bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Albino 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

Context

Insurance 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.

Methodology

Between 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.

Results

Most 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.

Conclusion

When 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.
A data‐based approach to determining the optimal water ponding scale and zone for small urban wetland restoration
Authors: Nakashima Naohisa , Tsuji Osamu , Muneoka Toshimi , Kimura Masato
Published: April 2024

This study established a planning framework for effective small‐scale urban wetland restoration by adapting an analytical template used for watershed‐scale projects. We evaluated the optimal water ponding scale and location for small urban wetland restoration. We calculated the achievable water ponding area in Oyama Wetland, Hokkaido, Japan, by the use of an artificial water supply and elevation differences without reliance on precipitation. The volume of infiltration into the sediments, a component of the water balance equation, was estimated during a temporary suspension of the artificial water supply, and the estimate was then validated by modeling the decrease of the water ponding area from 2008, before the introduction of the artificial water supply, with high reproducibility (Nash–Sutcliffe efficiency = 0.68). The estimated attainable water ponding area was 1172 m2. We identified where a water ponding location could be most efficiently established through principal component and cluster analyses of groundwater level observation data collected from 2008 to 2010. Areas with high groundwater levels (first axis) and stable groundwater levels (second axis) accounted for approximately 73% of the cumulative contribution ratio. The calculated potentially achievable ponding area was consistent with the area achieved by the actual wetland restoration. This study shows how efficient and safe restoration of urban wetlands can be achieved with a dataset that volunteers and others can obtain independently. Long‐term data analysis using the adapted template allows for clear identification of discrepancies between desired reference conditions and current conditions, facilitating the setting of objectives that promote long‐term monitoring.
Association of HLA‐E single nucleotide polymorphisms with human myeloid leukemia
Authors: Sun Liyan , Hong Wenxu , Wang Songxing , Xu Yunping , Li Chengyao
Published: April 2024

Single nucleotide polymorphisms (SNPs) of HLA‐E are related to the occurrence of many diseases, but their functions remain unclear. In this study, the function of SNPs at HLA‐E rs76971248 and rs1264457 on the myeloid leukemia cells was analyzed by a progressive procedure, included genotyping, mRNA transcription, regulatory element, protein expression, and anti‐tumor effect. The frequencies of rs76971248 G and rs1264457 G were found higher in myeloid leukemia patients than those in healthy blood donors (p < 0.05). For myeloid leukemia, rs76971248 T was protective, while rs1264457 G was susceptible. We also found that rs76971248 affected HLA‐E mRNA transcription and membrane HLA‐E (mHLA‐E) expression in K562 cells through differently binding to transcription factor HOXA5 (p < 0.0001), while rs1264457 affected mHLA‐E expression by changing mRNA transcription and an encoding amino acid (p < 0.01). In contrast, the expression of soluble HLA‐E (sHLA‐E) was not influenced by both rs1264457 and rs76971248. The higher HLA‐E expression was detected among myeloid leukemia patients, and the K562 cells with higher HLA‐E molecules played a significant inhibitory effect on the killing activity of NK‐92MI cells (p < 0.05). In conclusion, the higher HLA‐E expression of myeloid leukemia cells is promoted by rs76971248 G and rs1264457 G, which helps escape from NK‐92MI cells' killing.
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

Background

Surgical 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.

Methods

This 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.

Results

There 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.

Conclusion

SSI occurred in 8% of LT recipients and was predominantly related to operation‐related factors rather than patient‐ or antibiotic‐related factors.

image
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

Drought 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

The 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

Background

Standard 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 Methods

We 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.

Results

Twenty 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.

