julilili42/papers huggingface dataset:
Compound models and Pearson residuals for single-cell RNA-seq data without UMIs
2023-08-05

Abstract Recent work employed Pearson residuals from Poisson or negative binomial models to normalize UMI data. To extend this approach to non-UMI data, we model the additional amplification step with a compound distribution: we assume that sequenced RNA molecules follow a negative binomial distribution, and are then replicated following an amplification distribution. We show how this model leads to compound Pearson residuals, which yield meaningful gene selection and embeddings of Smart-seq2 datasets. Further, we suggest that amplification distributions across several sequencing protocols can be described by a broken power law. The resulting compound model captures previously unexplained overdispersion and zero-inflation patterns in non-UMI data.
Nitrite secretion by cyanobacteria is controlled by the small protein NirP1
2023-08-05

ABSTRACT When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. While it has been hypothesized that the secreted nitrite represents excess nitrogen that could not be further assimilated due to the missing carbon, the underlying molecular mechanism has remained enigmatic. Here, we characterized a hitherto unannotated gene with homologs in the genomes of 485 different cyanobacteria that is upregulated under low carbon conditions and controlled by the transcription factor NtcA, a central regulator of nitrogen homeostasis. To understand its function, we ectopically overexpressed it in Synechocystis sp. PCC 6803, which resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments revealed that this protein targets nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite, and was re-named to nitrite reductase regulator protein 1 (NirP1). Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting one of the central enzymes. In natural environments, the excreted nitrite will be utilized by other microorganisms; therefore, NirP1 ultimately impacts the activities and composition of the surrounding microbiome.
Unravelling technological behaviors through core reduction intensity. The case of the early Protoaurignacian assemblage from Fumane Cave.
2023-08-06

This paper investigates core reduction intensity in the early Protoaurignacian lithic assemblage from Fumane Cave in northeastern Italy. Here, reduction intensity was used as a means to characterize blank selection strategies and raw material management, explore the variability of knapping strategies throughout the reduction sequence by reconstructing the operatory field of core assemblages, and finally address the relationship between blades and bladelets. The latter aspect was particularly important to gain insights into the behavioral and chrono-cultural significance of laminar productions in the framework of the Aurignacian technocomplex. To meet these goals, experimental work was conducted thanks to 3D scanning technology to compare different methods and variables for measuring reduction intensity, including the percentage of non-cortical surface, the Scar Density Index (SDI), and a novel adaptation of the Volumetric Reconstruction Method (VRM). Results demonstrate the effectiveness and potential of adapting VRM for studying reduction intensity in Upper Paleolithic laminar cores, and the provided R scripts and datasets will enable this method to be applied to other contexts with little or no modification of the workflow. The reduction intensity measures applied to the Protoaurignacian assemblage from Fumane Cave reveal slight variations depending on the abundance and proximity of available raw materials selected for blank production. Not surprisingly, the most abundant raw material variety – the Maiolica – has the largest number of less reduced cores, although reduction is fairly high across all cores discarded at the site. The observed variability in the operatory field and the interrelation between blade and bladelet productions underscore the complexity and flexibility of Protoaurignacian human behavior, which also complicate a definitive separation between the operatory fields of blade and bladelet productions. These findings are particularly important to emphasize the importance of considering reduction intensity when examining technological variability and human behavior in Aurignacian studies. We hope that the proposed adaptation of the VRM and the effective combination with other measures of reduction will allow future studies to rightfully incorporate reduction intensity as a temporal component in studies on stone tool production to enhance our understanding of the adaptive behaviors of Homo sapiens in diverse ecological settings and better frame the development of the Upper Paleolithic.
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses
2023-08-07

Abstract Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high‐throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon‐specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty‐two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
Biophysical Determinants for the Viscosity of Concentrated Monoclonal Antibody Solutions
2023-08-07

