bluuebunny/crossref_metadata_2025_split huggingface dataset:
From microbiome composition to functional engineering, one step at a time
Authors: Burz Sebastian Dan , Causevic Senka , Dal Co Alma , Dmitrijeva Marija , Engel Philipp , Garrido-Sanz Daniel , Greub Gilbert , Hapfelmeier Siegfried , Hardt Wolf-Dietrich , Hatzimanikatis Vassily , Heiman Clara Margot , Herzog Mathias Klaus-Maria , Hockenberry Alyson , Keel Christoph , Keppler Andreas , Lee Soon-Jae , Luneau Julien , Malfertheiner Lukas , Mitri Sara , Ngyuen Bidong , Oftadeh Omid , Pacheco Alan R. , Peaudecerf François , Resch Grégory , Ruscheweyh Hans-Joachim , Sahin Asli , Sanders Ian R. , Slack Emma , Sunagawa Shinichi , Tackmann Janko , Tecon Robin , Ugolini Giovanni Stefano , Vacheron Jordan , van der Meer Jan Roelof , Vayena Evangelia , Vonaesch Pascale , Vorholt Julia A. 
Published: November 2023

SUMMARY

Communities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N
+
1/N−1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N−1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N−1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
Phytophthora capsici
genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing
Authors: Szadkowski Emmanuel , Lagnel Jacques , Touhami Nasradin , Sayeh Amalia , Lopez-Roques Céline , Bouchez Olivier , Lefebvre Véronique 
Published: November 2023

ABSTRACT

The oomycete
Phytophthora capsici
is a common pathogen of the Solanaceae and Cucurbitaceae families. An improved assembly for the reference isolate LT1534 was constructed using Oxford Nanopore Technologies and Illumina data. Additionally, an unpolished assembly was produced for the European isolate Pc285 collected on chili pepper using Oxford Nanopore reads.
Draft genome sequences of two
Pseudomonas
strains isolated from
129
I plumes at the Hanford Site
Authors: Robinson Courtney J. , Oliver Jerome J. O. , Anike Alexis , Howard M. Hope , Saunders Danielle L. , Lee Brady D. 
Published: November 2023

ABSTRACT

Pseudomonas
strains DVZ6 and DVZ24 were isolated from a sediment trap incubated in an
129
I plume at the Hanford Site (Washington State, USA). Whole-genome sequencing of the strains revealed that both genomes are 5.77 Mb in size, with a G + C content of 64.75%.
Characterizing the dynamics of the rumen microbiota, its metabolites, and blood metabolites across reproductive stages in Small-tailed Han sheep
Authors: Sha Yuzhu , Liu Xiu , Pu Xiaoning , He Yanyu , Wang Jiqing , Zhao Shengguo , Shao Pengyang , Wang Fanxiong , Xie Zhuanhui , Chen Xiaowei , Yang Wenxin 
Published: November 2023

ABSTRACT

Different reproductive stages of mammals involve complex biological processes, and the intestinal microbiota, as an endocrine organ or an “invisible organ,” is involved in the regulation of hormone levels, immune function, and metabolism. However, the effects of the rumen microbiota, its metabolites, and blood metabolites on the reproductive performance of ruminants remain unclear. This study revealed that the
Prevotella
abundance increased significantly during pregnancy (
P
< 0.01); the
Fibrobacter
abundance increased significantly during lactation (
P
< 0.05); and rumen microbial carbohydrate metabolism, glucose biosynthesis, and metabolic functions were significantly enriched during pregnancy (
P
< 0.05). Microbial metabolic profile analysis showed that the differentially abundant microbial metabolites during pregnancy and lactation were mainly enriched in the biosynthesis of ubiquinone and other terpenoid quinones, and there was a certain correlation with the microbiota. Among them, sapindoside A was increased during pregnancy, nicotinamide riboside and β-cryptoxanthin were reduced during pregnancy, and L-tryptophan was significantly increased during lactation. In addition, the volatile fatty acid levels in lactation were significantly higher than those in non-pregnancy and pregnancy (
P
< 0.05), and the NH
3
-N content during pregnancy was significantly higher than that during lactation and non-pregnancy (
P
< 0.05). Moreover, there were differences in the serum metabolite levels at different reproductive stages, and similar metabolites existed when comparing the rumen metabolites, which were mainly enriched in arachidonic acid metabolism, vitamin B6 metabolism, and ABC transporter protein, resulting in significantly higher serum IgA and IgM levels during lactation than during non-pregnancy and pregnancy (
P
< 0.05).

