bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seven‐year effects of sewage sludge biochar on soil organic carbon pools and yield: Understanding the role of biochar on carbon sequestration and productivity
Authors: Chagas Jhon Kenedy Moura , Nardoto Gabriela Bielefeld , Madari Beata Emoke , de Figueiredo Cícero Célio 
Published: December 2024

AbstractThe increasing need for sustainable agricultural practices and climate change mitigation has driven research into biochar's role in enhancing soil carbon (C) sequestration and fertility. This study aimed to investigate the long‐term effects of sewage sludge biochar (SSB), prepared at different temperatures (300 and 500°C), combined or not with mineral fertilizer application, on soil C stocks and organic matter fractions, addressing whether SSB can improve soil C sequestration. In the first two growing seasons (2015–2016), SSB was applied at 15 t ha−1 (dry weight) per crop and incorporated into the top 0.2 m of soil using a rotary hoe before planting. Over 7 years, soil samples were collected from the 0–0.2 m depth post‐harvest each season to analyse total C, total N, and various organic matter fractions, including easily oxidizable organic C, permanganate‐oxidizable C, non‐oxidizable C, humic substances, particulate C, and mineral‐associated C. Results demonstrate that SSB application enhances soil total C (up to 9.5%) and total N levels (up to 28.8%), indicating improved soil fertility and C sequestration potential. Notably, SSB amendments increased the non‐oxidizable organic C pool (up to 11.9%), contributing to soil organic matter stabilization. While the easily oxidizable organic C pool was increased under SSB at 300°C (up to 7.7%), the permanganate oxidizable C pool was not affected by treatments, suggesting that SSB primarily affects more recalcitrant C fractions, essential for long‐term C sequestration. Additionally, SSB application substantially increased crop yield, with higher grain yield (up to 105.0%) and shoot biomass (up to 75.1%) observed over multiple growing seasons. However, a decline in corn yield from the fourth season onwards in SSB‐only treatments highlights a limited capacity of biochar to sustain long‐term productivity. These findings underscore the effectiveness of SSB in enhancing soil C pools and its potential role in sustainable agricultural practices. Future research should focus on long‐term field studies under various environmental conditions and explore the potential of co‐pyrolysis of sewage sludge with other feedstocks to enhance C stability. The broader adoption of biochar technology could play a vital role in mitigating climate change and promoting sustainable agricultural development.
Implementation of isoniazid preventive therapy among children living with diagnosed pulmonary tuberculosis patients: A mixed methods study from Mumbai, India
Authors: Sreevidya P. A. , Acharya Shrikala , Raul Mayuri Umesh , Prakash Aparna 
Published: December 2024

AbstractBackgroundTuberculosis remains a significant public health issue, particularly among children who are in close contact with tuberculosis patients. India accounts for a large proportion of global tuberculosis cases. Despite global recommendations for Isoniazid Preventive Therapy to prevent latent tuberculosis infection from progressing to active disease, the initiation and adherence to Isoniazid Preventive Therapy remain suboptimal, especially in high‐burden settings. Understanding the barriers to Isoniazid Preventive Therapy implementation is crucial to improving treatment outcomes and achieving tuberculosis elimination goals.ObjectivesThis study aimed to quantify the uptake of isoniazid among children under 6 years who were started on Isoniazid Preventive Therapy and to identify the challenges from the perspectives of caregivers and healthcare providers.MethodsThe study was conducted in a slum in Mumbai, India, from June to December 2023, using a mixed‐methods design. The quantitative phase involved a house‐to‐house survey, covering all 96 contacts started on Isoniazid Preventive Therapy in 2022, using a semi‐structured questionnaire. The qualitative phase included key informant interviews with healthcare providers and in‐depth interviews with caregivers. Quantitative data were analysed using Fisher's exact test and chi‐square test, while qualitative data were analysed thematically.ResultsOf the 96 children, 11 (11.45%) completed therapy, with an average treatment duration of 2.5 months. Quantitative findings highlighted fear of side effects and family migration as major reasons for discontinuation. Completion of chemoprophylaxis was significantly associated with factors like male gender, support from extended family, home visits by tuberculosis health staff, and shorter travel time (under 30 min) to the tuberculosis unit. Qualitative data revealed challenges across themes of supply, staff, training, services, and adherence. Key challenges included lack of awareness, unavailability of isoniazid in syrup form, inadequate training for health workers, weak program monitoring, insufficient staffing, and fears related to tuberculosis exposure during outpatient department visits.ConclusionEffective counselling, regular follow‐ups, availability of medications in syrup form, increasing staffing based on case burden, timely training of staff, strengthening program monitoring, and ensuring infection control in tuberculosis outpatient departments are critical to achieving successful completion of isoniazid preventive therapy.
Cutaneous epitheliotropic T‐cell lymphoma in a sugar glider (Petaurus breviceps)
Authors: Amati Piercarlo , Dedola Carla , Demontis Roberta , Brachelente Chiara 
Published: December 2024

