julilili42/papers huggingface dataset:
Near‐infrared laser 808‐nm excitable palladium nano‐dots loaded on graphene oxide hybrid for the antibacterial activity
2021-07-15

Escherichia coli ( E. coli ) is considered the most common life‐threatening infectious bacteria in our daily life and poses a major challenge to human health. However, antibiotics frequently overused and misused has triggered increased multidrug resistance, hinders therapeutic outcomes, and causes higher mortalities. Herein, we addressed near‐infrared (NIR) laser‐excited human serum albumin (HSA) mediated graphene oxide loaded palladium nano‐dots (HSA‐GO‐Pd) that can effectively combat Gram‐negative E. coli in vitro. NIR laser‐excited designed hybrid material highly generates singlet oxygen and hydroxyl radical by electron spin‐resonance (ESR) analysis. Transmission electron microscope (TEM) images show small spherical sizes PdNPs on the surface of GO nano‐sheets. The zeta (ζ) potential study indicates that in an aqueous medium, the average PdNPs size and surface capped charge comes from human body protein (HSA), HSA‐GO‐Pd is 5–8 nm, and +25 mV, respectively. The spectroscopic characterization reveals that in the synthesized HSA‐GO‐Pd nanocomposite, PdNPs successfully well‐dispersed decorated on the surface of graphene oxide. The as‐synthesized HSA‐GO‐Pd shows excellent antibacterial activity against gram‐negative pathogen by killing 95% bacteria within 5 h. HSA‐GO‐Pd having very biocompatible and shows significant antibacterial activities. Owing to their intense photothermal conversation potential, low toxicity to normal cells, the as‐addressed hybrid (HSA‐GO‐Pd) combined with NIR‐irradiation will catch up valuable insight into the effective ablation of pathogenic bacteria.
Nemertean, Brachiopod, and Phoronid Neuropeptidomics Reveals Ancestral Spiralian Signaling Systems
2021-07-16

Abstract Neuropeptides are diverse signaling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide–receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for mollusks and annelids. Here, we analyze peptidergic systems in Nemertea, Brachiopoda, and Phoronida. We screened transcriptomes from 13 nemertean, 6 brachiopod, and 4 phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemertean Lineus longissimus, we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusk and annelid peptidergic systems also in nemerteans, brachiopods, and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusk APGWamides to RGWamides from annelids, with ortholog systems in nemerteans, brachiopods, and phoronids. We found that pleurin neuropeptides previously only found in mollusks are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signaling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids, and nemerteans. This analysis expands our knowledge of peptidergic signaling in spiralians and other protostomes. Our annotated data set of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signaling.
Melt in the Greenland EastGRIP ice core reveals Holocene warming events
2021-07-16

Abstract. We present a record of melt events obtained from the EastGRIP ice core, in central north eastern Greenland, covering the largest part of the Holocene. The data were acquired visually using an optical dark-field line scanner. We detect and describe bubble free layers and -lenses throughout the ice above the bubble-clathrate transition, located at 1100 m in the EastGRIP ice core, corresponding to an age of 9720 years b2k. We distinguish between melt layers (bubble free layers continuous over the width of the core), melt lenses (discontinuous), crusts (thin and sharp bubble free layers) and attribute three levels of confidence to each of these, depending on how clearly they are identified. Our record of melt events shows a large, distinct peak around 1014 years b2k (986 CE) and a broad peak around 7000 years b2k corresponding to the Holocene Climatic Optimum. We analyze melt layer thicknesses and correct for ice thinning, we account for missing layers due to core breaks, and ignore layers thinner than 1.5 mm. We define the brittle zone in the EastGRIP ice core from 650 m to 950 m depth, where we count on average more than three core breaks per meter. In total we can identify approximately 831 mm of melt (corrected for thinning) over the past 10,000 years. We compare our melt layer record to the GISP2 and Renland melt layer records. Our climatic interpretation matches well with the Little Ice Age, the Medieval and Roman Warm Periods, the Holocene Climatic Optimum, and the 8.2 kyr event. We also compare the most recent 2500 years to a tree ring composite and find an overlap between melt events and tree ring anomalies indicating warm summers. We open the discussion for sloping bubble free layers (tilt angle off horizontal &gt; 10°) being the effect of rheology and not climate. We also discuss our melt layers in connection to a coffee experiment (coffee as a colored substitute for melt infiltration into the snow pack) and the real time observations of the 2012 CE rain event at NEEM. We find that the melt event from 986 CE is most likely a large rain event, similar to 2012 CE, and that these two events are unprecedented throughout the Holocene. Furthermore, we suggest that the warm summer of 986 CE, with the exceptional melt event, was the trigger for the first Viking voyages to sail from Iceland to Greenland.
Repeated Genetic and Adaptive Phenotypic Divergence across Tidal Elevation in a Foundation Plant Species
2021-07-16

