bluuebunny/crossref_metadata_2025_split huggingface dataset:
Closed genomes of commercial inoculant rhizobia provide a blueprint for management of legume inoculation
Authors: Kohlmeier MacLean G. , O'Hara Graham W. , Ramsay Joshua P. , Terpolilli Jason J. 
Published: January 2025

ABSTRACT

Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N
2
into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N
2
-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera,
Bradyrhizobium
,
Mesorhizobium
,
Methylobacterium
,
Rhizobium
, and
Sinorhizobium
, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for
Rhizobium
sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.

IMPORTANCE
Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia’s legume inoculation program.
Draft genome sequence of
Mycobacterium
sp. SA01 isolated from
Sporobolus alterniflorus
seedlings collected in Cape Cod (USA)
Authors: Peredo Elena L. , Thomas Suzanne , Cardon Zoe G. 
Published: January 2025

ABSTRACT

A draft genome was generated for a strain of
Mycobacterium
closely related to
Mycobacterium
sp. ENV421 isolated
in vitro
from plants of smooth cordgrass germinated
in vitro
from seeds collected in a salt marsh in Cape Cod (USA). Genomic DNA was sequenced using paired-end Illumina technologies. Here, we report the classification and genome statistics of
Mycobacterium
sp. SA01. A strain of
Mycobacterium
was isolated from seedlings of
Sporobolus alterniflorus
germinated under in vitro conditions after surface sterilization. The seeds were collected in Little Swippewisett Marsh, Barnstable, MA, USA.
Trial of alginates in throat symptoms: protocol for a pragmatic, multicentre, placebo controlled, double blind, parallel, randomised controlled trial of liquid alginate (Gaviscon Advance) for the treatment of persistent throat symptoms
Authors: Morton Miranda , Smith Hesther , Fouweather Tony , Joyce Richard , Evans Lysbeth , Thompson Julie , Wood Ruth , Teare Dawn , Maier Rebecca , McGlashan Julian , Hamilton David , O’Hara James 
Published: January 2025

Introduction
Persistent throat symptoms (PTS) are indicators for over 60 000 new patient referrals to NHS secondary care annually. PTS have been attributed to manifestation of gastro-oesophageal reflux disease (GORD) with the hypothesis that gastric refluxate damages and irritates the mucosa of the upper aerodigestive tract. Symptoms of PTS and GORD are commonly treated with proton pump inhibitors (PPIs) or alginates are often, incorrectly, advocated. The Trial of PPIs in Throat Symptoms trial definitively demonstrated that lansoprazole is no more effective than placebo in treating symptoms of PTS, indicating that empirical PPI treatment for PTS should be discouraged. The impact of this is an anticipated increase in prescriptions of alginates for PTS, however, there is a lack of evidence of the efficacy of alginates in treating this condition. Trial of alginates in throat symptoms aims to compare symptomatic response of the symptoms of PTS in liquid alginate (Gaviscon Advance) in comparison to a near matched placebo over an 8-week period to provide definitive evidence of the use of alginates in treating PTS.

Methods and analysis
This is a multicentre, pragmatic, double blind, parallel, randomised controlled trial. 250 adults with PTS will be recruited from NHS secondary care sites and randomised to either liquid alginate (Gaviscon Advance) or near matched placebo in a 1:1 ratio. The primary objective is to compare the symptomatic response in patients with PTS to liquid alginate (Gaviscon Advance) compared with placebo using the outcome measure of total Reflux Symptom Index questionnaire score at 8 weeks.

Ethics and dissemination
Favourable ethical opinion was received from the East Midlands—Leicester South Research Ethics Committee (reference: 22/EM/0205). All participants will provide informed consent prior to any trial specific activity taking place. Results will be disseminated in peer reviewed publications, at national and international conferences, in peer reviewed journals and to participants and the public (using lay language).

Trial registration number

ISRCTN13949559
Neutropenic event incidence in women with early-stage breast cancer receiving neoadjuvant or adjuvant chemotherapy: a retrospective study
Authors: Englund Elin , Strandéus Michael , Engvall Kristina , Oliva Delmy 
Published: January 2025

