julilili42/papers huggingface dataset:
Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
2021-11-13

ABSTRACT Microbial biosurfactants are of major interest due to their multifunctional properties, biodegradable nature and low toxicity. Agroindustrial waste, such as fruit waste, can be used as substrates for producing bacteria. In this study, six samples of fruit waste, from oranges, mangoes and mixed fruits, were self-fermented, and then subjected to short-read metagenomic sequencing, so as to allow assessment of the potential of the associated microbiota for biosurfactant production. Taxonomic analysis using the DIAMOND+MEGAN analysis pipeline shows that all six samples are dominated by Proteobacteria, in particular, a common core consisting of the genera Klebsiella , Enterobacter , Stenotrophomonas , Acinetobacter and Escherichia . To support the interactive visualization and exploration of the surfactant-related genes in such samples, we have integrated the BiosurfDB classification into MEGAN and make this available. Functional analysis indicates high similarity among samples and that a significant number of reads map to genes that are involved in the biosynthesis of lipopeptide-class biosurfactants. Gene-centric analysis reveals Klebsiella as the main assignment for genes related to putisolvins biosynthesis. This suggests that fruit waste is a promising substrate for fermentative processes because the associated microbiota may be able to produce biosurfactants that are potentially useful for the agricultural, chemical, food and pharmaceutical industries.
The use of principal component and factor analysis to measure fundamental cognitive processes in neuropsychological data
2021-11-13

Abstract For years, dissociation studies on neurological single cases with brain lesions were the dominant method to infer fundamental cognitive functions in neuropsychology. In contrast, the association between deficits was considered to be of less epistemological value and even misleading. Still, principal component analysis (PCA) – an associational method for dimensionality reduction – recently became popular for the identification of fundamental functions. The current study evaluated the ability of PCA and factor analysis (FA) to overcome the association problem in behavioural data of neurological patients and to identify the fundamental variables underlying a battery of measures. Synthetic data were simulated to resemble neuropsychological data with typical dissociation patterns and, thereby, typical patterns of dependence between variables. In most experiments, PCA and FA succeeded to measure the underlying target variables with high up to almost perfect precision. However, this success was fragile and relied on the success of factor rotation, which failed its intended purpose when no test scores existed that primarily measured each underlying target variable. Further, commonly used strategies to estimate the number of meaningful factors appear to underfactor neuropsychological data, thereby consistently underestimating the dimensionality of the data. Finally, simulations suggested a high potential of PCA to denoise data, with factor rotation providing an additional filter function. This can be invaluable in neuropsychology, where measures are often inherently noisy, and PCA can be superior to common compound measures, such as the arithmetic mean, in the measurement of variables with high reliability. In summary, PCA and FA appear to be powerful tools in neuropsychology that are well capable to infer fundamental cognitive functions with high precision, but the typical structure of neuropsychological data and limited informative value of associations in neuropsychology place clear limitations and a risk of a complete failure on the methods.
Students’ Digital Media Usage at the University of Tübingen During the CoViD19 Semester 2020 Compared to 2018
2021-11-13

The purpose of this study was to compare students’ digital media use during the so-called corona semester in summer of 2020 when universities worldwide moved to online teaching and learning, with data from 2018. Two research questions were at the center of our study: To what extent did students’ media use during the digital summer semester 2020 differ from media use in 2018? In which ways is media use in 2020 related to individual factors (e.g., emotional states, social integration, self-efficacy)? In 2020, 207 students at the University of Tübingen participated in an online survey on their digital media use. This data was compared with an existing data set from the same university from 2018 (N = 808 students). Results show a significant increase in students’ media use across all categories, in particular Learning Management System, online exercises, learning videos, and video conferencing. We also found a significant relation of students’ usage of online tools for learning with their feeling of social integration, as well as connections between students’ digital media self-efficacy and their learning-relevant emotions. The article discusses these results in the light of other studies on students’ media uses and provides first practical implications for lecturers.
FLASHIda: Intelligent data acquisition for top-down proteomics that doubles proteoform level identification count
2021-11-13

Abstract Top-down proteomics (TDP) has gained a lot of interest in biomedical application for detailed analysis and structural characterization of proteoforms. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complex signal of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. We present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In analysis in E. coli lysates, FLASHIda increased the number of unique proteoform level identifications from 800 to 1,500, or generated a near-identical number of identifications in 1⁄3 of instrument time when compared to standard DDA mode. Furthermore, FLASHIda enabled sensitive mapping of post translational modifications and detection of chemical adducts. As an extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates.
Triple-Negative Breast Cancer Histological Subtypes with a Favourable Prognosis
2021-11-14

