julilili42/papers huggingface dataset:
Novel insights into the role of the mobilome in ecological diversification and success of Staphylococcus haemolyticus as an opportunistic pathogen
2022-01-17

Staphylococcus haemolyticus is a species of coagulase-negative staphylococci that has primarily been studied as a human skin microbiome member and an emerging nosocomial pathogen. Here, we present the first complete genome of S. haemolyticus strains SE3.9, SE3.8 and SE2.14 reported as an endophyte of rice seed. Detailed investigation of the genome dynamics of strains from diverse origins revealed an expanded genome size in clinical isolates, and a role of many insertion sequence (IS) elements in strain diversification. Interestingly, several of the IS elements are also unique or enriched in a particular habitat. Comparative studies also revealed the potential movement of mobile elements from rice endophytic S. haemolyticus to strains from other pathogenic species such as Staphylococcus aureus . The study highlights the importance of ecological studies in the systematic understanding of genome plasticity and management of medically important Staphylococcus species.
Spatial Coherence Patterns of Extreme Winter Precipitation In The United States
2022-01-17

<title>Abstract</title> Extreme precipitation events have a significant impact on life and property. The United States experiences huge economic losses due to severe floods caused by extreme precipitation. With the varied terrain, it becomes increasingly important to understand the spatial variability of extreme precipitation to conduct a proper risk assessment of natural hazards such as floods. In this work, we use a complex network based approach to identify distinct regions exhibiting spatially coherent precipitation patterns due to various underlying climate mechanisms. To quantify interactions between event series of different locations, we use a nonlinear similarity measure, called the edit-distance method, which considers not only the occurrence of the extreme events but also their intensity while measuring similarity. Using network measures, namely, degree and betweenness centrality, we are able to identify the specific regions affected by landfall of atmospheric rivers in addition to those regions where the extreme precipitation due to storm track activity is modulated by different mountain ranges such as the Rockies and the Appalachians. Our approach provides a comprehensive picture of the spatial patterns of extreme winter precipitation in the United States due to various climate processes despite its vast complex topography
Pioneer biocrust communities prevent soil erosion in temperate forests after disturbances
2022-01-17

Abstract. Soil erosion continues to be one of the most serious environmental problems of our time, which is exacerbated by progressive climate change. Until now, forests have been considered an ideal erosion control in this regard. However, even minor disturbances of the forest floor for example from heavy vehicle used for timber harvesting can cause substantial sediment transport. An important countermeasure is the quick restoration of the uncovered soil surface by vegetation. In this context, biological soil crusts (biocrusts) can play a vital role, as they are known for their soil-protective effect. This study examined the natural succession of pioneer vegetation in skid trails on four soil substrates in a central European temperate forest and investigated their influence on surface runoff and sediment discharge. We applied rainfall simulation experiments on small-scale runoff plots and continuously surveyed vegetation during the same period, primarily to map biocrust development. Skid trails on clayey substrates showed considerably higher biocrust cover and species richness. Biocrust cover was higher in center tracks than in wheel tracks, while there was no clear difference for biocrust species richness with regard to track position. Although biocrusts were quickly overtopped by vascular plants, they managed to coexist until their growth was restricted due to leaf litter fall. Brachythecium rutabulum and Oxyrrhynchium hians were the most important and persistent pioneer biocrust species, while Dicranella schreberiana and Pohlia lutescens were volatile and quickly disappeared after spreading in summer. Soil erosion was reduced with pioneer biocrust vegetation in summer, and again increased in winter. Total amount of sediment discharge was clearly site-dependent, indicating a high relevance of underlying substrates. Sediment discharge was 13.2 times higher in wheel tracks compared to undisturbed forest soil, and bare soil runoff plots produced 22-fold sediment discharge compared to undisturbed forest soil. Overall, bryophyte-dominated biocrusts contributed more to mitigating soil erosion than vascular plants. When soil coverage exceeded 50 %, biocrusts resulted in an average of 18 times less sediment loss compared to vascular plants.
Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues
2022-01-18

Understanding the molecular principles that govern the composition of the MHC-I immunopeptidome across different primary tissues is fundamentally important to predict how T cells respond in different contexts <i>in vivo</i>. Here, we performed a global analysis of the MHC-I immunopeptidome from 29 to 19 primary human and mouse tissues, respectively. First, we observed that different HLA-A, HLA-B, and HLA-C allotypes do not contribute evenly to the global composition of the MHC-I immunopeptidome across multiple human tissues. Second, we found that tissue-specific and housekeeping MHC-I peptides share very distinct properties. Third, we discovered that proteins that are evolutionarily hyperconserved represent the primary source of the MHC-I immunopeptidome at the organism-wide scale. Fourth, we uncovered new components of the antigen processing and presentation network, including the carboxypeptidases CPE, CNDP1/2, and CPVL. Together, this study opens up new avenues toward a system-wide understanding of antigen presentation <i>in vivo</i> across mammalian species.
Parasitic gaps aren’t parasitic, or, the case of the Uninvited Guest
2022-01-18

