bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multicenter study to assess the use of BL-DetecTool for the detection of CTX-M-type ESBLs and carbapenemases directly from clinical specimens
Authors: Fernandez-Pittol Mariana , Bosch Jordi , Ballesté-Delpierre Clara , Gonzalez Camille , Vasilakopoulou Alexandra , Berbel Dàmaris , Riccobono Eleonora , Gatermann Sören , Kamotsay Katalin , Reissier Sophie , Szabo Dora , Aszalos Albert Zoltan , Francius Laura , Volland Hervé , Stankov-Pugès Milovan , Rosenmöller Magda , Naas Thierry , Vila Jordi 
Published: February 2024

ABSTRACT

Antimicrobial resistance (AMR) is one of the major public health problems worldwide. Multiple strategies have been put in place to address this problem. One of them is the rapid detection of the mechanisms of resistance, such as extended-spectrum beta-lactamases (ESBLs) and/or carbapenemases. We conducted a multicenter study that included nine European centers for the assessment of prototypes of a novel lateral flow immunoassay-based device (BL-DetecTool) for a rapid detection of ESBL (NG-Test CTX-M-MULTI DetecTool) and/or carbapenemases (NG-Test CARBA 5 DetecTool) from
Enterobacterales
and
Pseudomonas aeruginosa
in positive urine, positive blood cultures, and rectal swabs. We performed a prospective analysis between January 2021 and June 2022, including overall 22,010 samples. Based on each hospital information, the sensitivity to detect CTX-M was 84%–100%, 90.9%–100%, and 75%–100% for urine, positive blood cultures, and enriched rectal swabs, respectively. On the other hand, the sensitivity to detect carbapenemases was 42.8%–100%, 75%–100%, and 66.6%–100% for urine, positive blood cultures, and enriched rectal swab, respectively. BL-DetecTool allows a rapid and reliable detection of ESBL and carbapenemases directly from urine, positive blood cultures, or enriched rectal swabs, being an easy technique to implement in the workflow of clinical microbiology laboratories.

IMPORTANCE
The assessed rapid assay to detect CTX-M beta-lactamases and carbapenemases directly from clinical samples can favor in the rapid detection of these mechanisms of resistance and hence the administration of a more adequate antimicrobial treatment.
Unraveling the dynamics of hepatitis C virus adaptive mutations and their impact on antiviral responses in primary human hepatocytes
Authors: Frericks Nicola , Brown Richard J. P. , Reinecke Birthe M. , Herrmann Maike , Brüggemann Yannick , Todt Daniel , Miskey Csaba , Vondran Florian W. R. , Steinmann Eike , Pietschmann Thomas , Sheldon Julie 
Published: February 2024

ABSTRACT

Hepatitis C virus (HCV) infection progresses to chronicity in the majority of infected individuals. Its high intra-host genetic variability enables HCV to evade the continuous selection pressure exerted by the host, contributing to persistent infection. Utilizing a cell culture-adapted HCV population (p100pop) which exhibits increased replicative capacity in various liver cell lines, this study investigated virus and host determinants that underlie enhanced viral fitness. Characterization of a panel of molecular p100 clones revealed that cell culture adaptive mutations optimize a range of virus-host interactions, resulting in expanded cell tropism, altered dependence on the cellular co-factor micro-RNA 122 and increased rates of virus spread. On the host side, comparative transcriptional profiling of hepatoma cells infected either with p100pop or its progenitor virus revealed that enhanced replicative fitness correlated with activation of endoplasmic reticulum stress signaling and the unfolded protein response. In contrast, infection of primary human hepatocytes with p100pop led to a mild attenuation of virion production which correlated with a greater induction of cell-intrinsic antiviral defense responses. In summary, long-term passage experiments in cells where selective pressure from innate immunity is lacking improves multiple virus-host interactions, enhancing HCV replicative fitness. However, this study further indicates that HCV has evolved to replicate at low levels in primary human hepatocytes to minimize innate immune activation, highlighting that an optimal balance between replicative fitness and innate immune induction is key to establish persistence.

