bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Graft Loss With Suspected Seventh‐Day Syndrome Following Pediatric Liver Transplantation
Authors: Hartjes Kayla , Koo Donna , Al‐Ibraheemi Alyaa , Sweeny Katherine F. , Wehrman Andrew , Elisofon Scott , Lee Christine K. , Cuenca Alex G. , Kim Heung Bae , Lee Eliza J. 
Published: June 2024

ABSTRACTIntroductionAllograft dysfunction within the first week posttransplant is an uncommon but known complication following liver transplantation. Seventh‐Day Syndrome (7DS) is a rare complication of allograft dysfunction following liver transplantation characterized by the rapid clinical deterioration of a formerly well‐functioning allograft within the first week posttransplant. The etiology of 7DS is unknown, and treatment options remain limited. While cases of graft survival have been reported, the risk of mortality remains exceedingly high without urgent retransplantation.MethodsPatient data was retrospectively analyzed and a literature review performed.ResultsWe present a unique case of split liver transplantation into two pediatric recipients in which one recipient developed rapidly progressive graft failure approximately 1 week postoperatively requiring urgent retransplantation while the other recipient had an unremarkable postoperative course. Upon clinical manifestation of progressive graft failure, the patient was treated with thymoglobulin, rituximab, intravenous immunoglobulin, and plasmapheresis. Despite this, the patient's clinical status continued to decline and she underwent retransplantation 11 days following her initial liver transplant.ConclusionSeventh‐Day Syndrome is a rare complication following liver transplantation that is associated with a high risk of morbidity and mortality. Our case adds to the limited literature on 7DS in children and is the first to report a comparative posttransplant clinical course in two recipients who received split grafts from the same donor.
A comparative evaluation of the effects of 635 nm laser on cell proliferation and osteogenic differentiation of buccal fat pad mesenchymal stem cells
Authors: Etemadi Ardavan , Karimi Mohammad Amin , Karimi Mohammadreza , Hodjat Mahshid , Pour Mahsa Sheibani , Karimi Alireza , Chiniforush Nasim 
Published: June 2024

AbstractThe purpose of this study was to evaluate the effects of 635 nm diode laser with different powers on undifferentiated mesenchymal stem cells obtained from buccal fat pad. Human buccal fat stem cells were cultured in DMEM containing 10% FBS, penicillin, and streptomycin under 5% CO2 and 95% humidity. Cells were cultured in 96‐well plate and 24 h later, laser irradiation with 635 nm diode laser was performed in four groups of 200, 300, 400, and 500 mW powers in addition to the control group with the same energy density of 4 J/cm2. MTT and flow cytometry assay was performed to evaluate cell proliferation and viability on 2 and 4 days after irradiation. Alizarin red assay and real‐time PCR (OPN, OCN, ALP, and RUNX‐2 genes) was performed to evaluate osteogenic differentiation. According to the MTT assay, none of the mentioned powers of 635 nm diode laser had significant effect on cell proliferation. Cells irradiated with power of 400 mW and 500 mW significantly showed a greater number of necrotic cells compared to the control group in Day 4. Cells irradiated with 300 mW power significantly exhibited a greater amount of nodule formation compared to all groups. Results of this study indicated that 635 nm diode laser with energy density of 4 J/cm2 has a positive effect inducing osteogenic differentiation when applying with a power of 300 mW in buccal fat pad mesenchymal stem cells.
Causal relationship between inflammatory skin diseases and breast cancer: A bidirectional Mendelian randomization study
Authors: Yang Yiling , Zhao Juhua 
Published: June 2024

