bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using
Streptomyces mirabilis
NRRL B-2400 in Columbia, MD
Authors: Kumar Soven Verma , Schaffer Nicholas , Bharmal Zainab , Mood Quinn ,   2022 UMBC Phage Hunters, Erill Ivan , Caruso Steven M. , Abdullah Nameerah , Ahsan Manal I. , Ali Samaneh F. , Anandkrishnan Mukundh , Anderson Nick , Badugu Preethi , Baker Devon , Bakry Heba A. , Balbuena Willmar , Bauer Paige , Beyene Eden A. , Bhargava Anukriti , Bhusal Anjali , Bhusal Kritika , Boateng Rachel-Anne O. , Bucci Katrina , Buchanan Angela H. , Chen Amanda , Chen Joyce , Chiapperino Julian , Cole Austin R. , Daniel-Okeke Victoria , Davis Kyle , Diebolt Julie , Dizon Jeannine , Dolan Kenny , Einsig Jonah , Ezeka Peace , Felouzis Natalie E. , Fienkeng Ralph M. , Fomengia Kayla , Froderman Allison M. , Galo Julie , Ghezai Bethel M. , Ghorakavi Samhita , Ginting Andra , Ha Summer , Hall McKenzie M. , Hawley Jenna , Haywood Alessandra B. , Hoffman Sophia E. , Howe Alexandria , Irfan Ashher , Ismail Phebe O. , Kanayo Amarachi , Kang Hanna , Kang Mona , Kargbo Porschderek L. , Katchekpele Kossi S. , Khuu Vivian , Knight Autumn M. , Kuan Dylan , Kwon Meghan S. , Lam Annalisa Q. , Lapid Francis , Lee Annie , Llaguri Kristen A. , Lopez Jillian A. , Maldonado-Robles Steffany L. , Marinko Emily , Marroquin Noe , Martinez Andrea E. , Matharu Manvir K. , Messiha Mary , Micarsos Eric J. , Miller Aysia , Mkpasi-Jr Jr , Motamedi Sara , Musa Amina , Myers October , Na Ethan , Nachadalingam Sibani G. , Nasir Mamoona , Neka Eden M. , Nguyen Rachel H. , Nguyen Taylor , Nguyen Trini V. , Nguyen Vivian V. , Ni Alissa , Norwood Lauren , Nwange Kristel E. , Nyakoe Moraa I. , Ogbenna Josh , Okorie Prisca , Olatunde Simi , Oluka Atinuke J. , Onuma Nnenna A. , Cortes Jessica , Osorio Eriberto , Patel Nishi R. , Pearson Savannah R. , Persaud Joel , Pham Matthew T. , Radhakrishnan Sriraghav , Richardson Milan E. , Sabirzhanova Tanya , Salzer Josh , Santizo Madison L. , Sequeira Andrea B. , Shah Aarsh H. , Sherif Timag A. , Siddiqui Zainab , Sodhi Anjali , Stanley Eva , Tatarian Harout , Tran Kirsten V. , Tran Sophia , Trinh Justin , Tu Hsinyen , Tuckley Shreya A. , Ukadike Vivica C. , Verbin-Hedger Tristan W. , Vo Mai N. , White Kierstyn , Zornes Destiny C. , Fiorino Alexis , Fryer Sydney C. , Khanam Nadia , Nguyen Chif , Nguyen Melissa , Quiambao Jeanelle M. , Sanyal Adrita , Andre Chase , Barry Payton , Chin Alexander , Mason Luke , Pandya Megha , Smith Zachary M. , Sun Winny 
Published: February 2024

ABSTRACT

Here, we present bacteriophage SoJo, a siphovirus infecting
Streptomyces mirabilis
, with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. SoJo was isolated from soil in Columbia, MD, USA.
Complete genome sequence of
Pseudomonas aeruginosa
phage Knedl
Authors: Maffei Enea , Manner Christina , Jenal Urs , Harms Alexander 
Published: February 2024