IMPORTANCE
Hepatitis C virus (HCV) infection remains a global health burden with 58 million people currently chronically infected. However, the detailed molecular mechanisms that underly persistence are incompletely defined. We utilized a long-term cell culture-adapted HCV, exhibiting enhanced replicative fitness in different human liver cell lines, in order to identify molecular principles by which HCV optimizes its replication fitness. Our experimental data revealed that cell culture adaptive mutations confer changes in the host response and usage of various host factors. The latter allows functional flexibility at different stages of the viral replication cycle. However, increased replicative fitness resulted in an increased activation of the innate immune system, which likely poses boundary for functional variation in authentic hepatocytes, explaining the observed attenuation of the adapted virus population in primary hepatocytes.
Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice
Authors: Guo Junjie , Ning Huiling , Li Yong , Xu Qicheng , Shen Qirong , Ling Ning , Guo Shiwei 
Published: February 2024

ABSTRACT

The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.

IMPORTANCE
The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.
Verification of a method using magnetic bead enrichment and nucleic acid extraction to improve the molecular detection of bacterial contamination in blood components
Authors: Na Byungjoon , Lee Jinyeop , Chang Ho Eun , Park Eunseon , Park Sojin , Lee Jiyoung , Oh Sujin , Shin Dong Woo , Hong Yun Ji , Park Kyoung Un 
Published: February 2024

ABSTRACT

Bacterial contamination of blood products poses a significant risk in transfusion medicine. Platelets are particularly vulnerable to bacterial growth because they must be stored at room temperature with constant agitation for >5 days. The limitations of bacterial detection using conventional methods, such as blood cultures and lateral flow assays, include the long detection times, low sensitivity, and the requirement for substantial volumes of blood components. To address these limitations, we assessed the performance of a bacterial enrichment technique using antibiotic-conjugated magnetic nanobeads (AcMNBs) and real-time PCR for the detection of bacterial contamination in plasma. AcMNBs successfully captured >80% of four bacterial strains, including
Staphylococcus aureus
,
Bacillus cereus
,
Escherichia coli
, and
Klebsiella pneumoniae
, in both plasma and phosphate-buffered saline. After 24-h incubation with bacterial enrichment,
S. aureus
and
B. cereus
were each detected at 10
1
CFU/mL in all trials (5/5),
E. coli
at 10
1
CFU/mL in 1/5 trials, and
K. pneumoniae
at 10² CFU/mL in 4/5 trials. Additionally, without incubation, the improvement was also achieved in samples with bacterial enrichment,
S. aureus
at 10² CFU/mL and
B. cereus
at 10
1
CFU/mL in 1/5 trials each,
E. coli
at 10³ CFU/mL in 3/5 trials, and
K. pneumoniae
at 10¹ CFU/mL in 2/5 trials. Overall, the findings from this study strongly support the superiority of bacterial enrichment in detecting low-level bacterial contamination in plasma when employing AcMNBs and PCR.

IMPORTANCE

The study presents a
break
through
approach to detect bacterial contamination in plasma, a critical concern in transfusion medicine. Traditional methods, such as blood cultures and lateral flow assays, are hampered by slow detection times, low sensitivity, and the need for large blood sample volumes. Our research introduces a novel technique using antibiotic-conjugated magnetic nanobeads combined with real-time PCR, enhancing the detection of bacteria in blood products, especially platelets. This method has shown exceptional efficiency in identifying even low levels of four different species of bacteria in plasma. The ability to detect bacterial contamination rapidly and accurately is vital for ensuring the safety of blood transfusions and can significantly reduce the risk of infections transmitted through blood products. This advancement is a pivotal step in improving patient outcomes and elevating the standards of care in transfusion medicine.
Ethical preparedness in genomic medicine: how NHS clinical scientists navigate ethical issues
Authors: Sahan Kate , Lyle Kate , Carley Helena , Hallowell Nina , Parker Michael J , Lucassen Anneke M 
Published: February 2024