Discussion

Slow, 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

Magnetic 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.
Black Twitter and Digital Counterpublics in South Africa
Authors: Aiseng Kealeboga
Published: April 2024

The growth of technology has made the Internet an essential tool in society. Scholars have argued that the Internet supports a more deliberative democracy. However, scholars have also raised concerns about the role of the Internet in political matters. While scholars agree that the Internet has facilitated broader public discussion, in many regards, its ‘virtual public sphere’ still mirrors existing social structures. Twitter has become a common social media platform for many South Africans. This has led to a virtual community of Twitter users engaged in real-time discourses primarily related to Black South Africans. Black Twitter in South Africa is used for social, political, and economic motivations. This study argues for the practice of Black Twitter as a digital counterpublic in South Africa. The aim is to spotlight how black people in South Africa have used Black Twitter as a digital counterpublic for the marginalized groups within South Africa. The research will investigate the potential challenges and opportunities associated with Black Twitter functioning as a digital counterpublic. Utilizing digital ethnography, the study gathered a dataset of tweets from Black Twitter in 2022, focusing on those addressing social, political, and economic issues. More than 700,000 tweets were identified under these specific thematic hashtags.
Total Cuntz semigroup, extension, and Elliott Conjecture with real rank zero
Authors: An Qingnan , Liu Zhichao
Published: April 2024

In 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

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.
Study of defects population and contaminations in silica/tantala coated mirrors
Authors: D’Ubaldo D. , Sbroscia M. , Ficca V. C. A. , Stellino E. , Pasqualetti A. , Sentenac D. , Gargiulo J. , Francescon L. , Pinard L. , Placidi E.
Published: April 2024

This article presents a study on the performance degradation of amorphous silica mirrors coated with silica/tantala, commonly utilized in gravitational wave interferometry measurements. The primary objective is to understand the factors contributing to the reduced performance, specifically the heightened noise observed after prolonged use of the mirrors in a vacuum. In this article, SiO2/Ta2O5 multilayered coated sample mirrors underwent analysis through x-ray photoemission spectro-microscopy, atomic force microscopy, and Raman spectroscopy, before and after exposure to a contaminating vacuum environment. Our findings revealed the possible correlation between the deterioration in mirror performance and an upsurge in contaminant carbon and defect populations within the silicon dioxide structure.
The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation
Authors: Henis Melad , Rücker Tabitha , Scharrenberg Robin , Richter Melanie , Baltussen Lucas , Hong Shuai , Meka Durga Praveen , Schwanke Birgit , Neelagandan Nagammal , Daaboul Danie , Murtaza Nadeem , Krisp Christoph , Harder Sönke , Schlüter Hartmut , Kneussel Matthias , Hermans-Borgmeyer Irm , de Wit Joris , Singh Karun K. , Duncan Kent E. , de Anda Froylan Calderón
Published: April 2024

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the
16p11.2
microdeletion, bear no obvious connection to translation. Here, we use proteomics, genetics, and translation assays in cultured cells and mouse brain to reveal altered translation mediated by loss of the kinase TAOK2 in
16p11.2
deletion models. We show that TAOK2 associates with the translational machinery and functions as a translational brake by phosphorylating eukaryotic elongation factor 2 (eEF2). Previously, all signal-mediated regulation of translation elongation via eEF2 phosphorylation was believed to be mediated by a single kinase, eEF2K. However, we show that TAOK2 can directly phosphorylate eEF2 on the same regulatory site, but functions independently of eEF2K signaling. Collectively, our results reveal an eEF2K-independent signaling pathway for control of translation elongation and suggest altered translation as a molecular component in the etiology of some forms of ASD.
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

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

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.
Localization and symbiotic status of probiotics in the coral holobiont
Authors: Cardoso P. M. , Hill L. J. , Villela H. D. M. , Vilela C. L. S. , Assis J. M. , Rosado P. M. , Rosado J. G. , Chacon M. A. , Majzoub M. E. , Duarte G. A. S. , Thomas T. , Peixoto R. S.
Published: April 2024

Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence
in situ
hybridization (FISH) to define their localization in the coral
Pocillopora damicornis
. Our results show the first evidence of the inherent presence of
Halomonas
sp. and
Cobetia
sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of
Halomonas
sp. and
Cobetia
sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.