AbstractIntroductionPrior research has explored the relationship between inflammatory skin disorders and breast cancer (BC), yet the causality of this association remains uncertain.MethodsUtilizing a bidirectional two‐sample Mendelian randomization (MR) approach, this study aimed to elucidate the causal dynamics between various inflammatory skin conditions—namely acne, atopic dermatitis, psoriasis vulgaris, urticaria, and rosacea—and BC. Genetic variants implicated in these disorders were sourced from comprehensive genome‐wide association studies representative of European ancestry. In the forward MR, BC was posited as the exposure, while the reverse MR treated each inflammatory skin disease as the exposure. A suite of analytical methodologies, including random effects inverse variance weighted (IVW), weighted median (WME), and MR‐Egger, were employed to probe the causative links between inflammatory skin diseases and BC. Sensitivity analyses, alongside evaluations for heterogeneity and pleiotropy, were conducted to substantiate the findings.ResultsThe MR analysis revealed an increased risk of acne associated with BC (IVW: OR = 1.063, 95% CI = 1.011–1.117, p = 0.016), while noting a decreased risk of atopic dermatitis (AD) in BC patients (IVW: OR = 0.941, 95% CI = 0.886–0.999, p = 0.047). No significant associations were observed between BC and psoriasis vulgaris, urticaria, or rosacea. Conversely, reverse MR analyses detected no effect of BC on the incidence of inflammatory skin diseases. The absence of pleiotropy and the consistency of these outcomes strengthen the study's conclusions.ConclusionFindings indicate an elevated incidence of acne and a reduced incidence of AD in individuals with BC within the European population.
Diversity and multifunctional potential for plant growth promotion in bacteria from soil and the rhizosphere
Authors: de Oliveira Larissa M. , Kavamura Vanessa N. , Clark Ian M. , Mauchline Tim H. , De Souza Jorge T. 
Published: June 2024

AbstractBeneficial microorganisms play essential roles in soil fertility, plant nutrition, and health. In this study, we examined the potential of a collection of 138 bacterial strains to promote plant growth. The strains were isolated from the rhizosphere of two monocotyledonous and two dicotyledonous plant species and from bare fallow soil, all from the same site. Our interest in this study was to investigate the diversity and the potential for growth promotion in this collection of culturable bacteria. The most common trait was phosphorus (P) solubilization from aluminium phosphate (in 66.7% of the strains), whereas solubilization of P from phytic acid (6.5%) and from iron phosphate (5.8%) was the least common and they were only detected in bacterial strains from faba bean and oilseed rape. All bacterial strains inhibited the growth of Fusarium graminearum (from 5.4% to 87.2%). In total, 10 genera were identified among the strains by 16S rRNA sequencing and Pseudomonas was the most common in monocotyledonous plants and in bulk soil, while Stenotrophomonas was dominant in the rhizosphere of the dicotyledonous plants. Combinations of bacterial strains improved the spectrum of in vitro activity in most cases, however, wheat growth was generally lower. These strains have potential to be used as biofertilizers and/or biocontrol agents and further studies should be pursued to develop them into practical solutions for a more sustainable agricultural production.
Demonstration scale chemical–physical treatment and agricultural reuse of highly saline textile wastewater
Authors: Arous Fatma , Hamdi Chadlia , Bessadok Salma , Boudagga Soumaya , Aydi Ayda , Li Wentao , Kyriacou Stathis , Pinelli Davide , Frascari Dario , Jaouani Atef 
Published: June 2024

AbstractThis study aimed to develop an energy‐efficient process for treating highly saline textile wastewater (TWW) in a 10 m3/day pilot plant and evaluate forage sorghum irrigation with treated wastewater in terms of crop production and soil and irrigation device performance. The TWW treatment pilot plant, consisting of a coagulation/flocculation unit followed by a sand filter and an anion exchange resin column, produced treated effluent that complied with the permissible limits specified in the ISO 16075‐2:2020 standard for Category C irrigation water. The corresponding average energy consumption was 1.77 kWh/m3. Reusing treated TWW for forage sorghum irrigation over a 13‐week cycle yielded crop performances comparable with freshwater irrigation, with no negative impact on the irrigation system. Although soil profiles were similar between treated TWW and freshwater irrigation, both soils featured an increase in electrical conductivity, which may reversibly or irreversibly affect soil quality and damage salt‐sensitive crops. These findings demonstrate the effective treatment and reuse of saline TWW for irrigating salt‐tolerant crops, offering significant implications for industrial wastewater management and cropping patterns in arid and semi‐arid regions.
“I Found Comfort in Exercising”: Exploring Experiences With Exercise for Adults With Attention-Deficit/Hyperactivity Disorder
Authors: Ramji Anusha V. , Dommett Eleanor J. , Runswick Oliver R. 
Published: June 2024