Much has been published about the ethical issues encountered by clinicians in genetics/genomics, but those experienced by clinical laboratory scientists are less well described. Clinical laboratory scientists now frequently face navigating ethical problems in their work, but how they should be best supported to do this is underexplored. This lack of attention is also reflected in the ethics tools available to clinical laboratory scientists such as guidance and deliberative ethics forums, developed primarily to manage issues arising within the clinic.We explore what ethical issues are being experienced by clinical scientists, how they think such issues could be best analysed and managed, and whether their practice might be enhanced by more situated approaches to ethics deliberation and practice such as ethical preparedness. From thematic analysis of cases presented by clinical scientists at a specially convened meeting of the UK Genethics Forum, we derived three main ethical themes: (1) the redistribution of labour and responsibilities resulting from the practice of genomic medicine; (2) the interpretation and certainty of results and (3) the proposal that better standardisation and consistency of ethical approaches (for example, more guidelines and policy) could resolve some of the challenges arising.We argue that although standardisation is important for promoting shared understandings of good (including ethical) practice, supplementary approaches to enhance and sustain ethical preparedness will be important to help clinical scientists and others in the recently expanded genetic/genomic medicine environment foster quality ethical thinking.
Development of the Pediatric Integrated Nutrition Pathway for Acute Care (P-INPAC) using a modified Delphi technique
Authors: Brunet-Wood Kim , Tul-Noor Zujaja , Bandsma Robert H.J. , Carter Laura , Fleming-Carroll Bonnie , Gramlich Leah , Hutchison Kim , Huysentruyt Koen , Kalnins Daina , Marchand Valerie , Martinez Andrea , Pai Nikhil , Vachon Mélanie , Hulst Jessie M. 
Published: February 2024

One in three hospitalized children have disease-related malnutrition (DRM) upon admission to hospital, and all children are at risk for further nutritional deterioration during hospital stay; however, systematic approaches to detect DRM in Canada are lacking. To standardise and improve hospital care, the multidisciplinary pediatric working group of the Canadian Malnutrition Taskforce aimed to develop a pediatric, inpatient nutritional care pathway based on available evidence, feasibility of resources, and expert consensus. The working group ( n = 13) undertook a total of four meetings: an in-person meeting to draft the pathway based on existing literature and modelled after the Integrated Nutrition Pathway for Acute Care (INPAC) in adults, followed by three online surveys and three rounds of online Delphi consensus meetings to achieve agreement on the draft pathway. In the first Delphi survey, 32 questions were asked, whereas in the second and third rounds 27 and 8 questions were asked, respectively. Consensus was defined as any question/issue in which at least 80% agreed. The modified Delphi process allowed the development of an evidence-informed, consensus-based pathway for inpatients, the Pediatric Integrated Nutrition Pathway for Acute Care (P-INPAC). It includes screening <24 h of admission, assessment with use of Subjective Global Nutritional Assessment (SGNA) <48 h of admission, as well as prevention, and treatment of DRM divided into standard, advanced, and specialized nutrition care plans. Research is necessary to explore feasibility of implementation and evaluate the effectiveness by integrating P-INPAC into clinical practice.
Women in Canada are consuming above the upper intake level of folic acid but few are meeting dietary choline recommendations in the second trimester of pregnancy: data from the CHILD cohort study
Authors: Wiedeman Alejandra M. , Miliku Kozeta , Moraes Theo J. , Mandhane Piushkumar J. , Simons Elinor , Subbarao Padmaja , Turvey Stuart E. , Zwicker Jill G. , Devlin Angela M. 
Published: February 2024

