bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substantive Legitimate Expectations: Re-shaping the Boundaries of Judicial Reach in Public Law Remedies in Commonwealth Jurisdictions
Authors: Maripe Bugalo 
Published: November 2024

Abstract
A legitimate expectation is a state of affairs established in a court of law, usually in proceedings for judicial review, in which a public authority that has made a promise, or has acted in terms of a regular practice, as to the conduct of public affairs, is held to the promise or practice, and can only be allowed to resile from the promise, or deviate from the practice, if it has accorded a beneficiary of the promise or practice, a prior hearing. Thus, the presence of a legitimate expectation imports an obligation on the part of an authority to accord a hearing to affected parties, the obligation to observe the audi alteram partem rule (simply the audi rule). For a long time, the only favorable result for a claimant of a legitimate expectation was the setting aside of the decision of the public authority on procedural grounds. This is what is described in this Article as the orthodox approach. With time courts in some countries, notably England, began enforcing the promises and practices, in the sense of granting relief in line with the legitimate expectations, thus granting substantive outcomes. This came amid some spirited reluctance, as it was thought that this was against principle. The main objection was that granting such relief amounted to usurpation of executive power and was judicial overreach into an area reserved for the executive, and therefore breaking the boundaries of separation of powers. Notwithstanding these objections, courts have continued to grant substantive relief.
This Article argues that granting substantive outcomes is the proper province of the judiciary and does not amount to judicial overreach, and that substantive outcomes in many cases provide appropriate protection to individuals in cases of broken promises and disappointed expectations. It will be argued that the courts in many countries have in the past, without saying so, in fact granted substantive relief. It is time that an express exposition be made to the effect that substantive relief in cases of proved legitimate expectations is available as a remedy, for the guidance of public administrators and the public alike.
Longitudinal Patterns and Predictors of Cognitive Impairment Classification Stability
Authors: McDowell Cynthia , Tamburri Nicholas , Gawryluk Jodie R , MacDonald Stuart W S 
Published: November 2024

Abstract

Objective
Classifications such as Cognitive Impairment, No Dementia (CIND) are thought to represent the transitory, pre-clinical phase of dementia. However, increasing research demonstrates that CIND represents a nonlinear, unstable entity that does not always lead to imminent dementia. The present study utilizes a longitudinal repeated measures design to gain a thorough understanding of CIND classification stability patterns and identify predictors of future stability. The objectives were to i) explore patterns of longitudinal stability in cognitive status across multiple assessments and ii) investigate whether select baseline variables could predict 6-year CIND stability patterns.

Method
Participants (N = 259) included older adults (aged 65–90 years) from Project MIND, a six-year longitudinal repeated measures design in which participants were classified as either normal cognition (NC) or CIND at each annual assessment. A latent transition analysis approach was adapted in order to identify and characterize transitions in CIND status across annual assessments. Participants were classified as either Stable NC, Stable CIND, Progressers, Reverters, or Fluctuaters. Multinomial logistic regression was employed to test whether baseline predictors were associated with cognitive status stability patterns.

Results
The sample demonstrated high rates of reversion and fluctuation in CIND status across annual assessments. Additionally, premorbid IQ and CIND severity (i.e., single vs. multi-domain impairment) at baseline were significantly associated with select stability outcomes.

Conclusions
CIND status was unstable for several years following baseline assessment and cognitive reserve may delay or protect against demonstrable cognitive impairment. Further, consideration of cognitive impairment severity at the time of initial classification may improve CIND classifications.
Microbiome analysis of monarch butterflies reveals effects of development and diet
Authors: Sanaei Ehsan , Chavez Joselyne , Harris Erica V , Alcaide Tiffanie Y , Baffour-Addo Keisha , Bugay Mahal J , Adams Kandis L , Zelaya Anna , de Roode Jacobus C , Gerardo Nicole M 
Published: November 2024