IMPORTANCE

Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as
Endozoicomonas
sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for
Halomonas
sp. and
Cobetia
sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.
Intra-arc rifting induced the fragmentation of microplate from the continental margin
Authors: Wu Limin , Zhao Guochun , Gao Jianfeng , Dong Xiaohan , Zhang Aimei , Peng Touping
Published: April 2024

Although abundant Neoproterozoic igneous rocks exposed along the periphery of the Yangtze Block of the South China Craton record the tectonic processes of the assembly and breakup of the Rodinia supercontinent, the mechanism that induced the rifting of the South China Craton from Rodinia and reconstruction of the paleogeographic position of the South China Craton in Rodinia remain controversial. We document two episodes of bimodal intrusions with emplacement ages of ca. 785 Ma and ca. 750 Ma in the Diancangshan Massif that provide critical constraints on the rifting processes and mechanisms. The rock association and the elemental and Hf-O isotopic signatures of these two episodes of bimodal intrusions illustrate that they are an important component of the Panxi-Hannan magmatic arc in the western Yangtze Block. The spatial pattern of Neoproterozoic sedimentary rocks to the west of the Panxi-Hannan arc and their provenance indicate that intra-arc rifting promoted the separation of microplates such as the Xuelongshan and Diancangshan massifs and even the Yidun Block from the western Yangtze Block and the mechanism induced synchronous deposits in these regions.
Evidence for ca. 1 Ga hypervelocity impact event found in northwest Greenland
Authors: Hyde William R. , Kenny Gavin G. , Jaret Steven J. , MacGregor Joseph A. , Beck Pierre , Whitehouse Martin J. , Larsen Nicolaj K.
Published: April 2024

There are likely many undiscovered impact structures on Earth, but several challenges prevent their detection, including possible concealment beneath large ice sheets. In recent years, geophysical, geochemical, and microphysical evidence has mounted for a ca. 58 Ma impact structure under the Hiawatha Glacier, northwest Greenland. Here, we report evidence for a second, much older hypervelocity impact event in this region, recorded in an impact melt rock sample collected from a glaciofluvial deposit in Inglefield Land. Secondary ion mass spectrometry U-Pb analyses of shock metamorphosed zircon grains yielded a previously unrecorded, Proterozoic best estimate impact age of 1039 ± 16 Ma (mean square of weighted deviates = 2.9). Based on Archean–Proterozoic target rock U-Pb ages obtained from unshocked zircon grains and the location of the melt rock sample along the ice margin, we suggest this sample was derived from a hypervelocity impact structure farther inland, concealed by the Greenland Ice Sheet. This study demonstrates the ability to uncover new impact events in some of the most inaccessible areas on Earth and the possibility of sampling multiple impact structures from one location when examining ex situ material. Our results have implications for current and future Martian and lunar returned samples that demonstrably bear complex impact histories.
Oligocene melting of subducted mélange and its mantle dynamics in northeast Asia
Authors: Hong Ke-Chun , Wang Feng , Zhang Si-Wen , Xu Wen-Liang , Wang Yi-Ni , Yang De-Bin
Published: April 2024

Melting of subducted mélange can potentially transport mass from the slab-mantle interface to the mantle wedge in subduction zones. The mélange diapir model was primarily proposed from the results of laboratory experiments and thermodynamic modeling. However, the melting mechanisms of mélange diapirs in subduction zones remain unclear. To further constrain the mantle dynamics of a mélange diapir, we studied Oligocene alkaline intermediate rocks on the northeast Asian continental margin. We report whole-rock geochemical and Sr-Nd-Pb-Mg-Zn isotope data and show that these rocks formed by partial melting of mélange. We conclude that a diapir was the mechanism for Oligocene melting of the mélange. We also identified younger rocks formed by melting of mélange in the eastern part of northeast Asia, implying an eastward shift in such magmatism since the Oligocene. Our results and the tectonic setting indicate that melting of mélange diapirs occurred preferentially during tectonic transitions, such as the formation of a back-arc basin triggered by trench-perpendicular mantle flow. The low-viscosity mantle with an incompressible stress field triggered melting of the mélange diapirs. Interactions occurred between the mélange diapirs and carbonated peridotites, constraining the depth of mélange-mantle interactions to the asthenosphere, which is deeper than the depth inferred in previous studies.
Predictive model for iris melanoma
Authors: Singh Arun , Melendez-Moreno Alexander , Krohn Jørgen , Zabor Emily C
Published: April 2024

