bluuebunny/crossref_metadata_2025_split huggingface dataset:
TaME-seq2: Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling
Authors: Løvestad Alexander Hesselberg , Stosic Milan , Costanzi Jean-Marc , Christiansen Irene Kraus , Aamot Hege Vangstein , Ambur Ole Herman , Rounge Trine B. 
Published: January 2023

Abstract
Background
Previously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the HPV DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the method's flexibility to a broader range of viruses, both DNA and RNA.
Results
Compared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approximately 40x faster. In total, 23 HPV-positive samples and seven SARS-CoV-2 clinical samples passed the threshold of 300x mean depth and were submitted to further analysis. The mean number of variable sites per 1000 bp was ~ 1.5x higher in SARS-CoV-2 than in HPV-positive samples. Reproducibility and repeatability of the method were tested on a subset of samples. A viral integration breakpoint followed by a partial genomic deletion was found in within-run replicates of HPV59-positive sample. Identified viral consensus sequence in two separate runs was >99.9 % identical between replicates, differing by a couple of nucleotides identified in only one of the replicates. Conversely, the number of identical minor nucleotide variants (MNVs) differed greatly between replicates, probably caused by PCR-introduced bias. The total number of detected MNVs, calculated gene variability and mutational signature analysis, were unaffected by the sequencing run.
Conclusion
TaME-seq2 proved well suited for consensus sequence identification, and the detection of low-frequency viral genome variation and viral-chromosomal integrations. The repertoire of TaME-seq2 now encompasses seven HR-HPV types. Our goal is to further include all HR-HPV types in the TaME-seq2 repertoire. Moreover, with a minor modification of previously developed primers, the same method was successfully applied for the analysis of SARS-CoV-2 positive samples, implying the ease of adapting TaME-seq2 to other viruses.
Qualitative assessment of the national initiative to implement antimicrobial stewardship centres in French administrative regions
Authors: Conlin Michèle , Leroy Anne-Gaëlle , Asquier-Khati Antoine , Boutoille David , Birgand Gabriel 
Published: January 2023

Abstract
Background: In May 2020, the French Ministry of Health funded the creation of regional antimicrobial stewardship (AMS) coordination centres (CRAtb) in preparation for the new national framework for the prevention of antimicrobial resistance. This study aimed to assess through qualitative methods the implementation process, the activities carried out, and the interactions with other regional stakeholders of the newly created CRAtb.
Methods: We conducted a mixed-method study based on a cross-sectional survey and semi-structured interviews by French regions among implemented CRAtb. Of the eight eligible French regions with an existing CRAtb, seven participated to the online survey. Regional partners involved in AMS from the eight regions were interviewed between September 2021 and April 2022. The survey questionnaire addressed, through closed questions, the organization of the CRAtb, articulation with other regional actors involved in AMS and infection prevention and control, and AMS activities. The semi-structured interviews approached the implementation and the role of the CRAtb, and the collaboration of other AMS and Infection Prevention and Control (IPC) stakeholders. Interview transcripts were analysed using thematic content analysis methodology.
Results: AMS activities carried out by CRAtb were mainly focusing on hospitals (n=3), primary care (n=2) and nursing homes (n=1), and mainly relied on education and training, online communications. CRAtb members reported still being more engaged in providing advices to professionals for individual antibiotic treatments rather than collective-level AMS activities. Interactions were frequent between CRAtb, IPC regional centres and health authorities, but rarely involved other stakeholders. Interviews were performed with 28 professionals involved in AMS from eight regions. Pre-existing networks and working relationships in AMS and more broadly facilitated the implementation of CRAtb. Streamlining and decompartmentalizing IPC and AMS regional activities were considered a way to optimise the prevention of antimicrobial resistance across sectors. The engagement with liberal health professionals was identified as a significant obstacle for CRAtb.
Conclusions: Two years after the launch of a new national framework, the implementation of CRAtb appeared complex in most regions. An integrative model joining IPC and AMS efforts, relying on existing networks, with engagement from liberal health profession organisations may be the next pivotal step.
“It Saved Us”: Parent Perspectives of the 2021 Expanded Child Tax Credit
Authors: Hamilton Leah , Bellisle Dylan , Brugger Laura , Roll Stephen , Fox-Dichter Sophia , Pitman Emily 
Published: January 2023