ObjectivesTo assess the incidence of neutropenia, febrile neutropenia, documented infection with neutropenia and fever associated with early-stage breast cancer (BC) in a real-life setting.MethodsA retrospective study that includes 88 women with BC who received a first dose of Epirubicin plus Cyclophosphamide with or without 5-Fluorouracil, in the county hospital of Ryhov, Sweden. The patients were included continuously from May 2017 to November 2020 and were ≥18 years old. All data was collected in a form and the G-CSF prophylaxis was checked to ensure that it was given during the treatments.ResultsThe median age among the patients was 59 (min 27-82max) years. 79 patients were treated with primary prophylaxis with Granulocyte-colony stimulating factor (G-CSF) support. Seven (8.0%) patients were affected by a neutropenic episode, including one (1.1%) patient with FN and two (2.3%) patients with documented infection (online supplemental table 1).ConclusionThe incidence of neutropenic events in this study is relatively low. A higher incidence of neutropenic episodes is observed in patients ≥ 60 years old compared with younger patients, despite lower doses of chemotherapy for the elderly. The use of G-CSF in the elderly, regardless of the dose of chemotherapy, may be needed to decrease the incidence of neutropenia and its consequences. The adverse effects of G-CSF and its cost-effectiveness are important perspectives which should be included in the treatment.
Abstracts of Recent Doctoral Dissertations in Computer Algebra
Authors: del Río Tereso 
Published: January 2025

Each quarter we are pleased to present abstracts of recent doctoral dissertations in Computer Algebra and Symbolic Computation. We encourage all recent Ph.D. graduates who have defended in the past two years (and their supervisors), to submit their abstracts for publication in CCA.
Please send abstracts to the CCA editors <editors_SIGSAM@acm.org> for consideration.
A Rare Case of Linear Phlebolith: Foreign Body Discovered in the Femoral Vein
Authors: Alanezi Tariq , Altoijry Abdulmajeed , Iqbal Kaisor , Alabduljabbar Saeed , Aldossary Mohammed Yousef , AlSheikh Sultan 
Published: January 2025

Introduction: Phlebolith is a term that refers to round‐shaped calcified thrombi commonly located in the pelvic region. The occurrence of dense, linear calcifications or phlebolith‐like formations within the soft tissues of the lower extremities, particularly in the superficial femoral, greater saphenous, or popliteal veins, is rare.Patient Concerns: This study presents the case of a 73‐year‐old woman who was being evaluated for postmenopausal bleeding. During the patient’s diagnostic workup, an incidental linear‐shaped phlebolith was discovered. She had a positive history of deep vein thrombosis (DVT) for 36 years following her previous vaginal delivery.Diagnosis: Upon further examination and imaging, the patient was found to have a chronic calcified thrombus in the iliofemoral, popliteal, great saphenous, and superficial femoral veins, which was initially reported as a foreign body in the femoral vein on computed tomography (CT).Interventions and Outcomes: Conservative management was undertaken, with no worsening of her condition upon further follow‐up.Conclusion: This study showcased a rare form of a radiographically visible calcified thrombus in the veins of the lower extremities of our patient. Calcified venous thrombosis in the lower extremities is rare, as previously documented cases of venous calcifications have been observed in the pelvis with round shapes or as phleboliths. The common presentations differ from those in our case, making it important to consider such cases when formulating a differential diagnosis. While the precise mechanisms behind the formation of calcified thrombi remain unclear, this study emphasizes the significance of further exploration and future case studies to shed light on this enigmatic phenomenon.
Mesenchymal Stem Cell–Sourced Exosomes as Potentially Novel Remedies for Severe Dry Eye Disease
Authors: Randall Harrell Carl , Djonov Valentin , Volarevic Ana , Arsenijevic Aleksandar , Volarevic Vladislav 
Published: January 2025

Severe dry eye disease (DED) is an inflammatory condition characterized by a lack of sufficient moisture or lubrication on the surface of the eye, significantly impacting the quality of life and visual function. Since detrimental immune response is crucially responsible for the development and aggravation of DED, therapeutic agents which modulate phenotype and function of eye‐infiltrated inflammatory immune cells could be used for the treatment of severe DED. Due to their potent immunomodulatory properties, mesenchymal stem cells (MSCs) represent potentially new remedies for the treatment of inflammatory eye diseases. The majority of MSC‐sourced bioactive factors are contained within MSC‐derived exosomes (MSC‐Exos), nano‐sized extracellular vesicles which, due to their nanosize dimension and lipid envelope, easily by pass all biological barriers in the body and deliver their cargo directly into the target immune cells. MSC‐Exos contain a variety of bioactive proteins (growth factors, immunoregulatory molecules, cytokines, and chemokines) lipids, and microRNAs (miRNAs) which affect viability, proliferation, phenotype, and function of eye‐infiltrated immune cells. Accordingly, MSC‐Exos may modulate the progression of inflammatory eye diseases, including DED. Therefore, in this review article, we summarized the current knowledge regarding molecular and cellular mechanisms which were responsible for trophic, anti‐inflammatory, immunoregulatory, and regenerative properties of MSC‐Exos in the treatment of severe DED. For this purpose, an extensive literature review was carried out in February 2024 across several databases (Medline, Embase, and Google Scholar), from 2000 to the present. Eligible studies delineated molecular and cellular mechanisms responsible for the MSC‐Exos–based modulation of immune cell–driven eye inflammation in DED, and their findings were analyzed in this review. Results obtained in these studies demonstrated beneficial effects of MSC‐Exos in the treatment of severe DED, paving the way for their future clinical use in ophthalmology.Trial Registration: ClinicalTrials.gov identifier: NCT04213248, NCT06475027, NCT06543667, NCT05738629
Use of Lung Volume Recruitment Technique in Patients With Chronic Respiratory Disease Among Brazilian Health Professionals
Authors: de Melo Robert , Alcantara Livia , Sarmet Max , Sheers Nicole L. , Berlowitz David J. , Maldaner Vinicius 
Published: January 2025