Abstract A parasitic gap construction typically occurs when an otherwise illicit gap in an island is ameliorated by a gap elsewhere in the sentence. In this paper, we consider the relationship between the unacceptability of extraction from subject islands (ExtrSubj) and the amelioration associated with parasitic gaps. We argue that there is no parasitic gap mechanism per se that has the effect of making extraction from an island grammatical. Rather, the link between the two is a matter of processing complexity. Our central claim is that in ExtrSubj, the presence of a distinct referring argument in the predicate contributes processing complexity. This referring argument is the ‘Uninvited Guest’. If an instance of ExtrSubj is of reduced acceptability, inclusion of the Uninvited Guest is likely to make it fully unacceptable, or ‘ungrammatical’ in conventional terms. On the other hand, linking of the argument position to the extracted A′ constituent – a ‘parasitic gap’ configuration – does not contribute additional processing complexity, thus giving rise to the appearance of amelioration.
Rare germline copy number variants (CNVs) and breast cancer risk
2022-01-18

Abstract Germline copy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. Gene burden tests detected the strongest association for deletions in BRCA1 ( P = 3.7E−18). Nine other genes were associated with a p -value &lt; 0.01 including known susceptibility genes CHEK2 ( P = 0.0008), ATM ( P = 0.002) and BRCA2 ( P = 0.008). Outside the known genes we detected associations with p -values &lt; 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci. To the best of our knowledge, this is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance.
Prognostic Value of Immunohistochemical Markers for Locally Advanced Rectal Cancer
2022-01-18

The aim of this study is to reveal the potential roles of apoptosis markers (Bcl2 and p53), proliferation markers (Ki-67 and CyclD1), and the neuroendocrine marker Chromogranin A as markers for the radioresistance of rectal cancer. Statistically significant differences were found in the expression of p53, Ki-67, and Chromogranin A in groups of patients with and without a favorable prognosis after radiotherapy. The survival analysis revealed that the marker of neuroendocrine differentiation, Chromogranin A, also demonstrated a high prognostic significance, indicating a poor prognosis. Markers of proliferation and apoptosis had no prognostic value for patients who received preoperative radiotherapy. Higher Chromogranin A values were predictors of poor prognosis. The results obtained from studying the Chromogranin A expression suggest that the secretion of biologically active substances by neuroendocrine cells causes an increase in tumor aggressiveness.
Effects of Face Masks on Physical Performance and Physiological Response during a Submaximal Bicycle Ergometer Test
2022-01-18

The ongoing COVID-19 pandemic requires wearing face masks in many areas of our daily life; hence, the potential side effects of mask use are discussed. Therefore, the present study explores whether wearing a medical face mask (MedMask) affects physical working capacity (PWC). Secondary, the influence of a filtering facepiece mask with exhalation valve class 2 (FFP2exhal) and a cotton fabric mask (community mask) on PWC was also investigated. Furthermore, corresponding physiological and subjective responses when wearing face masks as well as a potential moderating role of subjects’ individual cardiorespiratory fitness and sex on face mask effects were analyzed. Thirty-nine subjects (20 males, 19 females) with different cardiorespiratory fitness levels participated in a standardized submaximal bicycle ergometer protocol using either a MedMask, FFP2exhal, community mask, or no mask (control) on four days, in randomized order. PWC130 and PWC150 as the mechanical load at the heart rates of 130 and 150 beats per minute were measured as well as transcutaneous carbon dioxide partial pressure, saturation of peripheral capillary oxygen, breathing frequency, blood pressure, perceived respiratory effort, and physical exhaustion. Using the MedMask did not lead to changes in PWC or physiological response compared to control. Neither appeared changes exceeding normal ranges when the FFP2exhal or community mask was worn. Perceived respiratory effort was up to one point higher (zero-to-ten Likert scale) when using face masks (p &lt; 0.05) compared to control. Sex and cardiorespiratory fitness were not factors influencing the effects of the masks. The results of the present study provide reason to believe that wearing face masks for infection prevention during the COVID-19 pandemic does not pose relevant additional physical demands on the user although some more respiratory effort is required.
Diagnosis of Model Errors With a Sliding Time‐Window Bayesian Analysis
2022-01-18