Triple-negative breast cancers (TNBC), as a group of tumours, have a worse prognosis than stage-matched non-TNBC and lack the benefits of routinely available targeted therapy. However, TNBC is a heterogeneous group of neoplasms, which includes some special type carcinomas with a relatively indolent course. This review on behalf of the European Working Group for Breast Screening Pathology reviews the literature on the special histological types of BC that are reported to have a triple negative phenotype and indolent behaviour. These include adenoid cystic carcinoma of classical type, low-grade adenosquamous carcinoma, fibromatosis-like metaplastic carcinoma, low-grade mucoepidermoid carcinoma, secretory carcinoma, acinic cell carcinoma, and tall cell carcinoma with reversed polarity. The pathological and known molecular features as well as clinical data including treatment and prognosis of these special TNBC subtypes are summarised and it is concluded that many patients with these rare TNBC pure subtypes are unlikely to benefit from systemic chemotherapy. A consensus statement of the working group relating to the multidisciplinary approach and treatment of these rare tumour types concludes the review.
Water’s path from moss to soil: A multi-methodological study on water absorption and evaporation of soil-moss combinations
2021-11-14

Abstract Mosses are often overlooked; however, they are important for soil-atmosphere interfaces with regard to water exchange. This study investigated the influence of moss structural traits on maximum water storage capacities (WSCmax) and evaporation rates, and species-specific effects on water absorption and evaporation patterns in moss layers, moss-soil-interfaces and soil substrates using biocrust wetness probes. Five moss species typical for Central European temperate forests were selected: field-collected Brachythecium rutabulum , Eurhynchium striatum , Oxyrrhynchium hians and Plagiomnium undulatum ; and laboratory-cultivated Amblystegium serpens and Oxyrrhynchium hians . WSC max ranged from 14.10 g g −1 for Amblystegium serpens (Lab) to 7.31 g g −1 for Plagiomnium undulatum when immersed in water, and 11.04 g g −1 for Oxyrrhynchium hians (Lab) to 7.90 g g −1 for Oxyrrhynchium hians when sprayed, due to different morphologies depending on the growing location. Structural traits such as high leaf frequencies and small leaf areas increased WSC max . In terms of evaporation, leaf frequency displayed a positive correlation with evaporation, while leaf area index showed a negative correlation. Moisture alterations during watering and desiccation were largely controlled by species/substrate-specific patterns. Generally, moss cover prevented desiccation of soil surfaces and was not a barrier to infiltration. To understand water’s path from moss to soil, this study made a first contribution.
TP53 mutations are associated with primary endocrine resistance in luminal early breast cancer
2021-11-14

Abstract Background Whereas the genomic landscape of endocrine‐resistant breast cancer has been intensely characterized in previously treated cases with local or distant recurrence, comparably little is known about genomic alterations conveying primary non‐responsiveness to endocrine treatment in luminal early breast cancer. Methods In this study, 622 estrogen receptor‐expressing breast cancer cases treated with short‐term preoperative endocrine therapy (pET) from the WSG‐ADAPT trial (NCT01779206) were analyzed for genetic alterations associated with impaired endocrine proliferative response (EPR) to 3‐week pET with tamoxifen or aromatase inhibitors. EPR was categorized as optimal (post‐pET Ki67 &lt;10%) versus slightly, moderately, and severely impaired (post‐pET Ki67 10%–19%, 20%–34%, and ≥35%, respectively). Recently described gene mutations frequently found in previously treated advanced breast cancer were analyzed ( ARID1A , BRAF , ERBB2 , ESR1 , GATA3 , HRAS , KRAS , NRAS , PIK3CA , and TP53 ) by next‐generation sequencing. Amplifications of CCND1 , FGFR1 , ERBB2 , and PAK1 were determined by digital PCR or fluorescence in situ hybridization. Results ERBB2 amplification ( p = 0.0015) and mutations of TP53 ( p &lt; 0.0001) were significantly associated with impaired EPR. Impaired EPR in TP53 ‐mutated breast cancer cases was independent from the Oncotype DX Recurrence Score group and was seen both with tamoxifen‐ and aromatase inhibitor‐based pET ( p = 0.0005 each). Conclusion We conclude that impaired EPR to pET is suitable to identify cases with primary endocrine resistance in early luminal breast cancer and that TP53 ‐mutated luminal cancers might not be sufficiently treated by endocrine therapy alone.
LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy
2021-11-14