AbstractA 3‐year‐old male sugar glider presented with pruritus and alopecia primarily affecting the back and neck regions. Dermatologic diagnostics ruled out common causes. Skin biopsies revealed cutaneous epitheliotropic T‐cell lymphoma, a rare condition in sugar gliders. Despite treatment, the glider's condition worsened, leading to death. This case highlights the importance of thorough diagnostic evaluation in exotic pets.
DESIGN AND DEVELOPMENT OF THREE-DEGREES-OF-FREEDOM ROBOTIC ARM FOR ELECTRIC VEHICLE CHARGING STATION
Authors: Muhammad Nor Syamsulyusri Ruslan  , Mohd Nor Nur Safwati , Saputra Hendri Maja 
Published: December 2024

The exponential growth of the electric vehicle (EV) industry requires the development of more efficient and easily accessible charging infrastructures. The existing manual charging procedures provide significant difficulties, especially for those with impairments. The objective of this project was to overcome these difficulties by designing and developing a robotic arm that is particularly designed for automating the process of charging electric vehicles. The project aimed to improve operational efficiency and user accessibility by designing a three-degrees-of-freedom robotic arm using CAD software, SOLIDWORKS, and prototyping it using 3D printing technology. The main approaches employed were thorough Finite Element Analysis (FEA) to guarantee the structural integrity to confirm the operational dependability. The primary results indicate that the robotic arm design successfully automates the charging process, resulting in a substantial reduction in the human labor needed from users and an improvement in the accuracy of the charging connection. These results not only showcase the arm's capacity to completely transform EV charging methods but also emphasize its flexibility in different vehicle settings, indicating a wide range of possible uses in automated systems in the future.
Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa
Authors: Kyle Kathleen E. , Klassen Jonathan L. 
Published: December 2024

ABSTRACT

Advances in DNA metabarcoding have greatly expanded our knowledge of microbial communities in recent years. Pipelines and parameters have been tested extensively for bacterial metabarcoding using the 16S rRNA gene and best practices are largely established. For fungal metabarcoding using the internal transcribed spacer (ITS) gene, however, only a few studies have considered how such pipelines and parameters can affect community prediction. Here, we report a novel bias uncovered during ITS region 2 (ITS2) sequencing of
Trichoderma
-infected ant fungus gardens and confirmed this bias using mock communities. Abnormally low forward read quality caused
Trichoderma
ITS2 reads to be computationally filtered before and during read pair merging, thus almost entirely eliminating
Trichoderma
amplicon sequence variants from the resulting fungal community profiles. Sliding window quality trimming before filtering allowed most of these reads to pass filtering and merge successfully, producing community profiles that now correlated with visual signs of
Trichoderma
infection and matched the composition of the mock communities. Applying such sliding window trimming to a previously generated environmental ITS2 data set increased the detected fungal diversity and again overcame read quality biases against
Trichoderma
to detect it in nearly every sample instead and often at high relative abundances. This analysis additionally identified a similar, but distinct, bias against a second fungal genus
Meyerozyma
. The prevalence of such quality biases against other fungal ITS sequences is unknown but may be widespread. We, therefore, advocate for the routine use of sliding window quality trimming as a best practice in ITS2 metabarcoding analysis.

