julilili42/papers huggingface dataset:
Interseason waning of vaccine-induced hemagglutination inhibition antibody titers and contributing factors to pre-existing humoral immunity against influenza in community-dwelling older adults over 75 years of age
2022-12-28

Abstract Background: Seasonal influenza causes significant morbidity and mortality with a disproportionately high disease burden in older adults. Strain-specific hemagglutination-inhibition (HAI) antibody titer is a well-established measure of humoral immunity against influenza and pre-vaccination HAI antibody titer is a valuable indicator of pre-existing humoral immunity at the beginning of the influenza season in highly vaccinated older adults. While vaccine-induced HAI antibody titers are known to wane over time, accurate assessment of their interseason decline has been challenging. This is because pre-vaccination HAI antibody titers are conventionally measured using current season vaccine strain antigens instead of the prior season vaccines with which individuals were immunized, and do not accurately represent residual antibody titers from prior season vaccination. This study took advantage of available pre-vaccination HAI antibody titers measured using prior season vaccine strain antigens in a longitudinal influenza immunization study with participants enrolled for multiple consecutive influenza seasons from 2014 through 2017 during which influenza A virus (IAV) H3N2 and influenza B virus (IBV) strains were changed in 2015 and in 2016. While the IAV H1N1 vaccine strain remained the same from 2014 through 2016 seasons, it was changed in the 2017 season. Finally, we investigated factors contributing to pre-existing humoral immunity. Results: Interseason decline of HAI antibody titers was evident, but rates of decline varied among vaccine strains and study seasons, from 18% (p=0.43) to 61% (p&lt;0.01). Rates of decline were noticeably greater when pre-vaccination HAI titers were measured using the conventional approach, from 33% (p=0.12) to 83% (p&lt;0.01). All p values were adjusted for age at prior study season, sex, race, and education. This was largely because the conventional approach underestimated residual HAI antibody titers from prior season vaccinations. Moreover, interseason antibody decline and prior season post-vaccination HAI antibody titer had significant and independent associations with pre-vaccination HAI antibody titer. Conclusions: The conventional approach overestimates interseason HAI antibody decline as it underestimates residual antibody titers from prior season vaccination, particularly when virus strains in the vaccine formula change. Moreover, interseason antibody decline and prior season post-vaccination HAI antibody titers independently contribute to pre-existing humoral immunity in this highly vaccinated, community-dwelling older adult population.
The Cytokine Network in Colorectal Cancer: Implications for New Treatment Strategies
2022-12-29

Colorectal cancer (CRC) is one of the most frequent tumor entities worldwide with only limited therapeutic options. CRC is not only a genetic disease with several mutations in specific oncogenes and/or tumor suppressor genes such as APC, KRAS, PIC3CA, BRAF, SMAD4 or TP53 but also a multifactorial disease including environmental factors. Cancer cells communicate with their environment mostly via soluble factors such as cytokines, chemokines or growth factors to generate a favorable tumor microenvironment (TME). The TME, a heterogeneous population of differentiated and progenitor cells, plays a critical role in regulating tumor development, growth, invasion, metastasis and therapy resistance. In this context, cytokines from cancer cells and cells of the TME influence each other, eliciting an inflammatory milieu that can either enhance or suppress tumor growth and metastasis. Additionally, several lines of evidence exist that the composition of the microbiota regulates inflammatory processes, controlled by cytokine secretion, that play a role in carcinogenesis and tumor progression. In this review, we discuss the cytokine networks between cancer cells and the TME and microbiome in colorectal cancer and the related treatment strategies, with the goal to discuss cytokine-mediated strategies that could overcome the common therapeutic resistance of CRC tumors.
Care organisations role as intermediaries between the authorities and the marginalised in crisis management
2022-12-29

Social service providers work to alleviate social disadvantages, which may particularly loom during crises. These organisations have a close understanding of the needs of their clients. However, this knowledge is rarely taken into account in tailoring crisis measures, which may lead to increased vulnerability and create additional suffering. In this paper, we take a novel look at the role of care organisations as intermediaries between their clients and the authorities in representing the needs and capabilities of vulnerable people and explore the factors hindering or facilitating this representation. We focused on care organisations in Europe and collected data from 32 interviews, followed by 5 workshops and an international colloquium with 6 language-based discussion groups with participants from organisations offering care services to socially marginalised individuals. The results demonstrate the role these organisations had in advocating their clients' needs to the authorities to adapt the crisis measures accordingly ("bottom-up approach"), and communicating official information about the risks and government rules to their clients ("top-down approach"). We found effective mediation to stem from long-term, trusting client relationship to be able to reflect on clients' needs, while the lack of collaboration protocol and tradition can be seen as the main barrier to inclusive crisis management. Networking with social care services to bring their expertise into crisis management systems is essential to promote the resilience of the diverse society.
Direct modulation index: A measure of phase amplitude coupling for neurophysiology data
2022-12-29