Microgeographic genetic divergence can create fine-scale trait variation. When such divergence occurs within foundation species, then it might impact community structure and ecosystem function, and cause other cascading ecological effects. We tested for parallel microgeographic trait and genetic divergence in Spartina alterniflora , a foundation species that dominates salt marshes of the US Atlantic and Gulf coasts. Spartina is characterized by tall-form (1-2m) plants at lower tidal elevations and short-form (&lt;0.5m) plants at higher tidal elevations, yet whether this trait variation reflects plastic and/or genetically differentiated responses to these environmental conditions remains unclear. In the greenhouse, seedlings raised from tall-form plants grew taller than those from short-form plants, indicating a heritable difference in height. When we reciprocally transplanted seedlings back into the field for a growing season, composite fitness (survivorship and seed production) and key plant traits (plant height and biomass allocation) differed interactively across origin and transplant zones in a manner indicative of local adaptation. Further, a survey of single nucleotide polymorphisms revealed repeated, independent genetic differentiation between tall- and short-form Spartina at 5 of 6 tested marshes across the native range. The observed parallel, microgeographic genetic differentiation in Spartina likely underpins marsh health and functioning, and provides an underappreciated mechanism that might increase capacity of marshes to adapt to rising sea levels.
Distinct synaptic transfer functions in same-type photoreceptors
2021-07-16

Many sensory systems use ribbon-type synapses to transmit their signals to downstream circuits. The properties of this synaptic transfer fundamentally dictate which aspects in the original stimulus will be accentuated or suppressed, thereby partially defining the detection limits of the circuit. Accordingly, sensory neurons have evolved a wide variety of ribbon geometries and vesicle pool properties to best support their diverse functional requirements. However, the need for diverse synaptic functions does not only arise across neuron types, but also within . Here we show that UV-cones, a single type of photoreceptor of the larval zebrafish eye, exhibit striking differences in their synaptic ultrastructure and consequent calcium to glutamate transfer function depending on their location in the eye. We arrive at this conclusion by combining serial section electron microscopy and simultaneous ‘dual-colour’ two-photon imaging of calcium and glutamate signals from the same synapse in vivo. We further use the functional dataset to fit a cascade-like model of the ribbon synapse with different vesicle pool sizes, transfer rates, and other synaptic properties. Exploiting recent developments in simulation-based inference, we obtain full posterior estimates for the parameters and compare these across different retinal regions. The model enables us to extrapolate to new stimuli and to systematically investigate different response behaviours of various ribbon configurations. We also provide an interactive, easy-to-use version of this model as an online tool. Overall, we show that already on the synaptic level of single-neuron types there exist highly specialised mechanisms which are advantageous for the encoding of different visual features.
Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models
2021-07-16

Abstract Background The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Here we tested in vivo selection of anti-EGFR SR tumors in CRC patient-derived xenograft (PDX) models as a strategy for a molecular dissection of SR mechanisms. Methods We analyzed 21 KRAS, NRAS, BRAF, and PI3K wildtype CRC patient-derived xenograft (PDX) models for their anti-EGFR sensitivity. Furthermore, 31 anti-EGFR SR tumors were generated via chronic in vivo treatment with cetuximab. A multi-omics approach was employed to address molecular primary and secondary resistance mechanisms. Gene set enrichment analyses were used to uncover SR pathways. Targeted therapy of SR PDX models was applied to validate selected SR pathways. Results In vivo anti-EGFR SR could be established with high efficiency. Chronic anti-EGFR treatment of CRC PDX tumors induced parallel evolution of multiple resistant lesions with independent molecular SR mechanisms. Mutations in driver genes explained SR development in a subgroup of CRC PDX models, only. Transcriptional reprogramming inducing anti-EGFR SR was discovered as a common mechanism in CRC PDX models frequently leading to RAS signaling pathway activation. We identified cAMP and STAT3 signaling activation, as well as paracrine and autocrine signaling via growth factors as novel anti-EGFR secondary resistance mechanisms. Secondary resistant xenograft tumors could successfully be treated by addressing identified transcriptional changes by tailored targeted therapies. Conclusions Our study demonstrates that SR PDX tumors provide a unique platform to study molecular SR mechanisms and allow testing of multiple treatments for efficient targeting of SR mechanisms, not possible in the patient. Importantly, it suggests that the development of anti-EGFR tolerant cells via transcriptional reprogramming as a cause of anti-EGFR SR in CRC is likely more prevalent than previously anticipated. It emphasizes the need for analyses of SR tumor tissues at a multi-omics level for a comprehensive molecular understanding of anti-EGFR SR in CRC.
Parallelized label-free monitoring of cell adhesion on extracellular matrix proteins measured by single colour reflectometry
2021-07-16