Abstract
In early 2021, Congress expanded the existing Child Tax Credit (CTC), increasing the credit’s maximum value (up to $3,000 for school-age children and $3,600 for children under the age of six). Half of the credit was issued monthly to most families from July to December 2021. The temporary expansion was further made fully refundable, meaning that for one year, even very low-income families qualified. In this study, we draw on a novel, multi-wave probability-based panel survey of more than 1,000 CTC recipients to understand the credit’s impact on families. Using a mixed-methods approach that combines logistic regression and qualitative content analysis, we find that most respondents reported that the CTC made it easier for them to support their families, afford utility bills, and cover housing costs. Over one-third of respondents also stated that the CTC allowed them to pay for extracurricular activities for their children and save for their child’s future education, and spend more time with their children. In open-ended responses, parents describe that the CTC had a generally positive effect: it helped with bills/utilities, allowed families to save, helped with groceries/food, covered necessities for children, and reduced stress for parents. Conversely, some reported that it had no effects or made no difference. We also assess how participant demographics and political affiliation are associated with each theme.
A Deep Learning Model for the Identification of Active Contraction Properties of the Myocardium Using Limited Clinical Metrics
Authors: Nobrega Igor Augusto Paschoalotte , Mao Wenbin 
Published: January 2023

Abstract
Technological breakthroughs have enhanced our understanding of myocardial mechanics and physiological responses to detect early disease indicators. Using constitutive models to represent myocardium structure is critical for understanding the intricacies of such complex tissues. Several models have been developed to depict both passive response and active contraction of myocardium, however they require careful adjustment of material parameters for patient-specific scenarios and substantial time and computing resources. Thus, most models are unsuitable for employment outside of research. Deep learning (DL) has sparked interest in data-driven computational modeling for complex system analysis. We developed a DL model for assessing and forecasting the behavior of an active contraction model of the left ventricular (LV) myocardium under a patient-specific clinical setting. Our original technique analyzes a context in which clinical measures are limited: as model input, just a handful of clinical parameters and a pressure-volume (PV) loop are required. This technique aims to bridge the gap between theoretical calculations and clinical applications by allowing doctors to use traditional metrics without administering additional data and processing resources. Our DL model's main objectives are to produce a waveform of active contraction property that properly portrays patient-specific data during a cardiac cycle and to estimate fiber angles at the endocardium and epicardium. Our model accurately represented the mechanical response of the LV myocardium for various PV curves, and it applies to both idealized and patient-specific geometries. Integrating artificial intelligence with constitutive-based models allows for the autonomous selection of hidden model parameters and facilitates their application in clinical settings.
A Study on use of Waste Materials as Partial Replacement of Coarse Aggregate in Concrete
Authors: JAIN AYUSH , AGRAWAL GAURAV KUMAR , VERMA PRIYANKA 
Published: January 2023