Abstract Neural communication across different spatial and temporal scales is a topic of great interest in clinical and basic science. Phase‐amplitude coupling (PAC) has attracted particular interest due to its functional role in a wide range of cognitive and motor functions. Here, we introduce a novel measure termed the direct modulation index (dMI). Based on the classical modulation index, dMI provides an estimate of PAC that is (1) bound to an absolute interval between 0 and +1, (2) resistant against noise, and (3) reliable even for small amounts of data. To highlight the properties of this newly‐proposed measure, we evaluated dMI by comparing it to the classical modulation index, mean vector length, and phase‐locking value using simulated data. We ascertained that dMI provides a more accurate estimate of PAC than the existing methods and that is resilient to varying noise levels and signal lengths. As such, dMI permits a reliable investigation of PAC, which may reveal insights crucial to our understanding of functional brain architecture in key contexts such as behaviour and cognition. A Python toolbox that implements dMI and other measures of PAC is freely available at https://github.com/neurophysiological-analysis/FiNN .
Robotic radical cystectomy – more precision needed?
2022-12-29

Purpose of review Recently, several trials as well as registry-data analyses investigating the role of robot-assisted radical cystectomy with extra or intracorporal urinary diversion were completed and follow up matured. This review aims to comment on the current evidence-based findings and interpret the future role of the robotic approach as a part of the treatment of bladder cancer. Recent findings Numerous trials and registry-data analyses revealed no significant differences in progression-free and overall survival after open radical cystectomy or robot-assisted radical cystectomy irrespective of urinary diversion. Perioperative parameters, especially intraoperative blood loss, transfusions, thromboembolic events, wound infections and hospitalization were significantly increased in open radical cystectomy. Patients’ convalescence, and especially early postsurgical quality of life, was improved by the robotic approach. The highly demanding surgery itself displayed by a flat learning curve required more than 130 surgeries per institution to reach a stable plateau of complications. The performance of high-quality radical cystectomy irrespective of the approach was significantly increased in high-volume centres. Local recurrence occurs in 11% after radical cystectomy. Current research focuses on intraoperatively usable detection methods and instruments to minimize the risk of residual tumour cells. Summary Taken together, the total intracorporal approach in radical cystectomy holds the potential to improve perioperative parameters and reduces hospitalization without impairing oncological performance of the procedure. To provide best results for the patient radical cystectomy and especially the technically challenging total intracorporal procedure will gain importance in bladder cancer treatment but should be limited to high-volume centres.
Development and Testing of a Compact Autorefractor Based on Double-Pass Imaging
2022-12-29

Autorefraction is an objective way to determine the refractive error of the eye, without the need for feedback by the patient or a well-educated practitioner. To make refractive measurements more accessible in the background of the growing prevalence of myopia, a compact autorefractor was built, containing only few optical components and relying on double-pass imaging and the physical properties of the point-spread function and digital image processing instead. A method was developed to analyze spherical defocus as well as the defocus and angle of astigmatism. The device was tested using calibrator eye models in a range of ± 15 D spherical defocus and −3 D astigmatic defocus. Reliable results could be achieved across the whole measurement range, with only a small increase in deviation toward high values of refractive errors, showing the feasibility of a PSF-based approach for a compact and low-cost solution for objective measurements of refractive error.
Adverse effects of COVID-19 pandemic on a multicenter randomized controlled trial
2022-12-29

Abstract Objective Describe the effects of the COVID-19 pandemic on subject enrollment in a multicenter randomized controlled trial. Study design We assessed the number of eligible infants approached and consented for enrollment over five separate epochs including baseline, peak pandemic, and gradual but incomplete recovery. Result The pandemic had a major effect on ability to approach parents for consent. Parents approached dropped from 95.4% baseline to 13.1% in the peak pandemic epoch and has not recovered to baseline even in the just-completed post-pandemic epoch (84.9%). Despite the decrease in subjects approached, there was no significant change in the overall consent rate for the study Conclusion The pandemic has significantly limited ability to approach parents of eligible infants for consent, with only partial recovery. Opportunities for interactions of investigators and study coordinators with parents continue to present challenges limiting full recovery.
Abiotic and biotic drivers of tree trait effects on soil microbial biomass and soil carbon concentration
2022-12-30