Abstract
Diet profoundly influences the composition of an animal’s microbiome, especially in holometabolous insects, offering a valuable model to explore the impact of diet on gut microbiome dynamics throughout metamorphosis. Here, we use monarch butterflies (Danaus plexippus), specialist herbivores that feed as larvae on many species of chemically well-defined milkweed plants (Asclepias sp.), to investigate the impacts of development and diet on the composition of the gut microbial community. While a few microbial taxa are conserved across life stages of monarchs, the microbiome appears to be highly dynamic throughout the life cycle. Microbial diversity gradually diminishes throughout the larval instars, ultimately reaching its lowest point during the pupal stage and then recovering again in the adult stage. The microbial composition then undergoes a substantial shift upon the transition from pupa to adult, with female adults having significantly different microbial communities than the eggs that they lay, indicating limited evidence for vertical transmission of gut microbiota. While diet did not significantly impact overall microbial composition, our results suggest that fourth instar larvae exhibit higher microbial diversity when consuming milkweed with high concentrations of toxic cardenolide phytochemicals. This study underscores how diet and developmental stage collectively shape the monarch’s gut microbiota.
A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum
Authors: Trojan Daniela , García-Robledo Emilio , Hausmann Bela , Revsbech Niels Peter , Woebken Dagmar , Eichorst Stephanie A 
Published: November 2024

Abstract
Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1 µM oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.
DIVULSUPERBAC: an outreach project to raise awareness of antimicrobial resistance
Authors: Maicas Sergi , Fouz Belén 
Published: November 2024

Abstract
DIVULSUPERBAC (DSB) is an outreach project involving a Service-Learning component aimed at the educational community. Launched in 2019, it has involved Biology degree students in a Microbiology-focused initiative within the Valencian Community (Spain) for four academic years. The DSB project includes various outreach activities designed to raise awareness of the threat posed by superbugs among preuniversity students. Under the supervision of their professors, university students created an exhibition featuring 14 infographics on antimicrobial resistance. These infographics were presented at 23 high schools (HS), where university students explained the issue to HS students (aged 15–16) and assessed their understanding of the topic. The activity was supported by HS teachers. Surveys indicated scores of around 4 out of 5 in terms of overall scientific interest and knowledge gained about antibiotic resistance. These positive results have inspired us to expand the project to other regions of the world.
Loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 doubled fruit firmness in strawberry
Authors: Jiménez Nicolás P , Bjornson Marta , Famula Randi A , Pincot Dominique D A , Hardigan Michael A , Madera Mary A , Lopez Ramirez Cindy M , Cole Glenn S , Feldmann Mitchell J , Knapp Steven J 
Published: November 2024

Abstract
Wildtype fruit of cultivated strawberry (Fragaria $\times$ ananassa) are typically soft and highly perishable when fully ripe. The development of firm-fruited cultivars by phenotypic selection has greatly increased shelf-life, decreased postharvest perishability, and driven the expansion of strawberry production worldwide. Hypotheses for the firm-fruited phenotype include mutations affecting the expression of genes encoding polygalacturonases (PGs) that soften fruit by degrading cell wall pectins. Here we show that loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 (FaPG1; PG1-6A1) double fruit firmness in strawberry. PG1-6A1 was one of three tandemly duplicated PG genes found to be in linkage disequilibrium (LD) with a quantitative trait locus (QTL) affecting fruit firmness on chromosome 6A. PG1-6A1 was strongly expressed in soft-fruited (wildtype) homozygotes and weakly expressed in firm-fruited (mutant) homozygotes. Genome-wide association, quantitative trait transcript, DNA sequence, and expression-QTL analyses identified genetic variants in LD with PG1-6A1 that were positively correlated with fruit firmness and negatively correlated with PG1-6A1 expression. An Enhancer/Suppressor-mutator (En/Spm) transposable element insertion was discovered upstream of PG1-6A1 in mutant homozygotes that we hypothesize transcriptionally downegulates the expression of PG1-6A1. The PG1-6A1 locus was incompletely dominant and explained 26–76% of the genetic variance for fruit firmness among phenotypically diverse individuals. Additional loci are hypothesized to underlie the missing heritability. Highly accurate codominant genotyping assays were developed for modifying fruit firmness by marker-assisted selection of the En/Spm insertion and single nucleotide polymorphisms associated with the PG1-6A1 locus.
The cytological mechanism of the peach haploid producing triploid offspring
Authors: Liu Xin , Li Dandan , Zhang Yu , Zhou Xin , Wang Shangde , Zhao Jianbo , Guo Jiying , Jiang Quan , Ren Fei 
Published: November 2024