Little is known about how adults with attention-deficit/hyperactivity disorder (ADHD) experience exercise, resulting in a lack of recommendations for supporting this population. We aimed to explore how adults with ADHD experience exercise as a management tool before and after diagnosis and how and why individuals experience issues related to exercise dependence. Fifteen active adults with a diagnosis of ADHD participated in semistructured interviews. Three overarching themes were identified: (a) exercise as a necessity for ADHD, reflecting the need to exercise before a formal ADHD diagnosis, and use of exercise as a management tool postdiagnosis; (b) goals and achievements to live by, reflecting how exercise patterns revolved around a need to make progress toward targets; and (c) activity or exercise: a roller coaster journey, covering the ups and downs of exercise journeys. This article highlights the importance of exercise for adults to manage ADHD and how this can be encouraged and supported.
Functional studies on tandem carbohydrate-binding modules of a multimodular enzyme possessing two catalytic domains
Authors: Liu Jiawen , Shi Jiani , Gao Jiahui , Shi Rui , Zhu Jingrong , Jensen Marcus Sepo , Li Chenchen , Yang Jing , Zhao Siyi , Sun Aofei , Sun Di , Zhang Ying , Liu Cong , Liu Weijie 
Published: June 2024

ABSTRACT

Although functional studies on carbohydrate-binding module (CBM) have been carried out extensively, the role of tandem CBMs in the enzyme containing multiple catalytic domains (CDs) is unclear. Here, we identified a multidomain enzyme (Lc25986) with a novel modular structure from lignocellulolytic bacterial consortium. It consists of a mannanase domain, two CBM65 domains (LcCBM65-1/LcCBM65-2), and an esterase domain. To investigate CBM function and domain interactions, full-length Lc25986 and its variants were constructed and used for enzymatic activity, binding, and bioinformatic analyses. The results showed that LcCBM65-1 and LcCBM65-2 both bind mannan and xyloglucan but not cellulose or β-1,3-1,4-glucan, which differs from the ligand specificity of reported CBM65s. Compared to LcCBM65-2, LcCBM65-1 showed a stronger ligand affinity and a preference for acetylation sites. Both CBM65s stimulated the enzymatic activities of their respective neighboring CDs against acetylated mannan, but did not contribute to the activities of the distal CDs. The time course of mannan hydrolysis indicated that the full-length Lc25986 was more effective in the complete degradation of mixed acetyl/non-acetyl substrates than the mixture of single-CD mutants. When acting on complex substrates, LcCBM65-1 not only improved the enzymatic activity of the mannanase domain, but also directed the esterase domain to the acetylated polysaccharides. LcCBM65-2 adopted a low affinity to reduce interference with the catalysis of the mannanase domain. These results demonstrate the importance of CBMs for the synergism between the two CDs of a multidomain enzyme and suggest that they contribute to the adequate degradation of complex substrates such as plant cell walls.

IMPORTANCE
Lignocellulolytic enzymes, particularly those of bacterial origin, often harbor multiple carbohydrate-binding modules (CBMs). However, the function of CBM multivalency remains poorly understood. This is especially true for enzymes that contain more than one catalytic domain (CD), as the interactions between CDs, CBMs, and CDs and CBMs can be complex. Our research demonstrates that homogeneous CBMs can have distinct functions in a multimodular enzyme. The tandem CBMs coordinate the CDs in catalytic conflict through their differences in binding affinity, ligand preference, and arrangement within the full-length enzyme. Additionally, although the synergism between mannanase and esterase is widely acknowledged, our study highlights the benefits of integrating the two enzymes into a single entity for the degradation of complex substrates. In summary, these findings enhance our understanding of the intra-synergism of a multimodular enzyme and emphasize the significance of multiple CBMs in this context.
Blue valorization of lignin-derived monomers via reprogramming marine bacterium
Roseovarius nubinhibens
Authors: Wei Ying , Wang Shu-Guang , Xia Peng-Fei 
Published: June 2024