IMPORTANCE

Our study illustrates the succession of the rumen microbiota and its metabolites in Small-tailed Han sheep at different reproductive stages. Among them, Firmicutes and
Prevotella
, which are related to energy metabolism, increased in abundance during pregnancy, while
Fibrobacter
, a fiber-degrading bacterium, increased in abundance during lactation. At the same time, the microbial metabolic profile and serum metabolic profile characteristics of different reproductive stages were revealed, and some functional pathways and metabolites related to energy and immunity were found. This study provides a reference for the health management of ruminants during non-pregnancy, pregnancy, and lactation.
Basalts of a Seamount on the Eastern Flank of the Charlie Gibbs Transform Fracture Zone, North Atlantic: Petrochemical and Isotopic Evidence of a Microplume-Affected Formation in the Axial Zone of the Mid-Atlantic Ridge
Authors: Skolotnev S. G. , Peyve A. A. , Dokashenko S. A. , Dobrolyubov V. N. , Okina O. I. , Ermolaev B. V. 
Published: November 2023

Abstract
The composition of basalts dredged from the slopes of a single seamount (guyot), which is located south of the eastern end of the Charlie Gibbs Fracture Zone in the North Atlantic, is studied. Groups of high- and low-Ti rocks, which belong to oceanic tholeiites of the E-MORB and T-MORB types, respectively, are recognized. The first group of basalts have higher contents of TiO2, Na2O, K2O, P2O5, Fe2O3, and incompatible trace elements. The basalts of both groups are similar in the normalized lithophile element patterns indicating their melting from a similar mantle substrate. The difference in their composition is probably caused by melting of high-Ti volcanic rocks at a deeper intermediate level between spinel and garnet facies. Our studies give grounds to believe that the seamount also formed as a large neovolcanic rise 64–67 Ma ago under the influence of a microplume, which was a branch of the Milne deep mantle plume.
How the marketing practices of commercial milk formula companies impact infant breastfeeding practices in China
Authors: Zhu Zhonghai , Narayan Anuradha , Zhang Shuyi , Wang Liang , Zhu Yingze , Yang Wenfang , Cheng Yue , Zeng Lingxia , Chang Suying 
Published: November 2023