ABSTRACT

Bacteriophage Knedl is the first reported
Pseudomonas aeruginosa
phage that targets the Psl exopolysaccharide as receptor. Here, we report the genome of Knedl, demonstrating that it belongs to the genus
Iggyvirus
of the
Queuovirinae
subfamily. Future studies on the infection mechanism of Knedl could inform phage-based approaches to eradicate biofilms.
Cholera toxin and O-specific polysaccharide immune responses after oral cholera vaccination with Dukoral in different age groups of Bangladeshi participants
Authors: Dash Pinki , Hakim Al , Akter Aklima , Banna Hasan Al , Kaisar M. Hasanul , Aktar Amena , Jahan Sultana Rownok , Ferdous Jannatul , Basher Salima Raiyan , Kamruzzaman Mohammad , Chowdhury Fahima , Akter Afroza , Tauheed Imam , Weil Ana A. , Charles Richelle C. , Calderwood Stephen B. , Ryan Edward T. , LaRocque Regina C. , Harris Jason B. , Bhuiyan Taufiqur Rahman , Qadri Firdausi 
Published: February 2024

ABSTRACT

Vaccination is important to prevent cholera. There are limited data comparing anti-O-specific polysaccharide (OSP) and anti-cholera toxin-specific immune responses following oral whole-cell with cholera toxin B-subunit (WC-rBS) vaccine (Dukoral, Valneva) administration in different age groups. An understanding of the differences is relevant because young children are less well protected by oral cholera vaccines than older children and adults. We compared responses in 50 adults and 49 children (ages 2 to <18) who were administered two doses of WC-rBS at a standard 14-day interval. All age groups had significant IgA and IgG plasma-blast responses to the OSP and cholera toxin B-subunit (CtxB) antigens that peaked 7 days after vaccination. However, in adults and older children (ages 5 to <18), antibody responses directed at the OSP antigen were largely IgA and IgG, with a minimal IgM response, while younger children (ages 2 to <5) mounted significant increases in IgM with minimal increases in IgA and IgG antibody responses 30 days after vaccination. In adults, anti-OSP and CtxB memory B-cell responses were detected after completion of the vaccination series, while children only mounted CtxB-specific IgG memory B-cell responses and no OSP-memory B-cell responses. In summary, children and adults living in a cholera endemic area mounted different responses to the WC-rBS vaccine, which may be a result of more prior exposure to
Vibrio cholerae
in older participants. The absence of class-switched antibody responses and memory B-cell responses to OSP may explain why protection wanes more rapidly after vaccination in young children compared to older vaccinees.

IMPORTANCE

Vaccination is an important strategy to prevent cholera. Though immune responses targeting the OSP of
V. cholerae
are believed to mediate protection against cholera, there are limited data on anti-OSP responses after vaccination in different age groups, which is important as young children are not well protected by current oral cholera vaccines. In this study, we found that adults mounted memory B-cell responses to OSP, which were not seen in children. Adults and older children mounted class-switched (IgG and IgA) serum antibody responses to OSP, which were not seen in young children who had only IgM responses to OSP. The lack of class-switched antibody responses and memory B-cell responses to OSP in younger participants may be due to lack of prior exposure to
V. cholerae
and could explain why protection wanes more rapidly after vaccination in young children.
Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications
Authors: Jiang Feng , Ruan Yao , Chen Xiao-Hui , Yu Hai-Long , Cheng Ting , Duan Xin-Ya , Liu Yan-Guang , Zhang Hong-Yu , Zhang Qing-Ye 
Published: February 2024