IMPORTANCE
Metabarcode sequencing produces DNA abundance profiles that are presumed to reflect the actual microbial composition of their corresponding input samples. However, this assumption is not always tested, and taxon-specific biases are often not apparent, especially for low-abundance taxa in complex communities. Here, we identified internal transcribed spacer region 2 (ITS2) read quality aberrations that caused dramatic reductions in the relative abundances of specific taxa in multiple data sets characterizing ant fungus gardens. Such taxon-specific biases in read quality may be widespread in other environments and for other fungal taxa, thereby causing incorrect descriptions of these mycobiomes.
Essential role of
cis
-encoded mature NS3 in the genome packaging of classical swine fever virus
Authors: Lamp Benjamin , Barth Sandra , Reuscher Carina , Affeldt Sebastian , Cechini Angelika , Netsch Anette , Lobedank Irmin , Rümenapf Till 
Published: December 2024

ABSTRACT

Classical swine fever virus (CSFV) is a member of the genus
Pestivirus
within the family
Flaviviridae
. The enveloped particles contain a plus-stranded RNA genome encoding a single large polyprotein. The processing of this polyprotein undergoes dynamic changes throughout the infection cycle. The release of mature NS3 from the polyprotein is mediated and regulated by the NS2 autoprotease and a cellular co-factor, restricting efficient cleavage to the early phases of infection. NS3 is a multifunctional viral enzyme exhibiting helicase, NTPase, and protease activities pivotal for viral replication. Hence, the release of mature NS3 fuels replication, whereas unprocessed NS2-3 precursors are vital for progeny virus production in later phases of infection. Thus far, no packaging signals have been identified for pestivirus RNA. To explore the prerequisites for particle assembly,
trans
-packaging experiments were conducted using CSFV subgenomes and coreless CSFV strains. Intriguingly, we discovered a significant role of mature NS3 in genome packaging, effective only when the protein is encoded by the RNA molecule itself. This finding was reinforced by employing artificially engineered CSFV strains with duplicated NS3 genes, separating uncleavable NS2-3 precursors from mature NS3 molecules. The model for NS2-3/NS3 functions in genome packaging of pestiviruses appears to be much more complicated than anticipated, involving distinct functions of the mature NS3 and its precursor molecule NS2-3. Moreover, the reliance of genome packaging on
cis
-encoded NS3 may act as a downstream quality control mechanism, averting the packaging of defective genomes and coordinating the encapsidation of RNA molecules before membrane acquisition.

IMPORTANCE

Pestiviruses are economically significant pathogens in livestock. Although genome organization and non-structural protein functions resemble those of other
Flaviviridae
genera, distinct differences can be observed. Previous studies showed that coreless CSFV strains can produce coreless virions mediated by single compensatory mutations in NS3. In this study, we could show that only RNA molecules encoding these mutations in the mature NS3 are packaged in the absence of the core protein. Unlike this selectivity, a pool of structural proteins in the host cell was readily available for packaging all CSFV genomes. Similarly, the NS2-3-4A precursor molecules required for packaging could also be provided in
trans
. Consequently, genome packaging in pestiviruses is governed by
cis
-encoded mature NS3. Reliance on
cis
-acting proteins restricts the acceptance of defective genomes and establishes packaging specificity regardless of RNA sequence-specific packaging signals. Understanding the role of NS3 in pestiviral genome packaging might uncover new targets for antiviral therapies.
Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria
Authors: Beauchemin Eve T. , Hunter Claire , Maurice Corinne F. 
Published: December 2024

ABSTRACT

The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development—especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both
ex vivo
and
in situ
in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community
ex vivo
during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading
Akkermansia
and the poorly described
Erysipelatoclostridium
genus. We further demonstrate that many taxa exhibit variable replication rates
in situ
during colitis, including
Akkermansia muciniphila
. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria
in situ
which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.

IMPORTANCE
It is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.
Endoscope-assisted vitreous surgery for rhegmatogenous retinal detachment in a patient with a small-aperture IC-8 intraocular lens
Authors: Yoshioka Kazuki , Yokoyama Sho , Kaga Tatsushi 
Published: December 2024