Abstract
Peach is one of the most economically valuable fruit trees. Haploid peach trees occur spontaneously at very low frequencies and they are usually highly sterile. Therefore, the haploid with partial fertility is an extremely rare germplasm, which is highly valuable to genetic research and breeding programs. In this study, we investigated the cytological mechanism underlying the fertility of a peach haploid mutant ‘9-D’ derived from a spontaneous mutation. Cytologic evaluation and flow cytometry analysis demonstrated that ‘9-D’ is a pure haploid. Scanning electron microscope analysis revealed a considerable proportion of abnormal pollen grains in ‘9-D’. Pollen viability assay by Alexander staining showed that 50.4% of pollen grains from ‘9-D’ were viable. However, the pollen germination assay showed that only 7.6% of the pollen grains could germinate normally. Investigation of the chromosomal behavior of pollen mother cells at different stages of meiosis showed that pollen mother cells of ‘9-D’ lacked the process between anaphase I and prophase II of meiosis. Various types of sporophyte morphology were observed in haploid pollen mother cells at the tetrad stage. Measurement of the diameter of pollen grains indicated the presence of pollen with 2x ploidy in ‘9-D’. The offspring of ‘9-D’ were predominantly triploid or triploid aneuploid. The triploid offspring were more likely derived from the 2x male gametophyte combined with the haploid female gametophyte, which may explain the reason why ‘9-D’ has fertility. This study not only expands our understanding of haploid fertility mechanisms, but is also useful for ploid breeding programs in peach.
Long-Term Course and Prognostic Factors in Pediatric Ulcerative Proctitis: A Multicenter Cohort Study
Authors: Miyazawa Ayako , Nambu Ryusuke , Shimizu Hirotaka , Kudo Takahiro , Nishizawa Takuya , Kumagai Hideki , Hagiwara Shin-Ichiro , Kaji Emiri , Mizuochi Tatsuki , Kurasawa Shingo , Kakuta Fumihiko , Ishige Takashi , Shimizu Toshiaki , Iwama Itaru , Arai Katsuhiro 
Published: November 2024

Abstract

Background
Although ulcerative proctitis (UP) in children is considered relatively mild, some patients have proximal disease extension and require immunosuppressive treatment. We investigated clinical characteristics and course of refractory UP in a multicenter pediatric cohort.

Methods
Analyzing data obtained between 2013 and 2022 at 10 institutions specializing in pediatric inflammatory bowel disease, we elucidated natural history and factors predicting a need for immunosuppressive UP treatment. We compared patients given immunosuppressants and/or biologic agents (immunosuppressive treatment group) with those given 5-aminosalicylic acid (5-ASA) alone (5-ASA group).

Results
Fifty-five patients were followed for 3.5 years. The median Pediatric Ulcerative Colitis Activity Index at diagnosis was 20. The commonest treatment, 5-ASA suppository monotherapy in 40% of patients, showed the worst compliance. Clinical remission was achieved at least once in 95% of all patients. Disease extension beyond the splenic flexure occurred in 51%. Immunosuppressive treatment was given to 37%; biologic agents were used for 18%. Rates of endoscopically demonstrated inflammation, including Ra/Rs at diagnosis and extension beyond the left-sided colon, were higher in the immunosuppressive treatment group (70% vs 38%, P &lt; 0.05; 95% vs 27%, P &lt; 0.0001). The log-rank test and multivariate Cox proportional hazards regression showed that time to first clinical remission exceeding 3 months predicted the need for biologics.