ABSTRACT

Seed metabolites are the combination of essential compounds required by an organism across various potential environmental conditions. The seed metabolites screening framework based on the network topology approach can capture important biological information of species. This study aims to identify comprehensively the relationship between seed metabolites and pathogenic bacteria. A large-scale data set was compiled, describing the seed metabolite sets and metabolite sets of 124,192 pathogenic strains from 34 genera, by constructing genome-scale metabolic models. The enrichment analysis method was used to screen the specific seed metabolites of each species/genus of pathogenic bacteria. The metabolites of pathogenic microorganisms database (MPMdb) (
http://qyzhanglab.hzau.edu.cn/MPMdb/
) was established for browsing, searching, predicting, or downloading metabolites and seed metabolites of pathogenic microorganisms. Based on the MPMdb, taxonomic and phylogenetic analyses of pathogenic bacteria were performed according to the function of seed metabolites and metabolites. The results showed that the seed metabolites could be used as a feature for microorganism chemotaxonomy, and they could mirror the phylogeny of pathogenic bacteria. In addition, our screened specific seed metabolites of pathogenic bacteria can be used not only for further tapping the nutritional resources and identifying auxotrophies of pathogenic bacteria but also for designing targeted bactericidal compounds by combining with existing antimicrobial agents.

IMPORTANCE
Metabolites serve as key communication links between pathogenic microorganisms and hosts, with seed metabolites being crucial for microbial growth, reproduction, external communication, and host infection. However, the large-scale screening of metabolites and the identification of seed metabolites have always been the main technical bottleneck due to the low throughput and costly analysis. Genome-scale metabolic models have become a recognized research paradigm to investigate the metabolic characteristics of species. The developed metabolites of pathogenic microorganisms database in this study is committed to systematically predicting and identifying the metabolites and seed metabolites of pathogenic microorganisms, which could provide a powerful resource platform for pathogenic bacteria research.
Deciphering differential exhumation in the Gangdese orogen in southern Tibet using exposed porphyry alteration systems and geomorphic analysis
Authors: Fu Hanze , Kereszturi Gabor , Cheng Qiuming , Wang Rui , Smith Adam G.G. 
Published: February 2024

Abstract
Topography and exhumation vary strongly in the Tibetan Plateau, reflecting different geodynamics and surface processes. The Gangdese orogen in southern Tibet is characterized by west-to-east variations in topography and occurrences of the Miocene porphyry copper deposits. We integrated remote sensing based hydrothermal alteration mapping and geomorphological analysis to detect patterns of differential exhumation since the Miocene. High abundances of propylitic and potassic alteration of the eastern Miocene granitoids are identified, indicating &gt;2 km of exhumation since the Miocene. The western Gangdese has intensive phyllic and argillic alteration representing ~1 km of exhumation. Geomorphic analyses also show E-W changes that most likely resulted from differential rock uplift histories. Channel steepness index values indicate the eastern Gangdese has channel gradients between 211 m1.02 and 457 m1.02, compared to values between 30 m1.02 and 160 m1.02 in the west. Linear inversion of tributaries of the Yarlung river shows a pulse of rock uplift between 25 Ma and 7 Ma with a maximum rate of 110 m/ m.y. in the east. In contrast, the western Gangdese exhibits slower and persistent rock uplift rates between 20 m/m.y. and 40 m/m.y. since 20 Ma. The integrated results record differential exhumation and rock uplift since the Miocene. We invoke the geometric variations of the subducted Indian lithosphere to interpret the E-W differential exhumation since the Miocene. Steeper subduction of the Indian lithosphere beneath the eastern Gangdese induced mantle upwelling, triggering rapid rock uplift and deep exhumation. Conversely, the shallower subduction of the Indian slab in the west generated slow and prolonged rock uplift with less exhumation. Our study refines the exhumation process of the Gangdese since the Miocene.
Neurosensory, cognitive and academic outcomes at 8 years in children born 22–23 weeks’ gestation compared with more mature births
Authors: Marks India RM , Doyle Lex W , Mainzer Rheanna M , Spittle Alicia J , Clark Marissa , Boland Rosemarie A , Anderson Peter J , Cheong Jeanie LY 
Published: February 2024