Monoclonal antibodies (mAbs) are particularly relevant for therapeutics due to their high specificity and versatility, and mAb-based drugs are hence used to treat numerous diseases. The increased patient compliance of self-administration motivates the formulation of products for subcutaneous (SC) administration. The associated challenge is to formulate highly concentrated antibody solutions to achieve a significant therapeutic effect, while limiting their viscosity and preserving their physicochemical stability. Protein-protein interactions (PPIs) are in fact the root cause of several potential problems concerning the stability, manufacturability, and delivery of a drug product. The understanding of macroscopic viscosity requires an in-depth knowledge on protein diffusion, PPIs, and self-association/aggregation. Here, we study the self-diffusion of different mAbs of the IgG1 subtype in aqueous solution as a function of the concentration and temperature by quasi-elastic neutron scattering (QENS). QENS allows us to probe the short-time self-diffusion of the molecules and therefore to determine the hydrodynamic mAb cluster size and to gain information on the internal mAb dynamics. Small-angle neutron scattering (SANS) is jointly employed to probe structural details and to understand the nature and intensity of PPIs. Complementary information is provided by molecular dynamics (MD) simulations and viscometry, thus obtaining a comprehensive picture of mAb diffusion.
Sustainable Immobilization of Arsenic by Man-Made Aerenchymatous Tissues in Paddy Soil
2023-08-07

Arsenic (As) is a major environmental pollutant and poses a significant health risk to humans through rice consumption. Elevating the soil redox potential (Eh) has been shown to reduce As bioavailability and decrease As accumulation in rice grains. However, sustainable methods for managing the Eh of rice paddies are lacking. To address this issue, we propose a new approach that uses man-made aerenchymatous tissues (MAT) to increase soil Eh by mimicking O<sub>2</sub> release from wet plant roots. Our study demonstrated that the MAT method sustainably increased the soil Eh levels from -119 to -80.7 mV (∼30%), over approximately 100 days and within a radius of around 5 cm from the surface of the MAT. Moreover, it resulted in a significant reduction (-28.5% to -63.3%) in dissolved organic carbon, Fe, Mn, and As concentrations. MAT-induced Fe(III) (oxyhydr)oxide minerals served as additional adsorption sites for dissolved As in soil porewater. Furthermore, MAT promoted the oxidation of arsenite to the less mobile arsenate by significantly enhancing the relative abundance of the <i>aioA</i> gene (130% increase in the 0-5 cm soil zone around MAT). The decrease in As bioavailability significantly reduced As accumulation in rice grains (-30.0%). This work offers a low-cost and sustainable method for mitigating As release in rice paddies by addressing the issue of soil Eh management.
Information, doubt, and democracy: how digitization spurs democratic decay
2023-08-07

The amount of information available to citizens due to global digitization and new technologies is unprecedented. However, in established democracies where access to alternative sources of information is guaranteed and educational levels are high, we witness a rise in attitudes and actions that threaten democratic foundations. Some citizens succumb to misinformation that has led them down the path of radicalization and violence; others withdraw completely from political life. How do we explain these developments? Building on democratic theory and the concepts of informational learned helplessness and selective exposure, we introduce a theoretical framework that connects digitization and digital technologies to attitudes and behaviour that threaten democracy even before democratic decay manifests. We argue that AI-assisted digital technologies expose societies to an abundance of contradictory information, limit citizens' ability to assess their trustworthiness, and reinforce the tailored dissemination of misinformation. We present the US and Germany as empirical plausibility probes that show how these features drive some citizens towards informational agnosticism, which results in de-politicization and political apathy. Others might become misbelievers who display negative attitudes towards democracy and/or engage in anti-democratic actions. Our probe offers an initial empirical illustration that provides a basis for further systematic investigations of digital technology's effects on democracy.
Three-dimensional topology dataset of folded radar stratigraphy in northern Greenland
2023-08-07

Abstract We present a dataset of reconstructed three-dimensional (3D) englacial stratigraphic horizons in northern Greenland. The data cover four different regions representing key ice-dynamic settings in Greenland: (i) the onset of Petermann Glacier, (ii) a region upstream of the 79° North Glacier (Nioghalvfjerdsbræ), near the northern Greenland ice divide, (iii) the onset of the Northeast Greenland Ice Stream (NEGIS) and (iv) a 700 km wide region extending across the central ice divide over the entire northern part of central Greenland. In this paper, we promote the advantages of a 3D perspective of deformed englacial stratigraphy and explain how 3D horizons provide an improved basis for interpreting and reconstructing the ice-dynamic history. The 3D horizons are provided in various formats to allow a wide range of applications and reproducibility of results.
Diatom Indicators of Fluctuating/Intermittent Discharge from Springs in Two Bavarian Nature Conservation Areas
2023-08-07

