DiscussionSlow, step‐wise dilutions of freshly thawed samples of cryopreserved apheresis products to 1:20 yielded higher and more precise viability measurements compared to quickly washing samples to remove DMSO.
Three‐dimensional magnetic resonance cholangiography is superior to two‐dimensional single‐shot magnetic resonance cholangiography for visualization and image quality of the feline and canine biliary tract: A postmortem study
Authors: Rahmani Vahideh , Peltonen Juha , Hmelnikov Dmitri , Uosyte Raimonda , Männikkö Sofia , Spillmann Thomas , Ruohoniemi Mirja 
Published: April 2024

AbstractMagnetic resonance cholangiography (MRC) is an established diagnostic tool for noninvasive assessment of the biliary tract in humans. It has also been found to be feasible in companion animals, but no published studies have compared MRC sequences in veterinary medicine. The present study is part of a prospective, observational, analytical investigation on MR cholangiopancreatography performed on the donated bodies of 12 cats and eight dogs. The main aim of this study was to compare the images of 2D‐SSh‐TSE‐MRC and 3D‐TSE‐MRC sequences for visualization and image quality of the feline and canine biliary tract. Both sequences are T2‐weighted and noncontrast. Three independent readers scored the visibility of four segments of the biliary tract, namely the gallbladder (GB), cystic duct, common bile duct (CBD), and extrahepatic ducts, and the image quality of the two MRC sequences using five‐point Likert scales. Wilcoxon signed‐rank test was used to compare the scores between the MRC sequences separately for cats and dogs. Inter‐ and intraobserver agreements were measured using Gwet's AC2 with linear weighting. The 3D‐TSE‐MRC images were scored significantly higher than the 2D‐SSh‐TSE‐MRC for both visibility and image quality (P < .001–.016 for cats, P = .008–.031 for dogs); the only exception was GB in dogs. In both cats and dogs, interobserver agreement for segment visibility and image quality ranged from slight to substantial in 2D‐SSh‐TSE‐MRC and from poor to almost perfect in 3D‐TSE‐MRC. Most of the assessments (73% for segment visibility and 66% for image quality) had substantial to almost perfect intraobserver agreement. Findings from the current study support the use of 3D‐TSE‐MRC over 2D‐SSh‐TSE‐MRC for evaluation of the feline and canine biliary tract, but further studies on live animals are warranted.
Total Cuntz semigroup, extension, and Elliott Conjecture with real rank zero
Authors: An Qingnan , Liu Zhichao 
Published: April 2024

AbstractIn this paper, we exhibit two unital, separable, nuclear ‐algebras of stable rank one and real rank zero with the same ordered scaled total K‐theory, but they are not isomorphic with each other, which forms a counterexample to the Elliott Classification Conjecture for real rank zero setting. Thus, we introduce an additional normal condition and give a classification result in terms of the total K‐theory. For the general setting, with a new invariant, the total Cuntz semigroup [2], we classify a large class of ‐algebras obtained from extensions. The total Cuntz semigroup, which distinguishes the algebras of our counterexample, could possibly classify all the ‐algebras of stable rank one and real rank zero.
Continuum Growth Mechanics: Reconciling Two Common Frameworks
Authors: Ateshian Gerard A. , LaBelle Steven A. , Weiss Jeffrey A. 
Published: April 2024

Abstract
The objective of this study was to investigate whether the two most common growth mechanics modeling frameworks, the constrained-mixture growth model and the kinematic growth model, could be reconciled mathematically. The purpose of this effort was to provide practical guidelines for potential users of these modeling frameworks. Results showed that the kinematic growth model is mathematically consistent with a special form of the constrained-mixture growth model, where only one generation of a growing solid exists at any given time, overturning its entire solid mass at each instant of growth in order to adopt the reference configuration dictated by the growth deformation. The thermodynamics of the kinematic growth model, along with the specialized constrained-mixture growth model, requires a cellular supply of chemical energy to allow deposition of solid mass under a stressed state. A back-of-the-envelope calculation shows that the amount of chemical energy required to sustain biological growth under these models is negligibly small, when compared to the amount of energy normally consumed daily by the human body. In conclusion, this study successfully reconciled the two most popular growth theories for biological growth and explained the special circumstances under which the constrained-mixture growth model reduces to the kinematic growth model.
Effect modification of dosing strategy (AUC or trough) on AKI associated with vancomycin in combination with piperacillin/tazobactam or cefepime and meropenem
Authors: Mefford Breanne , Wallace Katie L. , Donaldson J. Chris , Bissell Turpin Brittany D. , Sen Parijat , Schadler Aric D. , Liu Lucas J. , Thompson Bastin Melissa L. 
Published: April 2024