Despite providing intensive care to more infants born <24 weeks’ gestation, data on school-age outcomes, critical for counselling and decision-making, are sparse.ObjectiveTo compare major neurosensory, cognitive and academic impairment among school-aged children born extremely preterm at 22–23 weeks’ gestation (EP22–23) with those born 24–25 weeks (EP24–25), 26–27 weeks (EP26–27) and term (≥37 weeks).DesignThree prospective longitudinal cohorts.SettingVictoria, Australia.ParticipantsAll EP live births (22–27 weeks) and term-born controls born in 1991–1992, 1997 and 2005.Main outcome measuresAt 8 years, major neurosensory disability (any of moderate/severe cerebral palsy, IQ <−2 SD relative to controls, blindness or deafness), motor, cognitive and academic impairment, executive dysfunction and poor health utility. Risk ratios (RRs) and risk differences between EP22–23 (reference) and other gestational age groups were estimated using generalised linear models, adjusted for era of birth, social risk and multiple birth.ResultsThe risk of major neurosensory disability was higher for EP22–23 (n=21) than more mature groups (168 EP24–25; 312 EP26–27; 576 term), with increasing magnitude of difference as the gestation increased (adjusted RR (95% CI) compared with EP24–25: 1.39 (0.70 to 2.76), p=0.35; EP26–27: 1.85 (0.95 to 3.61), p=0.07; term: 13.9 (5.75 to 33.7), p<0.001). Similar trends were seen with other outcomes. Two-thirds of EP22–23 survivors were free of major neurosensory disability.ConclusionsAlthough children born EP22–23 experienced higher rates of disability and impairment at 8 years than children born more maturely, many were free of major neurosensory disability. These data support providing active care to infants born EP22–23.
Comparing the effectiveness of pulsed radiofrequency treatment to lumbar dorsal root ganglion according to application times in patients with lumbar radicular pain: protocol for a randomised controlled trial
Authors: Park Soyoon , Jang Jae Ni , Park Ji-Hoon , Song Yumin , Sooil Choi , Kim Young Uk , Park Sukhee 
Published: February 2024

IntroductionLumbar radicular pain (LRP) is a common symptom characterised by a sharp, shooting or lancinating sensation localised to one or more dermatomes of the lumbar spine. Despite its high prevalence and significant impact on quality of life, the most effective conservative treatment for patients with LRP remains uncertain. When conventional treatment methods do not provide satisfactory results, the option of using epidural steroids and/or pulsed radiofrequency (PRF) treatment may be considered as a secondary approach for managing the condition. Ongoing advances in the field have led to a wide range of PRF parameters being investigated and extensively documented. Therefore, this study will aim to evaluate the treatment efficacy, sustainability and adverse effects of PRF application for different durations in patients with LRP.Methods and analysisThis study will be a double-blind, randomised, controlled trial. Eligible patients with LRP who visit the International St. Mary’s Hospital pain clinic in Korea will be assigned to three groups (1:1:1 ratio) based on the duration of PRF application: 240, 360 and 480 s. Outcome measures will include an assessment of radicular pain intensity, physical function, global improvement, treatment satisfaction and adverse events. The primary outcome will be a Numeric Rating Scale (NRS) score 3 months after the procedure. The secondary outcomes will be the number of subjects in each group reporting successful treatment defined as a significant decrease of NRS or improved physical function score or high satisfaction at the 3 and 6 months follow-up. X2or Fisher’s exact test and one-way analysis of variance will be used to compare the outcomes.Ethics and disseminationThis trial was approved by the Ethics Committee of Catholic Kwandong University International St. Mary’s Hospital (IS23EISE0018). The findings will be disseminated in peer-reviewed journals and at scientific conferences.Trial registration numberKCT0008612.
Telemedicine interventions in type 2 diabetes management: a protocol for systematic review and network meta-analysis
Authors: Maaitah Wasan , Abdelhay Osama , Tourkmani Ayla , Azzeh Mohammad , Abu-Soud Mohammad S , Atiani Serin 
Published: February 2024