Conclusion
The typical initial treatment of pediatric UP was 5-ASA suppositories, despite poor compliance. Biologics or other immunosuppressive treatments were needed in 37% of patients. Close follow-up with adjustment of treatment should be considered in children with UP as its clinical course varies.
Compartmentalized Human Immunodeficiency Virus Type 1 Reservoir in Intestinal Monocytes/Macrophages on Antiretroviral Therapy
Authors: Vellas Camille , Martres Dorine , Requena Mary , Nayrac Manon , Collercandy Nived , Latour Justine , Barange Karl , Alric Laurent , Martin-Blondel Guillaume , Izopet Jacques , Lagane Bernard , Delobel Pierre 
Published: November 2024

Abstract

Background
The intestinal mucosa contains many cells targeted by human immunodeficiency virus type 1 (HIV-1), and high levels of HIV-1 DNA persist in this compartment under antiretroviral therapy (ART). While CD4+ T cells are the best-characterized reservoir of HIV-1, the role of long-lived intestinal macrophages in HIV-1 persistence on ART remains controversial.

Methods
We collected duodenal and colonic biopsies from 12 people with HIV (PWH) on suppressive ART, enrolled in the ARNS EP61 GALT study. Total, integrated, intact and defective HIV-1 proviruses were quantified from sorted T cells and monocytes/macrophages. HIV-1 env quasispecies were analyzed by single-molecule next-generation sequencing and env-pseudotyped viruses were constructed to assess macrophage versus T-tropism.

Results
Total HIV-1 DNA levels in intestinal T cells were significantly higher than those in monocytes/macrophages (P &lt; .0001). Unintegrated HIV-1 DNA was detected in one-third of T-cell and monocyte/macrophage-positive samples. Intact HIV-1 proviruses were detected using the intact proviral DNA assay in 4 of 16 T-cell samples and 1 of 6 monocyte/macrophage samples with detectable HIV-1 DNA. HIV-1 sequences were compartmentalized between intestinal monocytes/macrophages and T cells in some subjects. Phenotypic analysis of pseudotyped viruses expressing HIV-1 envelopes from colonic monocytes/macrophages revealed T-tropism rather than M-tropism.

Conclusions
Our results show that monocytes/macrophages from the intestinal mucosa of PWH on ART can contain HIV-1 DNA, including intact or unintegrated forms, but at much lower levels than those found in T cells, and with some compartmentalization, although they do not exhibit a specific macrophage tropism, raising the question of the mechanisms of infection involved.
Sand Fly Surveillance for Molecular Identification and Characterization of Leishmania and Bartonella Species in Peru
Authors: Zorrilla Victor O , Espada Liz J , Lozano Marisa E , Potter Alexander M , Vasquez Gissella M 
Published: November 2024

Abstract
Leishmaniasis and Carrion's disease are endemic neglected diseases in Peru. Both diseases are transmitted by phlebotomine sand flies competent for infection with Leishmania species and Bartonella bacilliformis. In Peru, 149 sand fly species have been identified. Knowledge regarding sand fly species diversity and distribution in leishmaniasis and Carrion's disease transmission areas has grown in the past 2 decades through multiple surveillance efforts in endemic regions, including unexplored low and high jungle areas. Furthermore, molecular testing approaches have been implemented to enhance surveillance of Leishmania and Bartonella species in sand fly populations from these endemic regions. This review emphasizes the importance of entomological surveillance in Peru for the characterization of sand fly species and the discovery of a great diversity of Leishmania and Bartonella species in sand fly populations from Andean and Amazonian regions.
Maintenance of the Golgi ribbon structure by the KASH protein Jaw1
Authors: Fujita Morihisa 
Published: November 2024

Abstract
The Golgi apparatus is an organelle responsible for modification, secretion and transport of biomolecules. Its structure and morphology are crucial for the efficient processing and proper transport of proteins. The maintenance of this Golgi ribbon structure involves multiple proteins including GRASP and golgin proteins and the microtubule network. Particularly, the microtubule network extending from the Golgi is important for the Golgi ribbon formation and positioning. A recent report by Okumura et al. (J. Biochem. 2023; 173: 383–392) demonstrated that Jaw1, one of the Klarsicht/ANC-1/Syne/homology (KASH) proteins that are components of the linker of nucleoskeleton and cytoskeleton (LINC) complex, is essential for maintaining the Golgi ribbon structure. Knockdown of Jaw1 disrupted the Golgi ribbon structure leading to the fragmentation, whilst the Golgi ministacks were preserved. Acetylated tubulin, a marker of the Golgi-derived microtubule network, became more dispersed, losing its local compactness in the Jaw-depleted cells. These phenomena suggest that Jaw1 is required to maintain the proper organization of the Golgi-derived microtubule network.
Long-duration type 1 diabetes is associated with deficient cortical bone mechanical behavior and altered matrix composition in human femoral bone
Authors: Emerzian Shannon R , Chow Jarred , Behzad Ramina , Unal Mustafa , Brooks Daniel J , Wu I-Hsien , Gauthier John , Jangolla Surya Vishva Teja , Yu Marc Gregory , Shah Hetal S , King George L , Johannesdottir Fjola , Karim Lamya , Yu Elaine W , Bouxsein Mary L 
Published: November 2024