Abstract Deterministic hydrological models with uncertain, but inferred‐to‐be‐time‐invariant parameters typically show time‐dependent model errors. Such errors can occur if a hydrological process is active in certain time periods in nature, but is not resolved by the model or by its input. Such missing processes could become visible during calibration as time‐dependent best‐fit values of model parameters. We propose a formal time‐windowed Bayesian analysis to diagnose this type of model error, formalizing the question “In which period of the calibration time‐series does the model statistically disqualify itself as quasi‐true?” Using Bayesian model evidence (BME) as model performance metric, we determine how much the data in time windows of the calibration time‐series support or refute the model. Then, we track BME over sliding time windows to obtain a dynamic, time‐windowed BME (tBME) and search for sudden decreases that indicate an onset of model error. tBME also allows us to perform a formal, sliding likelihood‐ratio test of the model against the data. Our proposed approach is designed to detect error occurrence on various temporal scales, which is especially useful in hydrological modeling. We illustrate this by applying our proposed method to soil moisture modeling. We test tBME as model error indicator on several synthetic and real‐world test cases that we designed to vary in error sources (structure and input) and error time scales. Results prove the successful detection errors in dynamic models. Moreover, the time sequence of posterior parameter distributions helps to investigate the reasons for model error and provide guidance for model improvement.
A Review on CRISPR-mediated Epigenome Editing: A Future Directivefor Therapeutic Management of Cancer
2022-01-18

Abstract: Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
Local stability of ground states in locally gapped and weakly interacting quantum spin systems
2022-01-18

Abstract Based on a result by Yarotsky (J Stat Phys 118, 2005), we prove that localized but otherwise arbitrary perturbations of weakly interacting quantum spin systems with uniformly gapped on-site terms change the ground state of such a system only locally, even if they close the spectral gap. We call this a strong version of the local perturbations perturb locally (LPPL) principle which is known to hold for much more general gapped systems, but only for perturbations that do not close the spectral gap of the Hamiltonian. We also extend this strong LPPL-principle to Hamiltonians that have the appropriate structure of gapped on-site terms and weak interactions only locally in some region of space. While our results are technically corollaries to a theorem of Yarotsky, we expect that the paradigm of systems with a locally gapped ground state that is completely insensitive to the form of the Hamiltonian elsewhere extends to other situations and has important physical consequences.
Fish health in the Nidda as an indicator for ecosystem integrity: a case study for Central European small streams in densely populated areas
2022-01-18

Abstract Background In Germany and the EU, most headwaters are still far from reaching a good chemical and ecological status as it is required by the European Water Framework Directive (WFD), until 2027 the latest. Particularly, in densely populated areas, impacts from municipal and industrial wastewater discharges or diffuse agricultural emissions are still a matter of concern. This also applies to the Nidda River which is considered to be in a moderate to rather poor condition. In our study, we investigated short-term and long-term consequences of anthropogenic pollution on fish health via one monitoring with caged fish (CF) and two field sampling campaigns (FF). In the CF monitoring, rainbow trout ( Oncorhynchus mykiss ) were caged for seven weeks at four selected sites along the Nidda, whereas in the FF monitoring approach, feral fish, including brown trout ( Salmo trutta f. fario ), European chub ( Leuciscus cephalus ) and stone loach ( Barbatula barbatula ) were caught in June and September 2016. Results Histopathological analyses of liver and gills were conducted, accompanied by measurements of hepatic 7-ethoxyresorufin- O -deethylase (EROD) activity to assess the cytochrome P450 (CYP1A1) function, and genotoxicity via the micronucleus assay. Caged as well as field-captured fish exhibited impaired health conditions showing lesions particularly in the liver, and a presumably overwhelmed CYP1A1 system, whereas genotoxicity was not induced. The variation between sampling sites and seasons was rather low, but two trends were recognisable: (a) liver condition was poorest around spawning season and (b) tissue integrity and EROD activity were most affected downstream of industrial dischargers. Furthermore, effects were species dependent: the generally highly sensitive S. trutta f. fario proved to be impacted most, whereas L. cephalus with its pelagic lifestyle was affected less than the benthic B. barbatula, indicating a relevant contamination of sediments. Conclusion Our results confirm the impaired ecological state of the Nidda and emphasise that a sustainable improvement of aquatic ecosystem health needs to include both water quality and sediment contamination to approach the ambitious WFD goal.
An Automated Toolbox to Predict Single Subject Atrophy in Presymptomatic Granulin Mutation Carriers
2022-01-18