Aim

To develop a predictive model for the diagnosis of iris melanoma.

Methods

Retrospective consecutive case series that included 100 cases of pathologically confirmed iris melanoma and 112 cases of Iris naevus, either pathological confirmation or documented stability of >1 year. Patient demographic data, features of clinical presentation, tumour characteristics and follow-up were collected. Iris melanoma with ciliary body extension was excluded. Lasso logistic regression with 10-fold cross-validation was used to select the tuning parameter. Discrimination was assessed with the area under the curve (AUC) and calibration by a plot.

Results

There was a significant asymmetry in the location of both nevi and melanoma with preference for inferior iris quadrants (83, 74%) and (79, 79%), respectively (p=0.50). Tumour seeding, glaucoma and hyphaema were present only in melanoma. The features that favoured the diagnosis of melanoma were size (increased height (OR 3.35); increased the largest basal diameter (OR 1.64)), pupillary distortion (ectropion uvea or corectopia (OR 2.55)), peripheral extension (angle or iris root involvement (OR 2.83)), secondary effects (pigment dispersion (OR 1.12)) and vascularity (OR 6.79). The optimism-corrected AUC was 0.865. The calibration plot indicated good calibration with most of the points falling near the identity line and the confidence band containing the identity line through most of the range of probabilities.

Conclusions

The predictive model provides direct diagnostic prediction of the lesion being iris melanoma expressed as probability (%). Use of a prediction calculator (app) can enhance decision-making and patient counselling. Further refinements can be undertaken with additional datasets, forming the basis for automated diagnosis.
Relapse in ocular tuberculosis: relapse rate, risk factors and clinical management in a non-endemic country
Authors: Putera Ikhwanuliman , ten Berge Josianne C. E. M. , Thiadens Alberta A. H. J. , Dik Willem A. , Agrawal Rupesh , van Hagen P. Martin , La Distia Nora Rina , Rombach Saskia M.
Published: April 2024

Aims

To assess the risk of uveitis relapse in ocular tuberculosis (OTB) following clinical inactivity, to analyse clinical factors associated with relapses and to describe the management strategies for relapses.

Methods

A retrospective study was conducted on a 10-year patient registry of patients with OTB diagnosed at Erasmus MC in Rotterdam, The Netherlands. Time-to-relapse of uveitis was evaluated with Kaplan-Meier curve and risk factors for relapses were analysed.

Results

93 OTB cases were identified, of which 75 patients achieved clinical inactivity following treatment. The median time to achieve uveitis inactivity was 3.97 months. During a median follow-up of 20.7 months (Q1–Q3: 5.2–81.2) after clinical inactivity, uveitis relapse occurred in 25 of these 75 patients (33.3%). Patients who were considered poor treatment responders for their initial uveitis episode had a significantly higher risk of relapse after achieving clinical inactivity than good responders (adjusted HR=3.84, 95% CI: 1.28 to 11.51). 13 of the 25 relapsed patients experienced multiple uveitis relapse episodes, accounting for 78 eye-relapse episodes during the entire observation period. Over half (46 out of 78, 59.0%) of these episodes were anterior uveitis. A significant number of uveitis relapse episodes (31 episodes, 39.7%) were effectively managed with topical corticosteroids.