IntroductionThe consequences of type 2 diabetes mellitus (T2DM) heavily strain individuals and healthcare systems worldwide. Interventions via telemedicine have become a potential tactic to tackle the difficulties in effectively managing T2DM. However, more research is needed to determine how telemedicine interventions affect T2DM management. This study sets out to systematically analyse and report the effects of telemedicine treatments on T2DM management to gain essential insights into the potential of telemedicine as a cutting-edge strategy to improve the outcomes and care delivery for people with T2DM.Methods and analysisTo uncover relevant research, we will perform a comprehensive literature search across six databases (PubMed, IEEE, EMBASE, Web of Science, Google Scholar and Cochrane Library). Each piece of data will be extracted separately, and any discrepancies will be worked out through discussion or by a third reviewer. The studies included are randomised controlled trial. We chose by predefined inclusion standards. After the telemedicine intervention, glycated haemoglobin will be the primary outcome. The Cochrane risk-of-bias approach will be used to evaluate the quality of the included studies. RevMan V.5.3.5 software and RStiduo V.4.3.1 software can be used to analyse the data, including publication bias.Ethics and disseminationSince this research will employ publicly accessible documents, ethical approval is unnecessary. The review is registered prospectively on the PROSPERO database. The study’s findings will be published in a peer-reviewed journal.PROSPERO registration numberCRD42023421719.
Self-management behaviours in adults with non-alcoholic fatty liver disease: a cross-sectional survey from China
Authors: Zhou Run , Zhang Binbin , Zhang Wei , Kong Tingting , Fu Jie , Li Jie , Shi Junping 
Published: February 2024

ObjectivesThe prevalence of non-alcoholic fatty liver disease (NAFLD) in China has significantly increased due to changing lifestyles and rising obesity rates. Effective self-management behaviours are crucial for reversing NAFLD. This study aimed to assess the current self-management status and the influencing factors among the Chinese NAFLD population.DesignA cross-sectional study.SettingThis was a study conducted between 30 May 2022 and 30 May 2023 at a tertiary care hospital.ParticipantsA total of 380 patients diagnosed with NAFLD were included in this study. NAFLD patients included in this study were diagnosed by FibroScan and had a controlled attenuation parameter ≥248 dB/m.Primary outcomes and measuresThe primary outcomes were self-management, demographic characteristics and clinical features of patients with NAFLD. Self-management-related domains were assessed using the self-management questionnaire of NAFLD.ResultsThe study included 380 patients with an average age of 42.79±13.77 years, with 62.89% being male. The mean score on the self-management scale was 80.92±18.31, indicating a low level of self-management behaviours. Among the five dimensions of the self-management scale, lifestyle management received the highest score (10.68±2.53), while disease knowledge management received the lowest score (9.29±2.51). Furthermore, gender (β=0.118, p=0.009), education level (β=0.118, p=0.010), body mass index (BMI) (β=−0.141, p=0.002) and sleep quality (β=0.387, p<0.001) were found to influence the self-management behaviours of patients to some extent.ConclusionsThis cross-sectional survey in China revealed impaired self-management behaviours among adults with NAFLD. The study identified significant associations between self-management behaviours and gender, education level, BMI and sleep quality. Healthcare providers should focus on optimising the care of NAFLD patients to enhance their self-management behaviours.
Cluster analysis of long COVID in Japan and association of its trajectory of symptoms and quality of life
Authors: Ito Fumimaro , Terai Hideki , Kondo Masahiro , Takemura Ryo , Namkoong Ho , Asakura Takanori , Chubachi Shotaro , Masuzawa Keita , Nakayama Sohei , Suzuki Yusuke , Hashiguchi Mizuha , Kagyo Junko , Shiomi Tetsuya , Minematsu Naoto , Manabe Tadashi , Fukui Takahiro , Funatsu Yohei , Koh Hidefumi , Masaki Katsunori , Ohgino Keiko , Miyata Jun , Kawada Ichiro , Ishii Makoto , Sato Yasunori , Fukunaga Koichi 
Published: February 2024