Abstract The understanding of the initial cell adhesion to biomaterials is crucial for the survival of implants. The manifold possibilities to tailor an implant surface and the diverse requirements for different implant applications necessitate a timesaving and highly parallelized analytical methodology. Due to its intrinsic advantages (label-free, time-resolved, robust against temperature fluctuations, and particularly the multiplexing possibilities), single colour reflectometry (SCORE) is used for the first time to investigate cell adhesion to different extracellular matrix protein–coated surfaces. The excellent correlation between the novel SCORE technology and well-established reference methods proves that the results obtained by using this direct optical method are able to reflect the cell binding processes at the transducer surface. Additionally, the high time resolution of SCORE revealed the differences in the adhesion behaviour of the cells on the different extracellular matrix protein–coated glass slides during the initial adsorption phase and during the spreading of the cells on the surfaces. Therefore, we conclude that SCORE is a perfectly suited methodology for studying the entire cell adsorption process, including morphological changes, and shows great potential for other cell-based sensing applications. Graphical abstract
Accelerated T2-Weighted TSE Imaging of the Prostate Using Deep Learning Image Reconstruction: A Prospective Comparison with Standard T2-Weighted TSE Imaging
2021-07-17

Multiparametric MRI (mpMRI) of the prostate has become the standard of care in prostate cancer evaluation. Recently, deep learning image reconstruction (DLR) methods have been introduced with promising results regarding scan acceleration. Therefore, the aim of this study was to investigate the impact of deep learning image reconstruction (DLR) in a shortened acquisition process of T2-weighted TSE imaging, regarding the image quality and diagnostic confidence, as well as PI-RADS and T2 scoring, as compared to standard T2 TSE imaging. Sixty patients undergoing 3T mpMRI for the evaluation of prostate cancer were prospectively enrolled in this institutional review board-approved study between October 2020 and March 2021. After the acquisition of standard T2 TSE imaging (T2S), the novel T2 TSE sequence with DLR (T2DLR) was applied in three planes. Overall, the acquisition time for T2S resulted in 10:21 min versus 3:50 min for T2DLR. The image evaluation was performed by two radiologists independently using a Likert scale ranging from 1–4 (4 best) applying the following criteria: noise levels, artifacts, overall image quality, diagnostic confidence, and lesion conspicuity. Additionally, T2 and PI-RADS scoring were performed. The mean patient age was 69 ± 9 years (range, 49–85 years). The noise levels and the extent of the artifacts were evaluated to be significantly improved in T2DLR versus T2S by both readers (p &lt; 0.05). Overall image quality was also evaluated to be superior in T2DLR versus T2S in all three acquisition planes (p = 0.005–&lt;0.001). Both readers evaluated the item lesion conspicuity to be superior in T2DLR with a median of 4 versus a median of 3 in T2S (p = 0.001 and &lt;0.001, respectively). T2-weighted TSE imaging of the prostate in three planes with an acquisition time reduction of more than 60% including DLR is feasible with a significant improvement of image quality.
Spontaneous transient brain states in EEG source space in disorders of consciousness
2021-07-17

Spontaneous transient states were recently identified by functional magnetic resonance imaging and magnetoencephalography in healthy subjects. They organize and coordinate neural activity in brain networks. How spontaneous transient states are altered in abnormal brain conditions is unknown. Here, we conducted a transient state analysis on resting-state electroencephalography (EEG) source space and developed a state transfer analysis to patients with disorders of consciousness (DOC). They uncovered different neural coordination patterns, including spatial power patterns, temporal dynamics, spectral shifts, and connectivity construction varies at potentially very fast (millisecond) time scales, in groups with different consciousness levels: healthy subjects, patients in minimally conscious state (MCS), and patients with vegetative state/unresponsive wakefulness syndrome (VS/UWS). Machine learning based on transient state features reveal high classification accuracy between MCS and VS/UWS. This study developed methodology of transient states analysis on EEG source space and abnormal brain conditions. Findings correlate spontaneous transient states with human consciousness and suggest potential roles of transient states in brain disease assessment.
Values and Environmental Knowledge of Student Participants of Climate Strikes: A Comparative Perspective between Brazil and Germany
2021-07-17

Climate change and its consequences have called for actions to mitigate it, triggering society to act and speak out about sustainability policies. Movements like Fridays for Future (FFF) spread beyond the young people pressed for action to combat climate change. The present study aimed to (1) assess the environmental attitudes (EA) and knowledge (EK) of Brazilian and German students and (2) verify whether the frequency of participation in climate strikes changes according to these EA and EK. A total of 658 students participated in our study, 327 from Germany and 331 from Brazil (mean age 25.21 ± 7.91). We applied the Two Major Environmental Values (2-MEV) model and three-dimensional questionnaires to measure EA and EK, respectively. We applied a multivariate general linear model to assess the influence of the variables simultaneously. FFF participation is affected by EA, with strikers showing higher Preservation (PRE) and lower Utilization (UTL) scores; furthermore, our findings suggest that EK affects FFF participation, specifically system-related knowledge. The study adds to the increasing number of validations of the 2-MEV model in different languages and cultures and discusses the differences of EA and EK in student strikers and non-strikers between both countries.
Pro‐vaccination subjective norms moderate the relationship between conspiracy mentality and vaccination intentions
2021-07-18