Abstract
Background: More development approaches more litter, more litter makes natural worries of harmful danger. The use of litter materials for future new products would be a cost-effective and realistic solution to this problem, reducing the tremendous pressure on the country's landfills. Reusing litter as development materials save regular assets, saves energy, diminishes strong waste, brings down air and water contamination, and brings down ozone-depleting substance outflows. The development area can start to recognize and benefit from the advantages of using trash and repurposed materials. Acceptable litter, reused and reusable materials, and strategies have all been explored in numerous studies.
Scope and approach: Due to the scarcity and rising expense of raw materials, the use of shattered tiles, glass, granite in structural components is used in this study. Compressive strength, workability, unit weight, density, cost of concrete made of litter material will be tested in this study. A comparison of all test findings of concrete formed of litter materials with conventional concrete will be done to break down present practices in the building industry regarding litter use and reused materials.
Key findings and conclusion: This study provides an early knowledge of the practice's current strengths and flaws to assist the construction industry in formulating appropriate policies governing the use of trash and reused substances as improvement materials. Nine Samples were used with different proportion and mixes and it was found that 10 % partial replacement of coarse aggregate with glass achieved 26.83 % & 6.39 % more strength than target mean compressive strength (fm) of M20 conventional concrete for 7 & 28 days respectively. 7 day density & 28 day density of concrete cube made with 10 % partial replacement of glass with coarse aggregate was 1.75 % & 0.45 % less than the conventional concrete, this make concrete light and gives more target mean compressive strength (fm) than conventional concrete. All Samples come under medium degree of workability. Slump values are directly proportional to percentage of replacement. Use of this type of concrete will also reduce the dead load of the structure by 0.45 %. Saving of 10 % cost of aggregate can done by using concrete made with 10 % partial replacement of glass with coarse aggregate.
Effects of Annulation on Low-Reynolds-Number Flows over an Orthocone
Authors: Thakor Mitesh , Seh Kee Horng , Gladson Sareta R. , Fernandez Martin L. , Ivany Linda C. , Green Melissa , Sun Yiyang 
Published: January 2023

Abstract
This study examines the influences of transverse annulation around a cone surface on the characteristics of a flow over the orthocone. This work is inspired by Spyroceras, a fossilized genus of the nautiloid family during the Paleozoic era, whose method of locomotion is understudied. As a baseline case, a flow over a smooth orthoconic model with a blunt cone end is investigated numerically at Reynolds numbers from 500 to 1500. As Reynolds increases, two different shedding mechanisms - hairpin-vortex wake and spiral-vortex wake - are captured. We notice that an introduction of annulation over the cone surface changes the critical Reynolds number for the transition of the shedding mechanism. The dominant shedding frequency increases with the Reynolds number for the smooth and annulated cone flows. Moreover, the annulation reduces the dominant frequency for the same Reynolds number and increases the time-averaged drag coefficient. Modal decompositions - Proper Orthogonal Decomposition (POD) and Spectral Proper Orthogonal Decomposition (SPOD) - are used to capture the coherent structures and their oscillating frequencies. We have captured modes corresponding to the hairpin-vortex wake and spiral-vortex wake shedding mechanisms. Comparing the leading POD modes for the smooth and the annulated cone flows, we find that the annulation can reduce the twisting effects of the coherent structures in the wake. Additionally, we find that the SPOD analysis can identify modes presenting both hairpin-vortex wake and spiral-vortex wake in one flow condition as leading modes, while the POD leading modes only reveal one shedding mechanism in each flow.
The role of microhabitat for bryophyte establishment in reclamation of boreal wetlands
Authors: Vitt Dale H. , House Melissa , Glaeser Lilyan C. 
Published: January 2023

Abstract
Minerogenous peatlands that accumulate deep deposits of organic matter (fens) were an important part of the pre-disturbance landscape across Alberta’s oil sand mining area. Bryophytes occupy 80–100% of the ground layer in these site types and form an important part of the accumulated organic matter. Bryophytes are small plants that occur in microhabitats influenced by surrounding vascular plants and substrate features. The objective of this paper is to evaluate the resilience of bryophytes and initial success of an experimental wetland (Sandhill Wetland-SHW) by assessing the changing vegetation and substrate regimes over eight years after wet-up. Included in this analysis is an account of the ground layer flora between 2014 and 2021 along with evaluation of associated environmental factors. At SHW, a number of peatland bryophytes initially established in numerous areas across the wetland. However, in subsequent years increasing water tables with expanding Typha-dominating areas, high sedge productivity and fluctuating water tables, increasing vascular plant cover, and increasing sodicity have reduced the microhabitats available for bryophytes, with the result being a much-diminished set of peatland bryophyte species. We suggest that future reclamation designs for fens should include microhabitats for bryophytes, as bryophytes are foundational species and integral to fen development. In comparison, reclamation designs for non-peat forming ecosystems that do not have abundant bryophytes, such as marshes and saline wetlands, do not require these microhabitat conditions. Installing a recently harvested peat substrate appears to provide suitable conditions for early establishment of bryophytes.
The experiences of patients with advanced heart failure, family carers, and professional caregivers with palliative care services: a secondary reflexive thematic analysis of longitudinal interview data
Authors: Remawi Bader Nael , Gadoud Amy , Preston Nancy 
Published: January 2023