We present a case of rhegmatogenous retinal detachment in an eye with an implanted IC-8 intraocular lens (IOL). The IC-8, an extended depth of focus IOL, incorporates pinhole technology with a central 3.23-mm black circular mask and 1.36-mm aperture. The opaque ring can impede visualisation of the posterior segment.Initially, a 25-gauge 3-port pars plana core vitrectomy was performed using a Constellation Vision System and a Resight 700 wide-viewing system. However, poor visibility around the retinal breaks necessitated endoscopic visualisation for the subsequent procedures. Under endoscopic guidance, vitrectomy around the retinal breaks, peripheral vitrectomy, subretinal fluid drainage and retinal photocoagulation was completed successfully. Notably, the IC-8’s opaque ring did not impair endoscopic observations.This case highlights the enhanced safety and adaptability of vitreous surgery in eyes with IC-8 IOLs, demonstrating the effectiveness of both wide-angle viewing and endoscopic systems in challenging ophthalmic procedures.
Modern perspective of the Rice Diet for hypertension and other metabolic diseases
Authors: Sommerfeld Romeo , Ermler Paul , Fehr Jana , Bergner Benjamin , Lopez David , Sanoff Scott , Neelon Francis A , Kuo Anthony , McDowell William , Li Yi-Ju , Fox Smilla , Ghajar Abdullatif , Gensch Elena , Lorenz Cedric , Preiss Martin , Richter Tom , Luft Friedrich C , Klemmer Philip , Bohannon Anastacia , Lippert Christoph , Lin Pao-Hwa 
Published: December 2024

BackgroundIn the early 1940s, before antihypertensive drugs were available, the Rice Diet Programme (RDP) was developed to treat severe hypertension and, later, diabetes and obesity. Despite significant advancements in dietary management for these conditions since then, debates remain regarding the proper guidelines for sodium and macronutrients intakes. The patient care records of RDP offer a unique source of longitudinal examination of a very low sodium (<10 mmol/day), fat, cholesterol and protein diet on blood pressure (BP), other health markers and survival.MethodsIn 2019, the Rice Diet Database Project (RDDP) digitised handwritten patient care records and retinal photographs of 17 487 RDP participants, establishing a digital database for analyses. Manual transcription accuracy exceeded 97%. We used regression models to investigate the impact of dietary adherence on systolic BP (SBP) and body weight. Further, we performed Kaplan-Meier survival analysis to compare 5-year survival probability of participants defined by baseline level of SBP.ResultsThe database encompasses a wide array of health markers, including BP, weight, urine chloride (UCl) concentration and retinal features that offer a unique resource for studying the impact of the RDP on hypertension, diabetes and obesity. Initial analysis shows reductions in BP and weight as well as improved survival in participants with severe hypertension, underscoring the effectiveness of the diet. The data also permit examining the safety of extreme dietary sodium reduction.The database has numerous strengths (large patient population; extensive, long-term measurements and the use of UCl excretion to document dietary adherence) and limitations (missing data; temporal changes in methodologies over 50 years and lack of control subjects).ConclusionThe RDDP database allows exploration of the effects of a diet extremely low in sodium, protein, fat and cholesterol on health indicators and patient survival. This report highlights the database’s potential for detailed and intricate future analyses.
How does the level of functional impairment vary in individuals with non-communicable disease and comorbidity? Cross-sectional analysis of linked census and administrative data in Aotearoa New Zealand
Authors: Teng Andrea M , Underwood Lisa , Bowden Nicholas , Jamieson Hamish , Milne Barry 
Published: December 2024

ObjectivesThis study examines national patterns of functional impairment, and how they vary by the presence of non-communicable disease (NCD), type of health condition, comorbidity, age, sex, ethnicity, deprivation and living situation.DesignA cross-sectional examination using a national research database of linked administrative and survey data sets including census, tax and health data.SettingAotearoa New ZealandParticipantsAll individuals living in NZ on 30 June 2018, identified by the Statistics NZ Integrated Data Infrastructure estimated residential population (4.79 million individuals). Nine NCDs among these individuals were identified from national health data sets using existing and adapted algorithms.Primary and secondary outcome measuresFunctional impairment was assessed via hospitalisations, comorbidities (Elixhauser index), activity limitations (census) and income support.ResultsThree-tenths (29%) of the population had at least one NCD. Functional impairment was strongly patterned by NCD prevalence (3% activity limitation in people without any NCDs, 13% if one or more NCDs and 25% if two or more NCDs). Activity limitation was most common in individuals with dementia (68% activity limitation), stroke (42%) and coronary heart disease (26%). After age stratification, there was also a high level of activity limitation and income support in people with mental health conditions. Māori and Pacific peoples and people living in deprived areas or alone were more likely to have functional impairment.ConclusionsFunctional impairment was strongly patterned by NCD type. NCD prevention efforts and disability supports are needed to reduce the burden of disability experienced.