Abstract
Type 1 diabetes (T1D) is associated with an increased risk of hip fracture beyond what can be explained by reduced bone mineral density, possibly due to changes in bone material from accumulation of advanced glycation end-products (AGEs) and altered matrix composition, though data from human cortical bone in T1D are limited. The objective of this study was to evaluate cortical bone material behavior in T1D by examining specimens from cadaveric femora from older adults with long-duration T1D (≥50 yr; n = 20) and age- and sex-matched nondiabetic controls (n = 14). Cortical bone was assessed by mechanical testing (4-point bending, cyclic reference point indentation, impact microindentation), AGE quantification [total fluorescent AGEs, pentosidine, carboxymethyl lysine (CML)], and matrix composition via Raman spectroscopy. Cortical bone from older adults with T1D had diminished postyield toughness to fracture (−30%, p = .036), elevated levels of AGEs (pentosidine, +17%, p = .039), lower mineral crystallinity (−1.4%, p = .010), greater proline hydroxylation (+1.9%, p = .009), and reduced glycosaminoglycan (GAG) content (−1.3%, p &lt; .03) compared to nondiabetics. In multiple regression models to predict cortical bone toughness, cortical tissue mineral density, CML, and Raman spectroscopic measures of enzymatic collagen crosslinks and GAG content remained highly significant predictors of toughness, while diabetic status was no longer significant (adjusted R2 &gt; 0.60, p &lt; .001). Thus, the impairment of cortical bone to absorb energy following long-duration T1D is well explained by AGE accumulation and modifications to the bone matrix. These results provide novel insight into the pathogenesis of skeletal fragility in individuals with T1D.
A synthetic co-culture for bioproduction of ammonia from methane and air
Authors: Crumbley Anna Morgan , Garg Shivani , Pan Jonathan Lin , Gonzalez Ramon 
Published: November 2024

Abstract

Fixed nitrogen fertilizers feed 50% of the global population, but most fixed nitrogen production occurs using energy-intensive Haber–Bosch-based chemistry combining nitrogen (N2) from air with gaseous hydrogen (H2) from methane (CH4) at high temperatures and pressures in large-scale facilities sensitive to supply chain disruptions. This work demonstrates the biological transformation of atmospheric N2 into ammonia (NH3) using CH4 as the sole carbon and energy source in a single vessel at ambient pressure and temperature, representing a biological “room-pressure and room-temperature” route to NH3 that could ultimately be developed to support compact, remote, NH3 production facilities amenable to distributed biomanufacturing. The synthetic microbial co-culture of engineered methanotroph Methylomicrobium buryatense (now Methylotuvimicrobium buryatense) and diazotroph Azotobacter vinelandii converted three CH4 molecules to l-lactate (C3H6O3) and powered gaseous N2 conversion to NH3. The design used division of labor and mutualistic metabolism strategies to address the oxygen sensitivity of nitrogenase and maximize CH4 oxidation efficiency. Media pH and salinity were central variables supporting co-cultivation. Carbon concentration heavily influenced NH3 production. Smaller-scale NH3 production near dispersed, abundant, and renewable CH4 sources could reduce disruption risks and capitalize on untapped energy resources.

One-Sentence Summary
Co-culture of engineered microorganisms Methylomicrobium buryatense and Azotobacter vinelandii facilitated the use of methane gas as a sole carbon feedstock to produce ammonia in an ambient temperature, atmospheric pressure, single-vessel system.