Objectives Increasing vaccination hesitancy threatens societies’ capacity to contain pandemics and other diseases. One factor that is positively associated with vaccination intentions is a supportive subjective norm (i.e., the perception that close others approve of vaccination). On the downside, there is evidence that negative attitudes toward vaccinations are partly rooted in conspiracy mentality (i.e., the tendency to believe in conspiracies). The objective of this study is to examine the role of subjective norms in moderating the association between conspiracy mentality and vaccine hesitancy. We examined two competing predictions: Are those high in conspiracy mentality immune to subjective norms, or do subjective norms moderate the relationship between conspiracy mentality and vaccination intentions? Methods We conducted five studies (total N = 1,280) to test these hypotheses across several vaccination contexts (some real, some fictitious). We measured conspiracy mentality, vaccination intentions, subjective norms, attitudes toward vaccination, and perceived behavioural control. Results A merged analysis across the studies revealed an interaction effect of conspiracy mentality and subjective norm on vaccination intentions. When subjective norm was high (i.e., when participants perceived that close others approved of vaccines) conspiracy mentality no longer predicted vaccination intentions. This was consistent with the moderating hypothesis of subjective norms and inconsistent with the immunity hypothesis. Conclusions The typical negative relationship between conspiracy mentality and vaccination intentions is eliminated among those who perceive pro‐vaccination subjective norms. Although correlational, these data raise the possibility that pro‐vaccination views of friends and family can be leveraged to reduce vaccine hesitancy.
Sensitivity of Water Balance in the Qaidam Basin to the Mid‐Pliocene Climate
2021-07-18

Abstract The Qaidam Basin (QB) in the northeastern Tibetan Plateau held a megalake system during the Pliocene. Today, the lower elevations in the basin are hyperarid. To understand to what extent the climate plays a role in the maintenance of the megalake system during the Pliocene, we applied the Weather Research and Forecasting model for dynamical downscaling of ECHAM5 global climate simulations for the present day and the mid‐Pliocene. When imposing the mid‐Pliocene climate on the QB with its modern land surface settings, the annual water balance ( ), that is, the change in terrestrial water storage within the QB, increases. This positive imbalance of induced solely by the changes in the large‐scale climate state would lead to a readjustment of lake extent, until a new equilibrium state is reached, where loss due to evaporation over lake areas compensates for the input by runoff and precipitation. Atmospheric water transport (AWT) analysis at each border of the QB reveals that this imbalance of is caused by stronger moisture influx across the western border in winter, spring, and autumn and weaker moisture out‐flux across the eastern border in summer. These changes in AWT are associated with the strengthening of the midlatitude westerlies in all seasons, except for summer, and the intensification of the East Asian Summer Monsoon. Given that the mid‐Pliocene climate is an analog to the projected warm climate of the near future, our study contributes to a better understanding of climate change impacts in central Asia.
Engineering of Streptoalloteichus tenebrarius 2444 for Sustainable Production of Tobramycin
2021-07-18

Tobramycin is a broad-spectrum aminoglycoside antibiotic agent. The compound is obtained from the base-catalyzed hydrolysis of carbamoyltobramycin (CTB), which is naturally produced by the actinomycete Streptoalloteichus tenebrarius. However, the strain uses the same precursors to synthesize several structurally related aminoglycosides. Consequently, the production yields of tobramycin are low, and the compound’s purification is very challenging, costly, and time-consuming. In this study, the production of the main undesired product, apramycin, in the industrial isolate Streptoalloteichus tenebrarius 2444 was decreased by applying the fermentation media M10 and M11, which contained high concentrations of starch and dextrin. Furthermore, the strain was genetically engineered by the inactivation of the aprK gene (∆aprK), resulting in the abolishment of apramycin biosynthesis. In the next step of strain development, an additional copy of the tobramycin biosynthetic gene cluster (BGC) was introduced into the ∆aprK mutant. Fermentation by the engineered strain (∆aprK_1-17L) in M11 medium resulted in a 3- to 4-fold higher production than fermentation by the precursor strain (∆aprK). The phenotypic stability of the mutant without selection pressure was validated. The use of the engineered S. tenebrarius 2444 facilitates a step-saving, efficient, and, thus, more sustainable production of the valuable compound tobramycin on an industrial scale.