High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we showed that LIN28B expression was associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7-independent enrichment of transcripts encoding components of the translational and ribosomal apparatus and depletion of transcripts of neuronal developmental programs. We further observed that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrated that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a posttranscriptional driver of the metastatic phenotype.
A site formation model for Cuncaicha rock shelter: Depositional and postdepositional processes at the high‐altitude keysite in the Peruvian Andes
2021-11-14

Abstract We report results from geoarchaeological investigations at Cuncaicha rock shelter (4480 m above sea level) in the high Andes of southern Peru. Using field observations, geomorphological, micromorphological, micro‐Fourier transform infrared spectroscopy, Bayesian modeling of radiocarbon ages, and archaeological data, we analyzed the entire stratigraphic sequence to determine depositional and postdepositional processes and agents to assess the impact of bioturbation and to correlate the deposits with regional paleoenvironmental information. The archaeological record is represented well on a microscale, and bioturbation has not destroyed the stratigraphic integrity. The Terminal Pleistocene sediments that contain the oldest archaeological material at the site, dating to ~12.3–11.1 ka, are especially well preserved and capped by a layer of tufa. Depositional changes from autochthonous carbonate precipitation during the Terminal Pleistocene toward allochthonous aeolian sedimentation in the Early Holocene reflect changing environmental and climatic conditions. Formation of a soil during the Late‐Middle Holocene caused postdepositional alterations and likely correlates to variable environmental conditions. We use these results to formulate a site formation model for Cuncaicha rock shelter that integrates archaeological, chronological, and paleoenvironmental data.
Effects of flares on the habitable zones of M dwarfs accessible to TESS planet detections
2021-11-14

Abstract Photometric space missions such as Kepler and TESS continuously discover new exoplanets and advance the search for a second habitable world. The light curves (LCs) recorded by these telescopes also reveal signs of magnetic activity, such as star spot modulation and flares, which can influence habitability. Searching for these characteristics, we analyzed TESS LCs of 112 M dwarfs selected according to the criterion that TESS can spot planet transits over their entire habitable zone (HZ). We detected 2,532 flare events occurring on 35 stars; thus the flaring fraction is . For only of our stars, we found rotation periods. We calculated bolometric flare energies and luminosities, flare energy frequency distributions (FFDs), and the bolometric flux reaching the HZ at the peak of the flare. We estimated the effects of flaring on the atmosphere of an Earth‐like planet in the HZ from the viewpoint of both ozone depletion and the enabling of chemical reactions necessary to build ribonucleic acid (RNA). None of our targets exhibits highly energetic flares at a frequency large enough to trigger ozone depletion or RNA formation.
Phoenix auditory neurons as 3R cell model for high throughput screening of neurogenic compounds
2021-11-14

Auditory neurons connect the sensory hair cells from the inner ear to the brainstem. These bipolar neurons are relevant targets for pharmacological intervention aiming at protecting or improving the hearing function in various forms of sensorineural hearing loss. In the research laboratory, neurotrophic compounds are commonly used to improve survival and to promote regeneration of auditory neurons. One important roadblock delaying eventual clinical applications of these strategies in humans is the lack of powerful in vitro models allowing high throughput screening of otoprotective and regenerative compounds. The recently discovered auditory neuroprogenitors (ANPGs) derived from the A/J mouse with an unprecedented capacity to self-renew and to provide mature auditory neurons offer the possibility to overcome this bottleneck. In the present study, we further characterized the new phoenix ANPGs model and compared it to the current gold-standard spiral ganglion organotypic explant (SGE) model to assay neurite outgrowth, neurite length and glutamate-induced Ca<sup>2+</sup> response in response to neurotrophin-3 (NT-3) and brain derived neurotrophic factor (BDNF) treatment. Whereas both, SGEs and phoenix ANPGs exhibited a robust and sensitive response to neurotrophins, the phoenix ANPGs offer a considerable range of advantages including high throughput suitability, lower experimental variability, single cell resolution and an important reduction of animal numbers. The phoenix ANPGs in vitro model therefore provides a robust high-throughput platform to screen for otoprotective and regenerative neurotrophic compounds in line with 3R principles and is of interest for the field of auditory neuroscience.
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
2021-11-15