Background: Lung volume recruitment (LVR) is a stacked‐breath assisted inflation technique in which consecutive insufflations are delivered, without exhaling in between, until the maximum tolerable inflation capacity is reached. Although LVR is recommended in some neuromuscular disease guidelines, there is little information detailing when and how allied health professionals (AHPs) prescribe LVR.Objective: This study is aimed at describing the use of LVR in practice across Brazil.Methods: A cross‐sectional e‐survey (Sep–Nov 2023) explored LVR practices among qualified clinical or home care AHPs in Brazil. It gathered participant data on geographical region, profession, and experience. It delved into LVR specifics: clinical population and indications for use, prescription (frequency, dosage, and interfaces), related side effects, outcomes assessed, and combined therapies. Results were presented descriptively.Results: One hundred two surveys (74 physical therapists (PTs) and 28 speech and language pathologists (SLPs)) from diverse locations were collected. LVR was predominantly prescribed for adults (57%), with the most common diagnosis being amyotrophic lateral sclerosis (84%). Changes in peak cough flow and vital capacity were the most common reasons for LVR prescription. Maximal insufflation capacity was reportedly measured by 58% of PTs and 22% of SLPs. Chest wall soreness and discomfort were the most common side effects, and many respondents did not provide warnings about potential side effects (42% PTs and 50% SLPs). The study highlighted common use of other respiratory therapy devices alongside LVR.Conclusion: LVR is available in routine clinical and home care settings in Brazil. There is a lack of standardization regarding indications, prescription, and outcome measures among PTs and SLPs in Brazil. Clear recommendations and guidelines are needed to standardize these parameters, enabling more objective data and facilitating comparisons between centers.
Hypermethylation of
PM20D1
Is Associated With Carotid Bifurcation Intima‐Media Thickness in Dominican Republic Families
Authors: Dueker Nicole D. , Zhao Hongyu , Gardener Hannah , Kaur Sonya S. , Dong Chuanhui , Cabral Digna , Sacco Ralph L. , Blanton Susan H. , Rundek Tatjana , Wang Liyong 
Published: January 2025

Background
Carotid intima‐media thickness (IMT) is a measure of atherosclerosis and a predictor of vascular diseases. Traditional vascular risk factors and genetic variants do not completely explain the variation in carotid IMT. We sought to identify epigenetic factors that may contribute to the remaining carotid IMT variability.

Methods and Results

An epigenome‐wide association study was performed in 61 Dominican families with 769 individuals. A cytosine nucleotide that precedes a guanine nucleotide methylation in blood‐derived DNA was measured using the Human MethylationEPIC BeadChip. Linear mixed model analyses were performed regressing bifurcation carotid IMT (bIMT) on beta values for cytosine nucleotide that precedes a guanine nucleotide sites, adjusting for covariates, followed by differentially methylated region (DMR) analysis. One‐sample Mendelian randomization analysis was conducted to investigate causal associations between DMRs and bIMT. Twenty‐five DMRs were associated with bIMT (Sidak
P
<0.05), with the strongest DMR (Sidak
P
=2.45×10
−17
) overlapping with the promoter of
PM20D1
. All 11 cytosine nucleotides that precede a guanine nucleotide within the
PM20D1
DMR were positively associated with bIMT (
P
=0.0007–0.00006). Methylation of the
PM20D1
DMR was associated with
cis
variants, including rs823154 (β=0.26;
P
=1.1×10
−121
). As reported in GTEx (Genotype‐Tissue Expression project), rs823154 is an expression quantitative trait locus for
PM20D1
in multiple tissues, including the aorta (
P
=2.3×10
−60
) and blood (
P
=4.0×10
−73
), suggesting that hypermethylation of the
PM20D1
DMR directs lower expression of the gene. Mendelian randomization analysis supported a causal role for
PM20D1
DMR in bIMT (
P
=0.049).