Abstract
Background
Patients with heart failure have significant palliative care needs, but few are offered palliative care. Understanding the experiences of delivering and receiving palliative care from different perspectives can provide insight into the mechanisms of successful palliative care integration. There is limited research that explores multi-perspective and longitudinal experiences with palliative care provision. This study aimed to explore the longitudinal experiences of patients with heart failure, family carers, and professional caregivers with palliative care services.
Methods
A secondary analysis of 20 qualitative three-month apart interviews with patients with heart failure and family carers recruited from three community palliative care services in the UK. In addition, four group interviews with professional caregivers from four different services were analysed. Data were analysed using ‘reflexive thematic’ analysis. Results were explored through the lens of Normalisation Process Theory.
Results
Four themes were generated: Impact of heart failure, Coping and support, Recognising palliative phase, and Coordination of care. The impact of heart failure on patients and families was evident in several dimensions: physical, psychological, social, and financial. Patients developed different coping strategies and received most support from their families. Although professional caregivers endeavoured to support the patients and families, this was sometimes lacking. Professional caregivers found it difficult to recognise the palliative phase and when to initiate palliative care conversations. In turn, patients and family carers asked for better communication, collaboration, and care coordination along the whole disease trajectory.
Conclusions
The study provided broad insight into the experiences of patients, family carers, and professional caregivers with palliative care. It showed the impact of heart failure on patients and their families, how they cope, and how they could be supported to address their palliative care needs. The study findings can help researchers and healthcare professionals to design palliative care interventions focusing on the perceived care needs of patients and families.
Effect of climate change on Scots pine (Pinus sylvestris L.) growth across Europe: decrease of tree ring fluctuation and amplification of climate stress
Authors: Brichta Jakub , Šimůnek Václav , Bílek Lukáš , Vacek Zdeněk , Gallo Josef , Drozdowski Stanislaw , Bravo-Fernández José Alfredo , Mason Bill , Roig Sonia , Hájek Vojtěch , Vacek Stanislav , Štícha Václav 
Published: January 2023

Abstract
From an economic perspective, Scots pine (Pinus sylvestris L.) is one of Europe's most important tree species. It is characterized by its wide ecological adaptability across its natural range. This research aimed to evaluate the forest structure, productivity and especially radial growth of heterogenous pine stands in the 16 research plots in the Czech Republic, Poland, Spain and Scotland. The study assessed the tree-ring formation and its relationship to climate change for each country, using 163 dendrochronological samples. The tree-ring growth evaluation focused on two periods – before (Period 1: 1951–1985) and during the climate change (Period 2: 1986–2016). The stand volume of mature pine forest ranged between 91–510 m3 ha− 1, and carbon sequestration in tree biomass was 40–210 t ha− 1. The stands had a prevailing random distribution of trees with a high vertical structure close to selection forests. Spectral analyses showed a substantial decrease in fluctuations in the tree-ring index and a loss in natural growth cyclicity in the second period. Generally, 11-year growth solar cycles were most often found. In the second period, a higher effect of climate factors on radial growth was observed. The results also evinced that air temperature was the most important factor influencing the radial growth compared to precipitation totals. Pine thrives well in precipitation-stable locations, as shown by the results from Scotland. The conclusions of this study confirm the fundamental effect of ongoing global climate change on the dynamics and growth of pine forests in Europe.
3-NAntC: a novel Crotoxin B-derived peptide for the treatment of triple-negative breast cancer
Authors: Bezerra Patricia , Motti Eduardo 
Published: January 2023