There is concern that during a low-risk pregnancy, women are consuming more than recommended (400 µg/day) supplemental folic acid and may not meet recommendations for other nutrients. The objective of this study was to determine folic acid supplement use and dietary folate intakes in the second trimester (week 18) of pregnancy in women ( n = 2996) in the Canadian CHILD cohort study. Vitamin B12 and choline intakes were also assessed because they are metabolically related to folate. The majority of participants (71.6%) were consuming a daily prenatal supplement. Twenty-eight percent of women ( n = 847) reported consuming a folic acid supplement and of these women, 45.3% had daily supplemental folic acid intakes above the upper intake level (UL; 1000 µg/day). Daily dietary folate intakes were (mean (SD)) 575 (235) DFE µg/day. In contrast, only 24.8% of women met the dietary choline adequate intake (AI) recommendation (AI ≥ 450 mg/day) with a mean (SD) intake of 375 (151) mg/day. Further understanding of the impact of supplemental folic acid intake above the UL and low choline intake during pregnancy requires further investigation.
Soil responses to inclusion of corn, soybean, and cover crops under rainfed conditions in the northern Great Plains
Authors: Liebig Mark A. , Archer David W. , Halvorson Jonathan J. , Clemensen Andrea K. , Hendrickson John R. , Tanaka Donald L. 
Published: February 2024

Crop rotations in the northern Great Plains of North America increasingly include corn ( Zea mays L.) and soybean ( Glycine max (L.) Merr.). Use of cover crops, while less extensive, is also increasing given their purported agronomic and environmental benefits. To date, soil responses to the inclusion of corn, soybean, and cover crops in rainfed cropping systems have not been well documented in the region. Therefore, soil properties were evaluated 6 years after establishment of three crop rotations (spring wheat ( Triticum aestivum L.)–soybean (SW–S), spring wheat–corn–soybean (SW–C–S), and spring wheat–corn–cover crop (SW–C–cc)) each split by no and minimum tillage on a Dark Brown Chernozem near Mandan, ND, USA. Soil responses to treatments were subtle and exclusive to the 0–7.6 cm depth. Soil pH was lower in SW–S than SW–C–cc (5.28 vs. 5.48; P = 0.05), SO4-S was greater under SW–C–cc than SW–C–S (13.4 vs. 11.6 g S kg−1; P = 0.03), exchangeable K was greater under SW–C–S and SW–C–cc than SW–S (0.83 cmol kg−1 vs. 0.52 cmol kg−1; P = 0.05), and water-stable aggregates were greater in SW–S than SW–C–S (26% vs. 19%; P = 0.08). Soil organic carbon (SOC) and total N did not differ among crop rotations or between tillage treatments, while particulate organic matter N was greater under no tillage compared to minimum tillage ( P = 0.08). Between 2012 and 2018, soil pH decreased and SOC increased under SW–C–S. Frequent monitoring of near-surface soil conditions in rotations with soybean every other year is recommended. Furthermore, innovative management practices are needed to enhance soil C and N fractions in rotations with full-season cover crops.
Integrating Network Information Into Credit Classification Models
Authors: An Le T. T. , Anh Hoang T. K. , Anh Luu M. , Mien Mai T. , Oanh Phan T. K. 
Published: February 2024

Some qualitative studies have mentioned the impact of trading networks on the credit levels of countries or businesses. However, only a few studies quantified network information on simulated or actual data. This research studied the relationship between network characteristics and sovereign credit levels. Using a data set for 114 countries, we developed and compared the performance of five credit classification models with and without integrating network information. We used several measures to quantify the trading network information, such as Trading Weight, Closeness, Betweenness, PageRank, and Modularity. The analysis showed that they were closely related to credit levels. In particular, the Trading Weight usually belonged to the top five critical features for almost all classifiers. Overall, we saw that the correct prediction of the network models was consistently higher than those without a network. It meant we could improve the sovereign credit classifications with available trading network information.
Structure of the Plio-Quaternary coastal aquifer (Mediterranean Basin, Tunisia): insights from gravity and seismic analysis
Authors: Ayari Sana , Ghouili Nesrine , Gabtni Hakim , Zouhri Lahcen 
Published: February 2024