BackgroundMultiple prolonged symptoms observed in patients who recovered from COVID-19 are defined as long COVID. Although diverse phenotypic combinations are possible, they remain unclear. This study aimed to perform a cluster analysis of long COVID in Japan and clarify the association between its characteristics and background factors and quality of life (QOL).MethodsThis multicentre prospective cohort study collected various symptoms and QOL after COVID-19 from January 2020 to February 2021. This study included 935 patients aged ≥18 years with COVID-19 at 26 participating medical facilities. Hierarchical cluster analysis was performed using 24 long COVID symptom at 3 months after diagnosis.ResultsParticipants were divided into the following five clusters: numerous symptoms across multiple organs (cluster 1, n=54); no or minor symptoms (cluster 2, n=546); taste and olfactory disorders (cluster 3, n=76); fatigue, psychoneurotic symptoms and dyspnoea (low prevalence of cough and sputum) (cluster 4, n=207) and fatigue and dyspnoea (high prevalence of cough and sputum) (cluster 5, n=52). Cluster 1 included elderly patients with severe symptoms, while cluster 3 included young female with mild symptoms. No significant differences were observed in the comorbidities. Cluster 1 showed the most impaired QOL, followed by clusters 4 and 5; these changes as well as the composition of symptoms were observed over 1 year.ConclusionsWe identified patients with long COVID with diverse characteristics into five clusters. Future analysis of these different pathologies could result in individualised treatment of long COVID.Trial registration numberThe study protocol is registered at UMIN clinical trials registry (UMIN000042299).
Exploring the influence of baseline rheumatoid factor levels on TNF inhibitor retention rate in patients with rheumatoid arthritis: a multicentre and retrospective study
Authors: López-Medina Clementina , Calvo-Gutiérrez Jerusalem , Ábalos-Aguilera M Carmen , Cepas Francisco , Plasencia-Rodríguez Chamaida , Martínez-Feito Ana , Balsa Alejandro , Faré-García Regina , Juan-Mas Antoni , Ruiz-Esquide Virginia , Sainz Luis , Díaz-Torné César , Godoy-Navarrete Francisco Javier , Añón-Oñate Isabel , Mena-Vázquez Natalia , Manrique-Arija Sara , Moreno-García Marina Soledad , Ortega-Castro Rafaela , Escudero-Contreras Alejandro 
Published: February 2024

ObjectiveTo assess whether the retention rate of certolizumab pegol (CZP) was longer than that of other tumour necrosis factor inhibitors (TNFi) based on baseline rheumatoid factor (RF) levels.MethodsLongitudinal, retrospective and multicentre study including patients with RA who were treated with any TNFi (monoclonal antibodies (mAB), etanercept (ETA) or CZP). Log-rank test and Cox regressions were conducted to evaluate the retention rate in the three groups according to the level of RF, with the third quartile of the baseline levels used as cut-off: <200 (<Q3) and ≥200 (≥Q3) IU/mL. A sensitivity analysis matching patients using a propensity score technique based on age, concomitant use of methotrexate and previous targeted synthetic/biological disease-modifying antirheumatic drugs was performed to address the imbalance across groups.ResultsA total of 638 individuals and 752 treatments (132 CZP, 439 mAB and 181 ETA) were included. In non-naïve patients with ≥200 IU/mL of RF, those treated with CZP showed a significantly longer retention rate in comparison with mAB and ETA. After matching using the propensity score, patients with ≥200 IU/mL RF levels exhibited longer retention rates with CZP than with mAB (HR 2.3 (95% CI 1.2 to 4.3), or ETA (HR 2.8 (95% CI 1.5 to 5.2). No differences were found between groups in patients with <200 UI/mL.ConclusionsCZP showed a longer retention rate than mAB and ETA in patients with very high RF levels (≥200 IU/mL), while these differences were absent in patients with <200 IU/mL levels. The results suggest the potential effect of RF on binding the fragment crystallisable portion of certain TNFi.