ABSTRACT

Biological valorization of lignin, the second most abundant biopolymer on Earth, is an indispensable sector to build a circular economy and net-zero future. However, lignin is recalcitrant to bioupcycling, demanding innovative solutions. We report here the biological valorization of lignin-derived aromatic carbon to value-added chemicals without requesting extra organic carbon and freshwater via reprogramming the marine
Roseobacter
clade bacterium
Roseovarius nubinhibens
. We discovered the unusual advantages of this strain for the oxidation of lignin monomers and implemented a CRISPR interference (CRISPRi) system with the
lacI
-P
trc
inducible module, nuclease-deactivated Cas9, and programmable gRNAs. This is the first CRISPR-based regulatory system in
R. nubinhibens
, enabling precise and efficient repression of genes of interest. By deploying the customized CRISPRi, we reprogrammed the carbon flux from a lignin monomer, 4-hydroxybenzoate, to achieve the maximum production of protocatechuate, a pharmaceutical compound with antibacterial, antioxidant, and anticancer properties, with minimal carbon to maintain cell growth and drive biocatalysis. As a result, we achieved a 4.89-fold increase in protocatechuate yield with a dual-targeting CRISPRi system, and the system was demonstrated with real seawater. Our work underscores the power of CRISPRi in exploiting novel microbial chassis and will accelerate the development of marine synthetic biology. Meanwhile, the introduction of a new-to-the-field lineage of marine bacteria unveils the potential of blue biotechnology leveraging resources from the ocean.

IMPORTANCE

One often overlooked sector in carbon-conservative biotechnology is the water resource that sustains these enabling technologies. Similar to the “food-versus-fuel” debate, the competition of freshwater between human demands and bioproduction is another controversial issue, especially under global water scarcity. Here, we bring a new-to-the-field lineage of marine bacteria with unusual advantages to the stage of engineering biology for simultaneous carbon and water conservation. We report the valorization of lignin monomers to pharmaceutical compounds without requesting extra organic substrate (e.g., glucose) or freshwater by reprogramming the marine bacterium
Roseovarius nubinhibens
with a multiplex CRISPR interference system. Beyond the blue lignin valorization, we present a proof-of-principle of leveraging marine bacteria and engineering biology for a sustainable future.
Complete genome sequences of
Lactococcus petauri
strains 473AN and 473GN isolated from the blood culture of a Japanese patient with infective endocarditis
Authors: Imajoh Masayuki , Suzuki Marina , Okamoto Akira , Salif Maiga , Ogawa Riku , Mikami Aguri , Daibata Masanori 
Published: June 2024

ABSTRACT

Here, we report the complete genome sequences of
Lactococcus petauri
strains 473AN and 473GN, isolated from the blood culture of a Japanese patient with infective endocarditis. The complete genomes of 473AN and 473GN consist of single chromosomes of 2,065,772 and 2,094,461 bp, respectively.
Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA
Authors: Rasmussen Anna N. , Tolar Bradley B. , Bargar John R. , Boye Kristin , Francis Christopher A. 
Published: June 2024

ABSTRACT

We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling—particularly methane-cycling—microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (
n
= 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (
Methanoregulaceae
,
Methanotrichaceae
, and
Methanomassiliicoccales
), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (
Candidatus
Methanoperedens) in anoxic depths and uncultured bacteria (
Ca
. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered.
Ca.
Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot.
Ca
. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the
Ca
. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured
Thermoplasmata
archaea in the
Ca
. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.