This research paper presents an investigation of an aquifer structure using a combination of gravity and seismic analyses, calibrated by hydrogeological data. This work illustrates how crucial it is to study geological structures and fault networks as preliminary work to understand water- and pollutant-flow systems and aquifer vulnerability, especially with the increased frequency of drought events and climate change pressures. A Plio-Quaternary coastal northeastern aquifer in Tunisia was chosen as the study case.
First, a hydrogeological approach was performed using water wells, and piezometer data showed an important fluctuation in the piezometric level and a notable depression in the piezometric surface observed in the southern part of the study area.
Secondly, gravity data were analysed and calibrated using a seismic profile. The results demonstrated the presence of shallow NE–SW faults less than 300 m below the region's principal wadis, as well as deeper faults of varying depths (from 400 to 2600 m) that influence the basin structure, aquifer geometry and resulting water flow.
The combination of these approaches revealed that the variations in the aquifer thickness, piezometric surface depression zones and groundwater flow are mainly controlled by shallow and deep geological structures and their tectonic reactivation.
The Reach of Calls and Text Messages for Mailed FIT Outreach in the PROMPT Stepped-Wedge Colorectal Cancer Screening Trial
Authors: Coronado Gloria D. , Nyongesa Denis B. , Petrik Amanda F. , Thompson Jamie H. , Escaron Anne L. , Pham Tuan , Leo Michael C. 
Published: February 2024

Abstract

Background:
Mailed fecal immunochemical test (FIT) outreach can improve colorectal cancer screening participation. We assessed the reach and effectiveness of adding notifications to mailed FIT programs.

Methods:
We conducted secondary analyses of a stepped-wedge evaluation of an enhanced mailed FIT program (n = 15 clinics). Patients were stratified by prior FIT completion. Those with prior FIT were sent a text message (Group 1); those without were randomized 1:1 to receive a text message (Group 2) or live phone call (Group 3). All groups were sent automated phone call reminders. In stratified analysis, we measured reach and effectiveness (FIT completion within 6 months) and assessed patient-level associations using generalized estimating equations.

Results:
Patients (n = 16,934; 83% Latino; 72% completed prior FIT) were reached most often by text messages (78%), followed by live phone calls (71%), then automated phone calls (56%). FIT completion was higher in patients with prior FIT completion versus without [44% (Group 1) vs. 19% (Group 2 + Group 3); P &lt; 0.01]. For patients without prior FIT, effectiveness was higher in those allocated to a live phone call [20% (Group 3) vs. 18% (Group 2) for text message; P = 0.04] and in those who personally answered the live call (28% vs. 9% no call completed; P &lt; 0.01).

Conclusions:
Text messages reached the most patients, yet effectiveness was highest in those who personally answered the live phone call.

Impact:
Despite the broad reach and low cost of text messages, personalized approaches may more successfully boost FIT completion.
Addressing Social Risks to Accelerate Health Equity in Cancer Prevention and Control
Authors: McDougall Jean A. , Hastert Theresa A. , Teteh Dede K. , Rogers Charles R. , Moss Jennifer L. , Ochoa-Dominguez Carol Y. , Chebli Perla , Sutton Arnethea L. , Qin Bo , Warner Erica T. , Xiong Serena 
Published: February 2024

Abstract
Addressing social risks in cancer prevention and control presents a new opportunity for accelerating cancer health equity. As members of the American Society of Preventive Oncology (ASPO) Cancer Health Disparities Special Interest Group, we describe the current state of science on social risks in oncology research and practice. To reduce and eliminate the unjust burden of cancer, we also provide recommendations for multilevel research examining social risks as contributors to inequities and the development of social risks-focused interventions. Suggestions for research and practice are provided within levels of the socio-ecological model, including the interpersonal, organizational, community, and policy levels.