Conclusions

Our results suggest that approximately one-third of patients with OTB will experience relapse after achieving clinical inactivity. The initial disease course and poor response to treatment predict the likelihood of relapse in the long-term follow-up. Topical corticosteroids were particularly effective in relapse presenting as anterior uveitis.
Storylines of family medicine XI: professional identity formation—nurturing one’s own story
Authors: Ventres William B , Stone Leslie A , Wilson Hamish J , Sexton Sumi M , Doukas David J , Cerdeña Jessica P , Kelley David M , Fetters Michael D , Haney Jeffrey J , Frey John J
Published: April 2024

Storylines of Family Medicineis a 12-part series of thematically linked mini-essays with accompanying illustrations that explore the many dimensions of family medicine, as interpreted by individual family physicians and medical educators in the USA and elsewhere around the world. In ‘XI: professional identity formation—nurturing one’s own story’, authors address the following themes: ‘The social construction of professional identity’, ‘On becoming a family physician’, ‘What’s on the test?—professionalism for family physicians’, ‘The ugly doc-ling’, ‘Teachers—the essence of who we are’, ‘Family medicine research—it starts in the clinic’, ‘Socially accountability in medical education’, ‘Personal philosophy and how to find it’ and ‘Teaching and learning withStorylines of Family Medicine’. May these essays encourage readers to find their own creative spark in medicine.
Prospective evaluation to characterize the real-world performance of the EMBOVAC aspiration catheter for neurothrombectomy: a post-market clinical follow-up trial
Authors: Piano Mariangela , Jansen Olav , Marnat Gaultier , Gory Benjamin , Nordmeyer Hannes , Eckert Bernd , Pedicelli Alessandro , Cognard Christophe , Loehr Christian , Zanoni Matteo , Schaefer Axel , Macera Antonio , Fiehler Jens , Doyle Karen , Lobotesis Kyriakos
Published: April 2024

Background

A direct aspiration first pass technique (ADAPT) is an effective alternative to stent retriever thrombectomy for patients with large vessel occlusion (LVO). The PERFECT study evaluated direct aspiration with the EMBOVAC large bore aspiration catheter in patients with LVO strokes.

Methods

PERFECT was a prospective, post-market, single-arm, multicenter, observational study of patients enrolled across 11 European centers between October 2020 and July 2022. Three direct aspiration passes with EMBOVAC were mandated before switching strategy. The primary endpoint was core-lab assessed successful reperfusion (modified Thrombolysis In Cerebral Infarction (mTICI) ≥2b) post-procedure. Other outcomes included first pass mTICI ≥2c, independent 90-day modified Rankin Scale (mRS) evaluation, and symptomatic intracerebral hemorrhage (sICH) at 24 hours by a clinical events committee.

Results

EMBOVAC was used in 100 patients (mean age 70.4±14.0 years, 59.0% (59/100) female). Final mTICI ≥2b was achieved in 98.0% (97/99), final mTICI ≥2b with no change in frontline therapy or thrombolytics use during the procedure was achieved in 87.9% (87/99), final mTICI ≥2c in 86.9% (86/99), and first pass mTICI ≥2c in 53.5% (53/99). sICH at 24 hours was 0%. The 90-day mRS ≤2 rate was 56.6% (56/99) and all-cause mortality was 12.9%. One device-related serious adverse event occurred within 90 days (1.0%).

Conclusions

PERFECT demonstrates that EMBOVAC achieves successful reperfusion rates and favorable clinical outcomes when used in the endovascular treatment of acute ischemic stroke (AIS) using a direct aspiration technique as first line therapy in a real-world setting in patients with AIS secondary to large vessel occlusion.