Background: Magnetic resonance imaging (MRI) measures may be used as outcome markers in frontotemporal dementia (FTD). Objectives: To predict MRI cortical thickness (CT) at follow-up at the single subject level, using brain MRI acquired at baseline in preclinical FTD. Methods: 84 presymptomatic subjects carrying Granulin mutations underwent MRI scans at baseline and at follow-up (31.2±16.5 months). Multivariate nonlinear mixed-effects model was used for estimating individualized CT at follow-up based on baseline MRI data. The automated user-friendly preGRN-MRI script was coded. Results: Prediction accuracy was high for each considered brain region (i.e., prefrontal region, real CT at follow-up versus predicted CT at follow-up, mean error ≤1.87%). The sample size required to detect a reduction in decline in a 1-year clinical trial was equal to 52 subjects (power = 0.80, alpha = 0.05). Conclusion: The preGRN-MRI tool, using baseline MRI measures, was able to predict the expected MRI atrophy at follow-up in presymptomatic subjects carrying GRN mutations with good performances. This tool could be useful in clinical trials, where deviation of CT from the predicted model may be considered an effect of the intervention itself.
Joseph Turow. The voice catchers: How marketers listen in to exploit your feelings, your privacy, and your wallet
2022-01-18

“Voice profiling is a gateway drug to a new era of hyper-personalized targeting,” (p. 227) Joseph Turow concludes in his book The Voice Catchers: How Marketers Listen in to Exploit Your Feelings, Your Privacy, and Your Wallet. This crucial function of what Turow calls the “voice intelligence industry” explains the urgency of Turow’s most recent endeavor: a thorough examination of this industry which consists of different players, most centrally call center firms and the developers of voice assistants such as Amazon’s Alexa, the Google Assistant, Apple’s Siri, and Samsung’s Bixby. The industry is united by its interest in using voice as another source for collecting biometrical data. Such voiceprints, as Turow figuratively puts it, are the “gold in people’s speech” (p. 192). In contrast to the face as another source for biometrical data, voice has received comparatively little public attention.
Sensitizing Staphylococcus aureus to antibacterial agents by decoding and blocking the lipid flippase MprF
2022-01-19

The pandemic of antibiotic resistance represents a major human health threat demanding new antimicrobial strategies. Multiple peptide resistance factor (MprF) is the synthase and flippase of the phospholipid lysyl-phosphatidylglycerol that increases virulence and resistance of methicillin-resistant Staphylococcus aureus (MRSA) and other pathogens to cationic host defense peptides and antibiotics. With the aim to design MprF inhibitors that could sensitize MRSA to antimicrobial agents and support the clearance of staphylococcal infections with minimal selection pressure, we developed MprF-targeting monoclonal antibodies, which bound and blocked the MprF flippase subunit. Antibody M-C7.1 targeted a specific loop in the flippase domain that proved to be exposed at both sides of the bacterial membrane, thereby enhancing the mechanistic understanding of bacterial lipid translocation. M-C7.1 rendered MRSA susceptible to host antimicrobial peptides and antibiotics such as daptomycin, and it impaired MRSA survival in human phagocytes. Thus, MprF inhibitors are recommended for new antivirulence approaches against MRSA and other bacterial pathogens.
A Comparison of Model Averaging Techniques to Predict the Spatial Distribution of Soil Properties
2022-01-19

This study tested and evaluated a suite of nine individual base learners and seven model averaging techniques for predicting the spatial distribution of soil properties in central Iran. Based on the nested-cross validation approach, the results showed that the artificial neural network and Random Forest base learners were the most effective in predicting soil organic matter and electrical conductivity, respectively. However, all seven model averaging techniques performed better than the base learners. For example, the Granger–Ramanathan averaging approach resulted in the highest prediction accuracy for soil organic matter, while the Bayesian model averaging approach was most effective in predicting sand content. These results indicate that the model averaging approaches could improve the predictive accuracy for soil properties. The resulting maps, produced at a 30 m spatial resolution, can be used as valuable baseline information for managing environmental resources more effectively.
Blackbody-radiation-induced facilitated excitation of Rydberg atoms in optical tweezers
2022-01-19

Black-body radiation, omnipresent at room temperature, couples nearby Rydberg\\nstates. The resulting state mixture features strong dipolar interactions, which\\nmay induce dephasing in a Rydberg many-body system. Here we report on a single\\natom resolved study of this state contamination and the emerging pairwise\\ninteractions in optical tweezers. For near-resonant laser detuning we observe\\ncharacteristic correlations with a length scale set by the dipolar interaction.\\nOur study reveals the microscopic origin of avalanche excitation observed in\\nprevious experiments.\\n