Conclusions

Our study and previous expression quantitative trait locus studies provide converging evidence that reduced
PM20D1
expression via hypermethylation of the promoter is associated with increased atherosclerosis.
Salute the Classic: Revisiting Challenges of Machine Translation in
the Age of Large Language Models
Authors: Pang Jianhui , Ye Fanghua , Wong Derek Fai , Yu Dian , Shi Shuming , Tu Zhaopeng , Wang Longyue 
Published: January 2025

Abstract
The evolution of Neural Machine Translation (NMT) has been significantly influenced by six core challenges (Koehn and Knowles, 2017) that have acted as benchmarks for progress in this field. This study revisits these challenges, offering insights into their ongoing relevance in the context of advanced Large Language Models (LLMs): domain mismatch, amount of parallel data, rare word prediction, translation of long sentences, attention model as word alignment, and sub-optimal beam search. Our empirical findings show that LLMs effectively reduce reliance on parallel data for major languages during pretraining and significantly improve translation of long sentences containing approximately 80 words, even translating documents up to 512 words. Despite these improvements, challenges in domain mismatch and rare word prediction persist. While NMT-specific challenges like word alignment and beam search may not apply to LLMs, we identify three new challenges in LLM-based translation: inference efficiency, translation of low-resource languages during pretraining, and human-aligned evaluation.
Resolving Vertical and Fiscal Imbalances in India: A Task for the Sixteenth Finance Commission
Authors: Srivastava D. K. 
Published: January 2025

The Terms of Reference (ToR) of the Sixteenth Finance Commission (16th FC) have recently been announced. These ToR are based on the constitutional provisions relating to the sharing of central taxes and grants. Other clauses usually made part of the ToR of the earlier FCs have not been included. One such clause is usually related to the review of fiscal deficit and debt of the central and state governments. In this article, we argue that the subject of fiscal transfers is integrally linked to determining sustainable levels of fiscal deficit and debt and the 16th FC would need to review trends in receipts and expenditures of the two tiers of government as well as trends in fiscal deficit and debt. We observe that government finances in India have shown, in recent years, an increase in the centre’s fiscal deficit and debt relative to GDP together with a falling share of the centre’s revenue receipts in the combined revenue receipts post transfers. This has led to a significant fall in the centre’s primary expenditure relative to that of the states implying a loss of fiscal space for the centre. We show that this situation is unstable in the presence of competition for fiscal space between the central and state governments. In particular, a falling share of the centre in the combined revenue receipts post transfers would lead the central government to rely more and more on borrowing to preserve its comparative fiscal space. However, as the centre’s debt increases, its interest payments would increase and primary expenditures would fall, giving rise to further loss of fiscal space. We argue that the 16th FC should attempt to jointly resolve the issues of vertical and fiscal imbalances in the context of Fiscal Responsibility and Budget Management targets, which may also need to be reconsidered. JEL Codes: H63, H62, H7, H77
Establishment of liquid–liquid phase separation-related prognostic model in lung adenocarcinoma and systematic analysis of its clinical significance
Authors: Chen Yan , Huang Cheng , Wei Wei 
Published: January 2025

Purpose To detect the prognostic importance of liquid–liquid phase separation (LLPS) in lung adenocarcinoma. Methods The gene expression files, copy number variation data, and clinical data were downloaded from The Cancer Genome Atlas cohort. LLPS-related genes were acquired from the DrLLPS website. The prognostic model based on LLPS was constructed by the Cox regression and LASSO regression analyses after the identification of LLPS-related differentially expressed genes (DEGs). Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed. The LLPS-related prognostic risk score was validated by GSE31210 and GSE72094. The overall survival of lung adenocarcinoma patients was predicted by plotting a nomogram. The biological features of the high-risk lung adenocarcinoma were evaluated by the CIBERSORT, ESTIMATE, Gene Set Variation Analysis, and Genomics of Drug Sensitivity in Cancer. Reverse transcription-quantitative polymerase chain reaction detected hub gene expression. Results A total of 91 DEGs were screened out in LLPS, among which 9 genes were discovered as prognostic biomarkers of lung adenocarcinoma. GRIA1, CRTAC1, MAGEA4, and MAPK4 were identified as hub genes by the LASSO Cox regression analysis. High-risk and low-risk groups were divided according to the risk index, with the high-risk group displaying a markedly worse outcome. CRTAC1 expression was significantly decreased, MAGEA4 and MAPK4 expressions were increased, while GRIA1 expression was altered in lung adenocarcinoma cells. Tumor microenvironment, signaling pathway enrichment, and drug sensitivity significantly differed between different risk groups. Conclusions This work proposed a prognostic tool based on the LLPS-related gene signature to offer prospective and effective biomarkers for lung adenocarcinoma prognosis.