BackgroundThe marketing practices used by commercial milk formula (CMF) companies undermine breast feeding. However, it remains unclear how specific types of marketing practices result in suboptimal breast feeding.ObjectivesWe aimed to examine the associations of CMF marketing practices with breastfeeding outcomes, determine the influencing pathways, how it changes the perceptions and attitudes of mothers towards CMF, and how it impacts breastfeeding outcomes.MethodsA cross-sectional survey was conducted in Beijing and Jinan, China that mapped the CMF marketing practices in 2020. Mothers were interviewed about the feeding practices for the youngest child under the age of 18 months. Maternal attitude towards CMF was assessed using a set of five questions. Six common CMF marketing practices were reviewed. A logistic regression was performed to examine the associations between the CMF marketing practices and predominant breast feeding, with adjustments for maternal age, education, occupation, socioeconomic class and caesarean section. Furthermore, a path analysis was conducted to explore the pathways between the CMF marketing practices, maternal attitude towards CMF and predominant breast feeding.ResultsA total of 750 mothers were interviewed, with 20.0% of mothers predominantly breast feeding their young children. Two marketing practices, online engagement with CMF companies and promotions and discounts, were statistically associated with a lower likelihood of predominant breast feeding, with an adjusted ORs of 0.53 (95% CI 0.35 to 0.82) and 0.45 (95% CI 0.22 to 0.92). Furthermore, per CMF marketing practice increase mothers concurrently exposed to was associated with a 0.79 (95% CI 0.68 to 0.92) times lower likelihood of predominant breast feeding. In addition, online engagement and free formula samples distributed in hospitals had indirect effects on suboptimal breastfeeding outcomes, which was partly mediated by positive maternal attitude towards CMF.ConclusionsCMF marketing practices were associated with a lower likelihood of optimal breastfeeding through influencing the maternal attitude towards CMF.
The COVID-19 pandemic and disruptions to maternal and child health services in public primary care Malaysia: a retrospective time-series analysis
Authors: Mohd Ujang Izzatur Rahmi , Hamidi Normaizira , Ab Hamid Jabrullah , Awang Samsiah , Zulkifli Nur Wahida , Supadi Roslina , Mohamed Nur Ezdiani , Sooryanarayana Rajini 
Published: November 2023

IntroductionThe COVID-19 pandemic has posed significant challenges to healthcare systems worldwide. Maintaining essential health services, including maternal and child health (MCH), while addressing the pandemic is an enormous task. This study aimed to assess the impact of the COVID-19 pandemic on the utilisation of MCH services in Malaysian public primary care.MethodsA retrospective analysis was conducted using national administrative data from 1124 public primary care clinics. Eight indicators were selected to measure service utilisation covering antenatal, postnatal, women’s health, child health, and immunisation services. Interrupted time-series analysis was used to evaluate changes in levels and trends of indicators during four different periods: pre-pandemic (January 2019–February 2020), during pandemic and first lockdown (March–May 2020), after the first lockdown was lifted (June–December 2020) and after the second lockdown was implemented (January–June 2021).ResultsMost indicators showed no significant trend in monthly utilisation prior to the pandemic. The onset of the pandemic and first lockdown implementation were associated with significant decreasing trends in child health (−19.23%), women’s health (−10.12%), antenatal care (−8.10%), contraception (−6.50%), postnatal care (−4.85%) and postnatal care 1-week (−3.52%) indicators. These indicators showed varying degrees of recovery after the first lockdown was lifted. The implementation of the second lockdown caused transient reduction ranging from −11.29% to −25.92% in women’s health, contraception, child and two postnatal indicators, but no sustained reducing trend was seen afterwards. Two immunisation indicators appeared unaffected throughout the study period.ConclusionThe COVID-19 pandemic significantly impacted MCH services utilisation in Malaysia. While most MCH services were negatively affected by the lockdown implementation with varying degrees of recovery, infant immunisation showed resilience throughout. This highlights the need for a targeted preparedness plan to ensure the resilience of MCH services in future crises.
Incidence of admission ionised hypocalcaemia in paediatric major trauma: protocol for a systematic review and meta-analysis
Authors: Hibberd Owen , Price James , Harris Tim , Barnard Ed Benjamin Graham 
Published: November 2023