As a follow-up to the project “Springs in the Bavarian National Parks as Indicators of Climate Change (SpringNPB)”, a standard methodology for using springs as sentinel environments of climate change was transferred to the UNESCO Rhön Biosphere Reserve and other Bavarian middle-elevation mountain ranges. We studied diatoms from fifteen springs selected in the UNESCO Biosphere Reserve (9) and Steigerwald Nature Park (6). A total of 127 species belonging to 40 genera were found sampling 3 microhabitat types (lithic materials, hygrophilous or aquatic vegetation, and surface sediments). The cumulative percentage of endangered species according to the Red List was 41.5%. These very shaded, low–medium conductivity, low-discharge forest springs are fed by small surficial aquifers. As a consequence, the discharge fluctuates widely, and some springs even occasionally fall dry. Our results could contribute to the use of diatoms as indicators of discharge variability/desiccation in springs: springs affected by discharge variability have lower diatom species richness and distinct diatom communities; diatom indicators and metrics can be validated using invertebrates; larger databases will be necessary to identify the most suitable diatom indicators.
Exploring behavioral adjustments of proportion congruency manipulations in an Eriksen flanker task with visual and auditory distractor modalities
2023-08-07

Abstract The present study investigated global behavioral adaptation effects to conflict arising from different distractor modalities. Three experiments were conducted using an Eriksen flanker paradigm with constant visual targets, but randomly varying auditory or visual distractors. In Experiment 1, the proportion of congruent to incongruent trials was varied for both distractor modalities, whereas in Experiments 2A and 2B, this proportion congruency (PC) manipulation was applied to trials with one distractor modality (inducer) to test potential behavioral transfer effects to trials with the other distractor modality (diagnostic). In all experiments, mean proportion congruency effects (PCEs) were present in trials with a PC manipulation, but there was no evidence of transfer to diagnostic trials in Experiments 2A and 2B. Distributional analyses (delta plots) provided further evidence for distractor modality-specific global behavioral adaptations by showing differences in the slope of delta plots with visual but not auditory distractors when increasing the ratio of congruent trials. Thus, it is suggested that distractor modalities constrain global behavioral adaptation effects due to the learning of modality-specific memory traces (e.g., distractor–target associations) and/or the modality-specific cognitive control processes (e.g., suppression of modality-specific distractor-based activation). Moreover, additional analyses revealed partial transfer of the congruency sequence effect across trials with different distractor modalities suggesting that distractor modality may differentially affect local and global behavioral adaptations.
Solitary pulmonary metastases at first recurrence of osteosarcoma: Presentation, treatment, and survival of 219 patients of the Cooperative Osteosarcoma Study Group
2023-08-07

Abstract Background To evaluate patient and tumour characteristics, treatment and their impact on survival in patients with a solitary pulmonary metastasis at first relapse of high‐grade osteosarcoma. Procedure Two‐hundred and nineteen consecutive patients who had achieved a complete surgical remission and then developed a solitary pulmonary metastasis at first recurrence of high‐grade osteosarcoma were retrospectively reviewed. Results Two hundred and three (94.9%) of 214 patients achieved a second complete remission. After a median time from initial diagnosis of osteosarcoma to first relapse of 2.3 years (range, 0.3–18.8 years), actuarial post‐relapse overall survival after 2 and 5 years was 72.0% and 51.2%. Post‐relapse event‐free survival was 39.1% and 31.1%. Median follow‐up time was 3.2 years (range, 0.1–29.4 years). A longer time until first relapse and diagnosis due to imaging were positive prognostic factors in uni‐ and multivariate analyses, as were a second complete surgical remission and, in regard to death, the absence of a subsequent relapse. The use of salvage chemotherapy and radiotherapy were not associated with patient outcomes, nor was the surgical approach (thoracoscopy vs. thoracotomy) nor the exploration (uni‐ vs. bilateral). Conclusion Approximately half of the patients who experience a solitary pulmonary relapse at first recurrence of osteosarcoma remain alive 5 years after this first relapse. Only one third will remain disease‐free. A complete surgical resection of the lesion is essential for long‐term survival while relapse chemotherapy does not seem to improve survival. Innovative therapies are required to improve outcomes.
Supporting preservice economics teachers in creating high-quality instructional videos
2023-08-07