Trial registration

www.clinicaltrials.govUnique identifier:NCT04531904.
Needles in haystacks: monitoring the potential escape of bioaerosolised antibacterial resistance genes from wastewater treatment plants with air and phyllosphere sampling
Authors: George Paul B.L. , Hillary Luke S. , Leclerc Samantha , Cooledge Emily C. , Lemieux Joanie , Duchaine Caroline , Jones Davey L.
Published: April 2024

Wastewater treatment plants are well-known point sources of emissions of antibacterial resistance genes (ARGs) into the environment. Although most work to date has focused on ARG dispersal via effluent, aerial dispersal in bioaerosols is a poorly understood, but likely important vector for ARG dispersal. Recent evidence suggests that ARG profiles of the conifer needle phyllosphere could be used to measure bioaerosol dispersal from anthropogenic sources. Here, we assessed airborne dispersal of ARGs from wastewater treatment plants in Wales, UK and Quebec, Canada, using conifer needles as passive bioaerosol monitors. ARG profiles of wastewater were compared to those of conifer phyllosphere using high-throughput qPCR. ARG richness was significantly lower in conifer phyllosphere samples than wastewater samples, though no differences were observed across the dispersal gradients. Mean copy number of ARGs followed a similar trend. ARG profiles showed limited, but consistent patterns with increasing distance from wastewater treatment plants, but these did not align with those of wastewater samples. For example, proportional abundance of aminoglycosides decreased over the dispersal gradient in Wales, whereas mobile genetic elements showed the inverse relationship. In summary, while distinct ARG profiles exist along dispersal gradients, links to those of wastewater were not apparent.
Gluon distribution and mass decomposition of the pion and kaon
Authors: Han Chengdong , Kou Wei , Wang Rong , Chen Xurong
Published: April 2024

We present the gluon distribution functions of the pion and kaon in small-x and large-x regions, and compare them with the results obtained from lattice QCD and continuum Schwinger function methods. Whether in the small-x region or the large-x region, our gluon distribution of the pion is consistent with the results of lattice QCD and continuum Schwinger function methods. We also calculate the first four moments of gluon distributions of the pion and kaon at different $$Q^{2}$$

Q
2

scales. In addition, we present the mass decomposition of the pion and kaon with the dynamical parton distribution functions calculated by the DGLAP equation with parton–parton recombination corrections. The mass structures of the pion and kaon are completely different from that of the proton.
The crease flow on null hypersurfaces
Authors: Cotsakis Spiros
Published: April 2024

The crease flow, replacing the Hamiltonian system used for the evolution of crease sets on black hole horizons, is introduced and its bifurcation properties for null hypersurfaces are discussed. We state the conditions of nondegeneracy and typicality for the crease submanifolds, and find their normal forms and versal unfoldings (codimension 3). The allowed boundary singularities are thus prescribed by the Arnold–Kazaryan–Shcherbak theorem for 3-parameter versal families, and hence identified as swallowtails and Whitney umbrellas of particular kinds. We further present the bifurcation diagrams describing crease evolution at the crossings of the bifurcation sets and elsewhere, and a typical example is studied. Some remarks on the connection of these results to the crease evolution on black hole horizons are also given.
Nand to Tetris: Building a Modern Computer System from First Principles
Authors: Schocken Shimon
Published: April 2024

CS course walks students through a step-by-step construction of a complete, general-purpose computer system---hardware and software---in one semester.
The Dangers of Digitization, and the Importance of Data Backup
Authors: Bruderer Herbert , Vakulov Alex
Published: April 2024

In each issue of
Communications
, we publish selected posts or excerpts from the many blogs on our website. The views expressed by bloggers are their own and not necessarily held by
Communications
or the Association for Computing Machinery.

Read more blogs and join the discussion at https://cacm.acm.org/blog.

https://cacm.acm/blog

Herbert Bruderer considers the societal downsides of digital technologies, while Alex Vakulov discusses how to protect data by making copies.
Data Quality May Be All You Need
Authors: Edwards Chris
Published: April 2024

Size matters in machine learning, but will this continue to be true?
Community Is Critical Too
Authors: Clegg Tamara L.
Published: April 2024

Leveraging community to broaden the faces, places, and interlaces of computing.