IntroductionHypocalcaemia forms part of the ‘diamond of death’ in major trauma, alongside hypothermia, acidosis and coagulopathy. In adults, admission hypocalcaemia prior to transfusion is associated with increased mortality, increased blood transfusion requirements and coagulopathy. Data on paediatric major trauma patients are limited. This systematic review and meta-analysis aims to describe and synthesise the available evidence relevant to paediatric trauma, admission hypocalcaemia and outcome.Methods and analysisThe Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols guidelines will be used to construct this review. A planned literature search for articles in the English language will be conducted from inception to the date of searches using MEDLINE on the EBSCO platform, CINAHL on the EBSCO platform and Embase on the Ovid platform. The grey literature will also be searched. Both title and abstract screening and full-text screening will be done by two reviewers, with an adjudicating third reviewer. Heterogeneity will be assessed using the I2test, and the risk of bias will be assessed using the ROBINS-I tool. A meta-analysis will be undertaken using ratio measures (OR) and mean differences for measures of effect. When possible, the estimate of effect will be presented along with a CI and a p value.Ethical review and disseminationEthical review is not required, as no original data will be collected. Results will be disseminated through peer-reviewed publications and at academic conferences.PROSPERO registration numberCRD42023425172.
Views and experiences of long-acting reversible contraception among ethnic minorities in high-income countries: a systematic review of qualitative studies
Authors: Ahmed Sumayyah , McLoughlin Dymond Abigail , Correa Michele , Willcox Merlin L 
Published: November 2023

BackgroundEthnic minorities in high-income countries have higher rates of unintended pregnancies but are less likely to use highly efficacious long-acting reversible contraception (LARC). The reasons for this are unclear.AimTo understand the views and experiences of ethnic minorities within high-income countries about LARC.MethodologyMedline, CINAHL, EMBASE and Sociological Abstracts were searched systematically to find qualitative articles about views on LARC. Titles and abstracts were screened to select qualitative studies about LARC whose participants were mainly from ethnic minorities in high-income countries. Quality assessment was conducted using the Critical Appraisal Skills Programme (CASP) tool. Thematic synthesis was conducted.ResultsSeventeen studies (19 articles) met the inclusion criteria, 14 of which were from the USA (227 participants identified as Latina, 222 Black, 15 multiracial, 4 Asian). Two studies included 32 Chinese women in the UK and Australia and one included 20 Aboriginal women in Australia. Factors influencing uptake of LARC included side effects, convenience, and perceived efficacy of LARC compared with other methods; women’s ideas, concerns and expectations; and external influences (partner, family/friends, health professionals and society). Convenience of LARC, control over reproductive decisions, and desire to prevent pregnancy were the main facilitators. Barriers included specific cultural concerns about irregular bleeding, concerns about racial discrimination, and family/friends having negative views on LARC.ConclusionsEthnic minority women often have additional needs and concerns about LARC compared with the White majority. Further research is needed to develop and evaluate customised respectful counselling on contraception options for ethnic minority women and their partners.
Timed adoptive T cell transfer during chemotherapy in patients with recurrent platinum-sensitive epithelial ovarian cancer
Authors: Verdegaal Els M E , Santegoets Saskia J , Welters Marij J P , de Bruin Linda , Visser Marten , van der Minne Caroline E , de Kok Pita M , Loof Nikki M , Boekestijn Sanne , Roozen Inge , Westra Inge M , Meij Pauline , Van der Burg Sjoerd H , Kroep Judith R 
Published: November 2023