Instructional videos are a popular teaching and learning tool. Teachers use already existing videos and develop their own videos, in which they explain important domain concepts. The effectiveness of these videos depends on their instructional quality. To support future teachers in creating high-quality videos, we developed a training and compared the instructional quality of videos developed by pre-service economics teachers (N = 24) before and after the training period. The quality is assessed based on a theoretically funded framework. We identify small improvements regarding the overall instructional quality and provide an overview of the most common changes made by the preservice teachers. Overall, the study contributes to a better understanding of how future teachers can be supported in creating high-quality digital media.
Changes in college students' socioeconomic status aspirations during the COVID‐19 pandemic
2023-08-07

Abstract Although university students tend to be optimistic about their future socioeconomic status (SES), little is known how their SES aspirations changed during the context of the COVID‐19 pandemic. Using latent growth curve modeling techniques, we examined changes in subjective SES aspirations for students who began college before the pandemic (cohort 1; Fall 2019) and students who began college during the pandemic (cohort 2; Fall 2020). Moreover, we assessed how SES indicators (i.e., subjective family SES; first‐generation status; low‐income status) and a contextual financial indicator (i.e., pandemic‐related financial impacts) predicted changes in SES aspirations for both groups of students. Although SES aspirations were similar at the beginning of college for both groups of students, students who began college before the pandemic experienced a greater rate of downward change between the baseline assessment and the assessment shortly after the pandemic began. In both cohorts, students from higher‐SES families had higher SES aspirations at the beginning of college and steeper rates of downward change. Furthermore, despite having similar SES aspirations at the beginning of college, first‐generation students whose first year was interrupted by the pandemic experienced steeper downward changes in their SES aspirations. However, pandemic‐related financial impacts did not predict this downward change for either cohort. Our findings suggest that uncertainty in the early stages of the pandemic may have led to cautiousness in students' aspirations for their future SES attainment, particularly for first‐generation students.
Principles of quantum functional testing
2023-08-07

With the increasing commercial availability of quantum information processing devices the need for testing them efficiently for their specified functionality will arise. Complete quantum channel characterization is out of the question for anything more than the simplest quantum channels for one or two qubits. Quantum functional testing leads to a decision problem with outcomes corresponding to the rejection or acceptance of the claim of the producer that the device parameters are within certain specifications. In this context, we introduce and analyze three ingredients that can speed up this decision problem: the iteration of the channel, efficient decision criteria, and nongreedy adaptive experimental design.
Analysis of the complete plastomes of Albizia kalkora (Roxb.) Prain 1897 (Fabaceae)
2023-08-07

<i>Albizia kalkora</i> (Roxb.) Prain 1897, belonging to the family Fabaceae, is not only a landscape tree but also a medicinal plant. At present, few plastomes have been reported from <i>Albizia</i>, which delays the in-depth phylogenomic studies and the development of high-resolution discriminating markers for this genus. Herein, we sequenced the first plastome of <i>A. kalkora</i> by NGS technology. The genome is a circular structure (176,158 bp), containing a large single-copy (LSC) region (91,521 bp), a small copy (SSC) region (5237 bp), and two inverted repeat (IR) regions (39,700 bp each). It has 35.45% GC content and encodes 109 unique genes, which are 76 protein-coding, 4 rRNA, and 29 tRNA genes. The genetic distance analysis of the intergenic spacer regions for <i>A. kalkora</i>, <i>A. odoratissima</i> and <i>A. bracteate</i> shows four intergenic regions with very high K2p values, namely, <i>ccs</i>A-<i>ndh</i>D (15.04), <i>ma</i>tK-<i>rps</i>16 (10.77), <i>rps</i>11-<i>rpl</i>36 (17.63) and <i>rps</i>3-<i>rps</i>19 (20.08), which can discriminate the three <i>Albizia</i> species. In addition, we identified ten pairs of regions that could be utilized to design primers to discriminate the three <i>Albizia</i> species. The phylogenetic analysis showed <i>Albizia</i> was closely related to <i>Samanea</i>. The results in this study will provide valuable information to elucidate the classification, identification and evolutionary history of <i>Albizia</i>.
COVID-19 and chronic rhinosinusitis: management and comorbidity – what have we learned?
2023-08-08

Intranasal corticosteroids remain the standard treatment for CRS in patients with SARS-CoV-2 infection. Indications for surgical treatment of CRS should be critically evaluated and reserved for patients with complications and those with no other treatment options. For this purpose, COVID-19 status should be known if possible and, in case of unclear status (emergency), using appropriate personal protective equipment. Systemic corticosteroids should be avoided were possible. Biological treatment should be continued under careful monitoring in uninfected patients and should be temporarily interrupted during COVID-19 infection.