Abstract
Breast cancer is the most prevalent type of tumor and a major leading cause of cancer mortality. Triple-negative breast cancer (TNBC) has the worst prognosis due to its malignant characteristics and the absence of efficacious treatments. Crotoxin, a protein in Crotalus genus snake venom, has proven antitumor activity against aggressive solid tumors, but marked toxicity in humans. Crotoxin B-derived peptides were synthesized and evaluated in vitro for their antitumor activity, which resulted in the discovery of 3-NAntC. 3-NAntC (1µg/mL) treatment for 72 hours decreased the MDA-MB-231 cells viability to 49.0%±17.5% (p < 0.0001), while the same condition resulted in the viability of HMEC cells at 98.2%±13.8%. 3-NAntC exhibited higher antitumoral activity in vitro than cisplatin and similar effect of doxorubicin. 3-NAntC reduced MDA-MB-231 cell proliferation and caused a G2/M arrest. 3-NAntC primarily induced apoptosis, with a lower necrosis occurrence compared with doxorubicin. 3-NAntC caused a low LDH release, and its cytotoxicity was not impaired by the autophagy inhibitor 3-MA. In zebrafish in vivo model, 3-NAntC was very well tolerated, showing no lethal effect and a low malformation rate at ≤ 75mg/mL. 3-NAntC is a novel synthetic peptide with promising antitumor effects in vitro against TNBC cells and with low toxicity in vivo.
Identification of mutations that causes glucose-6-phosphate transporter defect in Tunisian patients with glycogenosis type 1b
Authors: Chkioua Latifa , Amri Yessine , Saheli Chayma , BenRhouma Ferdaws , Chehida Amel Ben , Tebib Neji , Messaoud Taieb , Abdennebi Hassen Ben , Laradi Sandrine 
Published: January 2023

Abstract
Background: Glycogen storage disease type 1b (GSD1b) is an autosomal recessive lysosomal storage disease caused by defective glucose-6-phosphate transporter encoded by SLC37A4 leading to the accumulation of glycogen in various tissues. The high rate of consanguineous marriages in Tunisian population provides an ideal environment to facilitate the identification of homozygous pathogenic mutations. We aimed to determine the clinical and genetic profiles of patients with GSD1b to evaluate SLC37A4 mutations spectrum in Tunisian patients.
Methods: All the 9 exons and flanking intron regions of SLC37A4 gene were screened by direct sequencing to identify mutations and polymorphisms in three unrelated families with GSD1b. Bioinformatics tools were then used to predict the impacts of identified mutations on the structure and function of protein in order to propose a function-structure relationship of the G6PT1 protein.
Results: Three patients (M.T, M.B and S.I) in Families I, II and III who had the severe phenotype were homoallelic for the two identified missense mutation and frameshift mutations: p.R300H (famillies I, II) and p.Trp393X (Family III), respectively. These two mutations were identified and previously reported. One of the alterations was a missense mutation p.R300H of exon 6 in SLC37A4 gene. The analysis of the protein structure flexibility upon p.R300H mutation using DynaMut tool and CABS-flex 2.0 server showed that the reported mutation increase the molecule flexibility of in the cytosol region and would probably lead to significant conformational changes. The other deleterious SLC37A4 gene alteration was a nonsense mutation p.Trp393X in exon 8 previously found homozygous.
Conclusion: This is the first Tunisian report of SLC37A4 mutations identified in Tunisia causing the glycogenosis type Ib disease. Bioinformatics analysis allowed us to establish an approximate structure-function relationship for the G6PT1 protein, thereby providing better genotype/phenotype correlation knowledge.