IMPORTANCE

The cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the
Ca
. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
Augmenting bacterial similarity measures using a graph-based genome representation
Authors: Ramanan Vivek , Sarkar Indra Neil 
Published: June 2024

ABSTRACT

Relationships between bacterial taxa are traditionally defined using 16S rRNA nucleotide similarity or average nucleotide identity. Improvements in sequencing technology provide additional pairwise information on genome sequences, which may provide valuable information on genomic relationships. Mapping orthologous gene locations between genome pairs, known as synteny, is typically implemented in the discovery of new species and has not been systematically applied to bacterial genomes. Using a data set of 378 bacterial genomes, we developed and tested a new measure of synteny similarity between a pair of genomes, which was scaled onto 16S rRNA distance using covariance matrices. Based on the input gene functions used (i.e., core, antibiotic resistance, and virulence), we observed varying topological arrangements of bacterial relationship networks by applying (i) complete linkage hierarchical clustering and (ii) K-nearest neighbor graph structures to synteny-scaled 16S data. Our metric improved clustering quality comparatively to state-of-the-art average nucleotide identity metrics while preserving clustering assignments for the highest similarity relationships. Our findings indicate that syntenic relationships provide more granular and interpretable relationships for within-genera taxa compared to pairwise similarity measures, particularly in functional contexts.

IMPORTANCE
Given the prevalence and necessity of the 16S rRNA measure in bacterial identification and analysis, this additional analysis adds a functional and synteny-based layer to the identification of relatives and clustering of bacteria genomes. It is also of computational interest to model the bacterial genome as a graph structure, which presents new avenues of genomic analysis for bacteria and their closely related strains and species.
Predictors of readmission and mortality in adults with diabetes or stress hyperglycemia after initial hospitalization for COVID-19
Authors: Chaugule Akshata , Howard Kyra , Simonson Donald C , McDonnell Marie E , Garg Rajesh , Gopalakrishnan Geetha , Mitri Joanna , Lebastchi Jasmin , Palermo Nadine E , Westcott Gregory , Weinstock Ruth S 
Published: June 2024

IntroductionWe previously reported predictors of mortality in 1786 adults with diabetes or stress hyperglycemia (glucose>180 mg/dL twice in 24 hours) admitted with COVID-19 from March 2020 to February 2021 to five university hospitals. Here, we examine predictors of readmission.Research design and methodsData were collected locally through retrospective reviews of electronic medical records from 1786 adults with diabetes or stress hyperglycemia who had a hemoglobin A1c (HbA1c) test on initial admission with COVID-19 infection or within 3 months prior to initial admission. Data were entered into a Research Electronic Data Capture (REDCap) web-based repository, and de-identified. Descriptive data are shown as mean±SD, per cent (%) or median (IQR). Student’s t-test was used for comparing continuous variables with normal distribution and Mann-Whitney U test was used for data not normally distributed. X2test was used for categorical variable.ResultsOf 1502 patients who were alive after initial hospitalization, 19.4% were readmitted; 90.3% within 30 days (median (IQR) 4 (0–14) days). Older age, lower estimated glomerular filtration rate (eGFR), comorbidities, intensive care unit (ICU) admission, mechanical ventilation, diabetic ketoacidosis (DKA), and longer length of stay (LOS) during the initial hospitalization were associated with readmission. Higher HbA1c, glycemic gap, or body mass index (BMI) were not associated with readmission. Mortality during readmission was 8.0% (n=23). Those who died were older than those who survived (74.9±9.5 vs 65.2±14.4 years, p=0.002) and more likely had DKA during the first hospitalization (p<0.001). Shorter LOS during the initial admission was associated with ICU stay during readmission, suggesting that a subset of patients may have been initially discharged prematurely.ConclusionsUnderstanding predictors of readmission after initial hospitalization for COVID-19, including older age, lower eGFR, comorbidities, ICU admission, mechanical ventilation, statin use and DKA but not HbA1c, glycemic gap or BMI, can help guide treatment approaches and future research in adults with diabetes.