ABSTRACT

Piperacillin-tazobactam (TZP), cefepime (FEP), or meropenem (MEM) and vancomycin (VAN) are commonly used in combination for sepsis. Studies have shown an increased risk of acute kidney injury (AKI) with TZP and VAN compared to FEP or MEM. VAN guidelines recommend area under the curve (AUC) monitoring over trough (Tr) to minimize the risk of AKI. We investigated the association of AKI and MAKE-30 with the two VAN monitoring strategies when used in combination with TZP or FEP/MEM. Adult patients between 2015 and 2019 with VAN > 72 hours were included. Patients with AKI prior to or within 48 hours of VAN or baseline CrCl of ≤30 mL/min were excluded. Four cohorts were defined: FEP/MEM/Tr, FEP/MEM/AUC, TZP/Tr, and TZP/AUC. A Cox Proportional Hazard Model was used to model AKI as a function of the incidence rate of at-risk days, testing monitoring strategy as a treatment effect modification. Multivariable logistic regression was used to model MAKE-30. Overall incidence of AKI was 18.6%; FEP/MEM/Tr = 115 (14.6%), FEP/MEM/AUC = 52 (14.9%), TZP/Tr = 189 (26%), and TZP/AUC = 96 (17.1%) (
P
< 0.001). Both drug group [(TZP;
P
= 0.0085)] and monitoring strategy [(Tr;
P
= 0.0007)] were highly associated with the development of AKI; however, the effect was not modified with interaction term [(TZP*Tr); 0.085)]. The odds of developing MAKE-30 were not different between any group and FEP/MEM/AUC. The effect of VAN/TZP on the development of AKI was not modified by the VAN monitoring strategy (AUC vs trough). MAKE-30 outcomes were not different among the four cohorts.
The global nitrogen regulator GlnR is a direct transcriptional repressor of the key gluconeogenic gene
pckA
in actinomycetes
Authors: Liu Xinqiang , Wang Xinyun , Shao Zhihui , Dang Jun , Wang Wei , Liu Chaoyue , Wang Jin , Yuan Hua , Zhao Guoping 
Published: April 2024

ABSTRACT

In most actinomycetes, GlnR governs both nitrogen and non-nitrogen metabolisms (e.g., carbon, phosphate, and secondary metabolisms). Although GlnR has been recognized as a global regulator, its regulatory role in central carbon metabolism [e.g., glycolysis, gluconeogenesis, and the tricarboxylic acid (TCA) cycle] is largely unknown. In this study, we characterized GlnR as a direct transcriptional repressor of the
pckA
gene that encodes phosphoenolpyruvate carboxykinase, catalyzing the conversion of the TCA cycle intermediate oxaloacetate to phosphoenolpyruvate, a key step in gluconeogenesis. Through the transcriptomic and quantitative real-time PCR analyses, we first showed that the
pckA
transcription was upregulated in the
glnR
null mutant of
Amycolatopsis mediterranei
. Next, we proved that the
pckA
gene was essential for
A. mediterranei
gluconeogenesis when the TCA cycle intermediate was used as a sole carbon source. Furthermore, with the employment of the electrophoretic mobility shift assay and DNase I footprinting assay, we revealed that GlnR was able to specifically bind to the
pckA
promoter region from both
A. mediterranei
and two other representative actinomycetes (
Streptomyces coelicolor
and
Mycobacterium smegmatis
). Therefore, our data suggest that GlnR may repress
pckA
transcription in actinomycetes, which highlights the global regulatory role of GlnR in both nitrogen and central carbon metabolisms in response to environmental nutrient stresses.

IMPORTANCE

The GlnR regulator of actinomycetes controls nitrogen metabolism genes and many other genes involved in carbon, phosphate, and secondary metabolisms. Currently, the known GlnR-regulated genes in carbon metabolism are involved in the transport of carbon sources, the assimilation of short-chain fatty acid, and the 2-methylcitrate cycle, although little is known about the relationship between GlnR and the TCA cycle and gluconeogenesis. Here, based on the biochemical and genetic results, we identified GlnR as a direct transcriptional repressor of
pckA
, the gene that encodes phosphoenolpyruvate carboxykinase, a key enzyme for gluconeogenesis, thus highlighting that GlnR plays a central and complex role for dynamic orchestration of cellular carbon, nitrogen, and phosphate fluxes and bioactive secondary metabolites in actinomycetes to adapt to changing surroundings.