BackgroundThe presence of T cells and suppressive myeloid cells in epithelial ovarian cancer (EOC) correlate with good and bad clinical outcome, respectively. This suggests that EOC may be sensitive to adoptive cell therapy with autologous tumor-infiltrating lymphocytes (TIL), provided that immunosuppression by myeloid-derived suppressor cells and M2 macrophages is reduced. Platinum-based chemotherapy can alleviate such immunosuppression, potentially creating a window of opportunity for T cell-based immunotherapy.MethodsWe initiated a phase I/II trial (NCT04072263) in patients with recurrent platinum-sensitive EOC receiving TIL during platinum-based chemotherapy. TILs were administered 2 weeks after the second, third and fourth chemotherapy course. Patients were treated in two cohorts with or without interferon-α (IFNa), as conditioning and TIL support regimen. The primary endpoint was to evaluate the feasibility and safety according to CTCAE V.4.03 criteria and the clinical response and immune modulatory effects of this treatment were evaluated as secondary endpoints.ResultsSixteen patients were enrolled. TIL could be successfully expanded for all patients. TIL treatment during chemotherapy without IFNa (n=13) was safe but the combination with IFNa added to the chemotherapy-induced toxicity with 2 out of 3 patients developing thrombocytopenia as dose-limiting toxicity. Fourteen patients completed treatment with a full TIL cycle and were further evaluated for clinical and immunological response. Platinum-based chemotherapy resulted in reduction of circulating myeloid cell numbers and IL-6 plasma levels, confirming its immunosuppression-alleviating effect. Three complete (CR), nine partial responses and two stable diseases were recorded, resulting in an objective response rate of 86% (Response Evaluation Criteria In Solid Tumors V.1.1). Interestingly, progression free survival that exceeded the previous platinum-free interval was detected in two patients, including an exceptionally long and ongoing CR in one patient that coincided with sustained alleviation of immune suppression.ConclusionTIL therapy can be safely combined with platinum-based chemotherapy but not in combination with IFNa. The chemotherapy-mediated reduction in immunosuppression and the increase in platinum-free interval for two patients warrants further exploration of properly-timed TIL infusions during platinum-based chemotherapy, possibly further benefiting from IL-2 support, as a novel treatment option for EOC patients.
Sex-specific difference in cardiac function in patients with systemic sclerosis: association with cardiovascular outcomes
Authors: Gegenava Tea , Fortuni Federico , van Leeuwen Nina Marijn , Tennoe Anders H , Hoffmann-Vold Anna-Maria , Jurcut Ruxandra , Giuca Adrian , Groseanu Laura , Tanner Felix , Distler Oliver , Bax Jeroen J , De Vries-Bouwstra Jeska , Ajmone Marsan Nina 
Published: November 2023

BackgroundCardiovascular involvement is one of the leading causes of mortality in systemic sclerosis (SSc) and is reported to be higher in men as compared with women. However, the cause of this difference is largely unknown. The objective of this study was to assess sex differences in echocardiographic characteristics, including left ventricular global longitudinal strain (LV GLS), as a potential explanation of sex differences in outcomes.MethodsA total of 746 patients with SSc from four centres, including 628 (84%, 54±13 years) women and 118 (16%, 55±15 years) men, were evaluated with standard and advanced echocardiographic examinations. The independent association of the echocardiographic parameters with the combined endpoint of cardiovascular events-hospitalisation/death was evaluated.ResultsMen and women with SSc showed significant differences in disease characteristics and cardiac function. After adjusting for the most important clinical characteristics, while LV ejection fraction and diastolic function were not significantly different anymore, men still presented with more impaired LV GLS as compared with women (−19% (IQR −20% to −17%) vs −21% (IQR: −22% to −19%), p<0.001). After a median follow-up of 48 months (IQR: 26–80), the combined endpoint occurred in 182 patients. Men with SSc experienced higher cumulative rates of cardiovascular events-hospitalisation/mortality (χ2=8.648; Log-rank=0.003), and sex differences were maintained after adjusting for clinical confounders, but neutralised when matching the groups for LV GLS.ConclusionIn patients with SSc, male sex is associated with worse cardiovascular outcomes even after adjusting for important clinical characteristics. LV GLS was more impaired in men as compared with women and potentially explains the sex difference in cardiovascular outcomes.
f(G, T) and its cosmological implications
Authors: Yousaf Z. , Bhatti M.Z. , Ganesan T. , Aman H. 
Published: November 2023

A coupled formulation of the Gauss–Bonnet invariant term G and the energy–momentum trace T term, which provide a modified f( G, T) gravity, has been analyzed in this study. The functional form for the f( G, T) gravity has been taken as f( G, T) = α T + β G n , where α and β are free parameters. The field equations are produced in general, which then used a dust case to extract a novel Hubble parameter. The stability of the assumed model and explanation for the late-time acceleration have been studied by the energy bound. Furthermore, the dynamical variables are used to analyze the behavior of the equation of state parameter by restricting different parameters with respect to the recent observational data. A quintessence-like evolution has been achieved as a result of this study.