Abstract Forests are ecosystems critical to understanding the global carbon budget, due to their carbon sequestration potential in both aboveground and belowground compartments, especially in species‐rich forests. Soil carbon sequestration is strongly linked to soil microbial communities, and this link is mediated by the tree community, likely due to modifications of microenvironmental conditions (i.e., biotic conditions, soil properties, and microclimate). We studied soil carbon concentration and the soil microbial biomass of 180 local neighborhoods along a gradient of tree species richness ranging from 1 to 16 tree species per plot in a Chinese subtropical forest experiment (BEF‐China). Tree productivity and different tree functional traits were measured at the neighborhood level. We tested the effects of tree productivity, functional trait identity, and dissimilarity on soil carbon concentrations, and their mediation by the soil microbial biomass and microenvironmental conditions. Our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentrations. In addition, soil carbon concentration increased with tree productivity and tree root diameter, while it decreased with litterfall C:N content. Moreover, tree productivity and tree functional traits (e.g., fungal root association and litterfall C:N ratio) modulated microenvironmental conditions with substantial consequences for soil microbial biomass. We also showed that soil history and topography should be considered in future experiments and tree plantations, as soil carbon concentrations were higher at sites where historical (i.e., at the beginning of the experiment) carbon concentrations were high, themselves being strongly affected by the topography. Altogether, these results implied that the quantification of the different soil carbon pools is critical for understanding microbial community–soil carbon stock relationships and their dependence on tree diversity and microenvironmental conditions.
Identification of stage I/II melanoma patients at high risk for recurrence using a model combining clinicopathologic factors with gene expression profiling (CP-GEP)
2022-12-30

CP-GEP can be used to identify primary cutaneous melanoma patients with a high risk for disease recurrence - especially for stage I/IIA, who are considered low risk by AJCC 8th. These patients may benefit from adjuvant therapy. Also, in the future, when SLNB may become irrelevant, CP-GEP may serve as a risk stratification tool.
Recent Advanced Development of Acid-Resistant Thin-Film Composite Nanofiltration Membrane Preparation and Separation Performance in Acidic Environments
2022-12-30

Membrane filtration technology has attracted extensive attention in academia and industry due to its advantages of eco-friendliness related to environmental protection and high efficiency. Polyamide thin-film composite nanofiltration (PA TFC NF) membranes have been widely used due to their high separation performance. Non-acid-resistant PA TFC NF membranes face tremendous challenges in an acidic environment. Novel and relatively acid-resistant polysulfonamide-based and triazine-based TFC NF membranes have been developed, but these have a serious trade-off in terms of permeability and selectivity. Hence, how to improve acid resistance of TFC NF membranes and their separation performance in acidic environments is a pivotal issue for the design and preparation of these membranes. This review first highlights current strategies for improving the acid resistance of PA TFC NF membranes by regulating the composition and structure of the separation layer of the membrane performed by manipulating and optimizing the construction method and then summarizes the separation performances of these acid-resistant TFC NF membranes in acidic environments, as studied in recent years.
Hot white dwarfs and pre-white dwarfs discovered with SALT
2022-12-30

ABSTRACT The Southern African Large Telescope survey of helium-rich hot subdwarfs aims to explore evolutionary pathways among groups of highly evolved stars. The selection criteria mean that several hot white dwarfs and related objects have also been included. This paper reports the discovery and analysis of eight new very hot white dwarf and pre-white dwarf stars with effective temperatures exceeding 100 000 K. They include two PG1159 stars, one DO white dwarf, three O(He), and two O(H) stars. One of the O(H) stars is the central star of a newly discovered planetary nebula, and the other is the hottest ‘naked’ O(H) star. Both of the PG1159 stars are GW Vir variables, one being the hottest GW Vir star measured and a crucial test for pulsation stability models. The DO white dwarf is also the hottest in its class.
Learning Multicast Patterns for Efficient BIER Forwarding With P4
2022-12-30