Corynebacterium glutamicum belongs to the microbes of enormous biotechnological relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at an industrial scale. Its apparent robustness also turns it into a favorable platform host for a wide range of further compounds, mainly because of emerging bio-based economies. A deep understanding of the biochemical processes in C. glutamicum is essential for a sustainable enhancement of the microbe's productivity. Computational systems biology has the potential to provide a valuable basis for driving metabolic engineering and biotechnological advances, such as increased yields of healthy producer strains based on genome-scale metabolic models (GEMs). Advanced reconstruction pipelines are now available that facilitate the reconstruction of GEMs and support their manual curation. This article presents i CGB21FR, an updated and unified GEM of C. glutamicum ATCC 13032 with high quality regarding comprehensiveness and data standards, built with the latest modeling techniques and advanced reconstruction pipelines. It comprises 1042 metabolites, 1539 reactions, and 805 genes with detailed annotations and database cross-references. The model validation took place using different media and resulted in realistic growth rate predictions under aerobic and anaerobic conditions. The new GEM produces all canonical amino acids, and its phenotypic predictions are consistent with laboratory data. The in silico model proved fruitful in adding knowledge to the metabolism of C. glutamicum : i CGB21FR still produces L-glutamate with the knock-out of the enzyme pyruvate carboxylase, despite the common belief to be relevant for the amino acid's production. We conclude that integrating high standards into the reconstruction of GEMs facilitates replicating validated knowledge, closing knowledge gaps, and making it a useful basis for metabolic engineering. The model is freely available from BioModels Database under identifier MODEL2102050001 .
Peritoneal Expression of SGLT-2, GLUT1, and GLUT3 in Peritoneal Dialysis Patients
2021-11-15

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; In peritoneal dialysis (PD) patients, the peritoneal membrane is affected by glucose-based solutions used as peritoneal dialysate fluids. This exposure leads to changes of the membrane which may eventually culminate in fibrosis and method failure. In vitro or animal studies demonstrated that glucose transporters are upregulated upon exposure to these solutions. Expression studies of glucose transporters in human peritoneum have not been reported yet. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Expression of SGLT-2, GLUT1, and GLUT3 in human peritoneal biopsies was analyzed by real-time polymerase chain reaction and Western blot analysis. The localization of these glucose transporters in the peritoneum was evaluated by immunohistochemistry using a Histo-Score. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Peritoneal biopsies of patients (healthy controls, uremic, PD, and encapsulating peritoneal sclerosis [EPS]) were analyzed. We found evidence of SGLT-2, GLUT1, and GLUT3 expression in the peritoneal membrane. Protein expression of SGLT-2 increases with PD duration and is significantly enhanced in EPS patients. All transporters were predominantly, but not exclusively, located adjacent to the vessel walls of the peritoneal membrane. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; Our study showed that SGLT-2, GLUT1, and GLUT3 were regularly expressed in the human peritoneum. SGLT-2 was particularly upregulated in PD patients with EPS, suggesting that this upregulation may be associated with pathological changes in the peritoneal membrane in this syndrome. Since preclinical studies in mice show that SGLT-2 inhibitors or downregulation of SGLT-2 ameliorated pathological changes in the peritoneum, SGLT-2 inhibitors may be potentially promising agents for therapy in PD patients that could reduce glucose absorption and delay functional deterioration of the peritoneal membrane in the long term.
The effects of parenting on early adolescents’ noncognitive skills: Evidence from a sample of twins in Germany
2021-11-15

Many theories in the social sciences assume that parenting affects child development. Previous research mostly supports the notion that parenting affects the skill development of children in early childhood. There are fewer studies testing whether parenting in early adolescence has such an influence. We estimate the effects of parenting on early adolescents’ noncognitive skills using data from the German Twin Family Panel (TwinLife). Specifically, we look at the effects of parenting styles, parental activities, and extracurricular activities on the academic self-concept, motivation, self-esteem, self-efficacy, and locus of control of 10 to 14 years old children. To control for unobserved heterogeneity and reverse causality, we employ twin fixed-effects models combined with longitudinal information. In addition, MZ twin fixed effects models also control for genetic confounding. Our findings provide no support to the notion that parenting styles, parental activities, and extracurricular activities in early adolescence affect the development of children's noncognitive skills. We conclude that our results, in combination with the majority of evidence from previous research, are in line with a model according to which parenting has larger effects on the skill development of children in early childhood than in early adolescence.