Bit Index Explicit Replication (BIER) is an efficient domain-based transport mechanism for IP multicast (IPMC) that indicates receivers of a packet through a bitstring in the packet header. Recently, BIER forwarding has been implemented on 100 Gbit/s per port hardware using the P4 programming language. However, the implementation requires packet recirculation to iteratively serve one next-hop after another. The objective of this paper is to reduce this inefficiency. Static multicast groups can be configured on P4 switches so that traffic can be sent to all next-hops without recirculation. We leverage that feature to make BIER forwarding more efficient. However, only a limited number of static multicast groups can be configured on a switch, which is not sufficient to cover all potential port patterns. In a first step, we develop efficient BIER forwarding that utilizes static multicast groups derived from so-called configured port clusters. Then, we design port clustering algorithms that observe multicast patterns and compute configured port clusters which are more efficient than randomly selected port clusters. These methods are based on Spectral Clustering, an unsupervised machine learning technique. We perform simulations that underline the effectiveness of this approach to reduce inefficient packet recirculations. We further implement the new forwarding behaviour on programmable hardware and provide a controller that samples BIER packets on the switch, runs the port clustering algorithms, and updates the configured static multicast groups. We validate this open source implementation in a testbed and show that the experimental results are in line with the simulation results.
Foundations for future math achievement: early numeracy, home learning, and the absence of math anxiety
2022-12-30

Mathematics achievement is an important predictor of later life and career prospects. Therefore, it is highly relevant to identify early determinants of math achievement. Recently, non-cognitive aspects such as home learning environment (home numeracy) and math anxiety were observed to significantly predict mathematics achievement beyond domain- specific early numerical skills. However, these aspects have hardly been considered jointly in one study. Therefore, this longitudinal study evaluated the predictive power of early numeracy skills, home learning environment, and math anxiety assessed at the end of kindergarten for mathematics achievement at the beginning of second grade in a normative sample of 85 children. Correlations and regression analyses indicated that early numeracy skills, home environment, and math anxiety have a unique and essential influence on math school achievement. It is, however, important to note that predictions seemed selective for different components of math achievement such as written computation, sequences, and comparisons. Results indicated that home numeracy only predicted performance on sequences, whereas math anxiety seemed to affect written computation. Overall achievement as well as performance on the equation’s subtest were best predicted by early numeracy skills. Taken together, these results suggest that non-cognitive aspects of home numeracy and math anxiety significantly influence children’s future math achievement. Importantly, however, results also argue for selective influences that should be considered in future studies.
An integrated systems-biology platform for power-to-gas technology
2022-12-30

Abstract Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in the growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments. In the first experiment, with molecular hydrogen and carbon dioxide, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Systems biology investigations, including implementing a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. This comparison enabled us to identify crucial differences in formate anabolism. In the second experiment, with sodium formate, we found stable growth with an M. thermautotrophicus ΔH plasmid-carrying strain with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. Our findings reveal that formate anabolism influences the diversion of carbon to biomass and methane with implications for biotechnological applications of Methanothermobacter spp. in power-to-gas technology and for chemical production. Graphical Abstract Broader context Renewable energy sources (e.g., wind and solar) provide carbon-free electric power. However, their intermittency and offset between peak production and demand generate the need to store this electric power. Furthermore, these technologies alone do not satisfy the demand for carbon-based commodities. Power-to-gas technology provides a means to store intermittent renewable electric power with concomitant carbon dioxide recycling into a chemical energy carrier, such as methane, on a centralized and decentralized scale. This is particularly important to establish equitable energy strategies for all countries, as is highlighted by the United Nations Sustainable Development Goals. With this work, we provide an integrated systems-biology platform for Methanothermobacter spp. to optimize biological power-to-gas technology and formulate strategies to produce other value-added products besides methane.
ArchaeoScale Protocol: Inserting digital scale bars into scientific images – Full step-by-step guideline for anthropological and archaeological specimen photography v1
2022-12-30

Geometric scale bars, also known as photography scales or photomacrographic rulers, are small but important details used in digital photography that allow for a quick visual understanding of size dimensions in images and should therefore be included in all scientific photographs. Scale bars exist in different sizes, shapes, and types, but they all aim to help the audience make proper connections between the presented photograph and the real subject. Inserting scale bars into pictures thus reduces interpretation biases and improves scientific readability, transparency, and quality. It should not be taken for granted that dimensions can be correctly understood based on mere intuition. However, scale bars are still often missing from many archaeological and anthropological publications, or their position tends to be inadequate. This protocol aims to change this by presenting a fast, step-by-step guideline for how to create digital scale bars in every photograph using the free and open-source image processing software ImageJ© (Schneider et al. 2012). Additionally, this protocol presents helpful tips regarding the type, size, creation, placement, and location of digital scale bars. The suggested workflow can easily be implemented in any photographic workflow as it does not require sophisticated and expensive equipment. Researchers that already work with scale bars on a regular basis might also find interest in this protocol, as there are certain aspects to the choice, type, position, and location of scale bars that are often not considered and that can reduce their effectiveness and usefulness.