julilili42/papers huggingface dataset:
Evaluation of Injectable Composite Material Comprising Biphasic Bone Substitutes and Crosslinked Collagen
2023-07-07

Bone tissue engineering has emerged as a promising approach to regenerate bone tissue, and injectable biomaterials have shown potential for bone regeneration applications due to their ease of administration and ability to fill irregularly shaped defects. This study aims to develop and characterize an injectable composite material comprising biphasic bone substitutes (BBS) and crosslinked porcine collagen type I for bone regeneration applications. The collagen is crosslinked via a UVA‐riboflavin crosslinking strategy and evaluated by testing the physicochemical properties, including the rheological behavior, dynamic storage modulus ( G′ ) and loss modulus ( G′′ ), and in vitro degradation process. The results show that the crosslinked collagen (xCol) exhibits suitable physicochemical properties for injectability and improved viscoelasticity and degradation resistance. Furthermore, xCol is then combined with BBS in a predetermined ratio, obtaining the injectable composite material. The biocompatibility of the materials is evaluated in vitro by XTT and BrdU assays on fibroblasts and preosteoblasts. The results demonstrate that the composite material is biocompatible and supporting pre‐osteoblasts proliferation. In conclusion, the injectable composite material BBS‐xCol has promising physiochemical and biological properties for bone regeneration applications. Further studies are warranted to evaluate its efficacy in vivo and optimize its composition for clinical translation.
Biological soil crusts as a major ecosystem component in sandization areas of the Brazilian Pampa
2023-07-08

In the Brazilian Pampa, vegetation disturbance and soil degradation led to an expansion of sediment remobilization areas, a process locally termed as sandization. Transported sands generate severe environmental problems and hamper the growth of vegetation. However, parts of these sandization areas are quickly covered by biological soil crusts (biocrusts), which have not been investigated in this biome before. This study describes biocrust occurence in sandization areas of the Brazilian Pampa for the first time and analyses their distribution patterns related to the local topography. We studied biocrusts at two research sites where their presence appeared to be essential for soil protection. First, the occurrence of different biocrust types were assessed and a taxonomic survey was conducted. Second, UAV-based imagery was created and biocrusts were classified, using a random forest approach to understand the relation of their abundance to topography. We observed that biocrusts occurred widely in areas prone to sandization with an approx. 25% distribution on the land surface. They are mostly dominated by cyanobacteria and secondarily by bryophytes. Among the observed genera, the cyanobacterial genus Stigonema sp. was dominating in both study sites. Campylopus pilifer was the dominating moss species. The mapped biocrusts represented all major morphological types and were classified as rolling, pinnacled, rugose, and smooth crusts. Local topography was a major driver for biocrust distribution, but also the establishment of vascular plants. Slope and aspect had a strong influence on biocrust development, but the presence of protective topographic positions against atmospheric influences most prominently facilitated their occurrence. This pilot study proves that biocrusts can potentially play a key role as ecosystem engineers in the Brazilian Pampa with a positive effect on general vegetation growth and soil-stabilization. In this biome, however, they have been largely overlooked compared to other areas globally. Thus, biocrusts need to be further studied and their effects considered in land management to constrain further soil degradation.
A promoter trap in transgenic citrus mediates recognition of a broad spectrum of Xanthomonas citri pv. citriTALEs, including in planta‐evolved derivatives
2023-07-08

Summary Citrus bacterial canker (CBC), caused by Xanthomonas citri subsp. citri ( Xcc ), causes dramatic losses to the citrus industry worldwide. Transcription activator‐like effectors (TALEs), which bind to effector binding elements ( EBEs ) in host promoters and activate transcription of downstream host genes, contribute significantly to Xcc virulence. The discovery of the biochemical context for the binding of TALEs to matching EBE motifs, an interaction commonly referred to as the TALE code, enabled the in silico prediction of EBEs for each TALE protein. Using the TALE code, we engineered a synthetic resistance ( R ) gene, called the Xcc‐TALE‐trap , in which 14 tandemly arranged EBEs , each capable of autonomously recognizing a particular Xcc TALE, drive the expression of Xanthomonas avrGf2 , which encodes a bacterial effector that induces plant cell death. Analysis of a corresponding transgenic Duncan grapefruit showed that transcription of the cell death‐inducing executor gene, avrGf2 , was strictly TALE‐dependent and could be activated by several different Xcc TALE proteins. Evaluation of Xcc strains from different continents showed that the Xcc ‐ TALE ‐ trap mediates resistance to this global panel of Xcc isolates. We also studied in planta ‐evolved TALEs (eTALEs) with novel DNA‐binding domains and found that these eTALEs also activate the Xcc‐TALE‐trap , suggesting that the Xcc‐TALE‐trap is likely to confer durable resistance to Xcc . Finally, we show that the Xcc‐TALE‐trap confers resistance not only in laboratory infection assays but also in more agriculturally relevant field studies. In conclusion, transgenic plants containing the Xcc‐TALE‐trap offer a promising sustainable approach to control CBC.
A Saddle‐Shaped Expanded Porphyrinoid Fitting C60**
2023-07-08

Abstract We present the synthesis of a new type of an expanded porphyrinoid macrocycle with a saddle‐shaped morphology and its complexation of C 60 guest molecules. The new macrocycle contains four carbazole and four triazole moieties and can be readily synthesized via a copper‐catalyzed click reaction. It shows specific photo‐physical properties including fluorescence with a high quantum yield of 60 %. The combination of the saddle‐shaped geometry with the expanded π‐system allows for host–guest interactions with C 60 in a stacked polymer fashion. Evidence for the presence of a host–guest complex is provided both in solution by NMR spectroscopy and in the solid state by X‐ray structure analysis.
Impact of text contrast polarity on the retinal activity in myopes and emmetropes using modified pattern ERG
2023-07-09

Abstract Environmental factors favoring myopia development are still being studied and there is accumulating evidence for a significant role of nearwork. Recently, reading standard black-on-white text was found to activate the retinal OFF pathway and induce choroidal thinning, which is associated with myopia onset. Contrarily, reading white-on-black text led to thicker choroids, being protective against myopia. Respective effects on retinal processing are yet unknown. Here, we exploratively assessed the impact of contrast polarity on the retinal activity and possible interactions with eccentricity and refractive error. We recorded pattern electroretinograms in myopic and emmetropic adults while presenting a dead leaves stimulus (DLS), overlaid by masks of different size in ring or circle shape, either filled with uniform gray or text of inverted or standard contrast. In myopes, retinal responses for DLS with standard and inverted contrast were larger when the perifovea was stimulated (6–12 deg), however, including the fovea resulted in smaller amplitudes for inverted contrast than in emmetropes. The retina of emmetropes was more sensitive to inverted contrast than to standard and gray within 12 deg, but most sensitive for gray in the perifovea. This demonstrates that the refractive error influences the sensitivity to text contrast polarity, with a special role of the peripheral retina, which is in line with previous studies about blur sensitivity. Defining whether the differences derive from retinal processing or anatomical features of a myopic eye requires further investigation. Our approach might be a first step to explain how nearwork promotes the eye’s elongation.
Novel multifunctional glycan probes to elucidate specificities of diverse glycan recognition systems
2023-07-09

Abstract Glycan microarrays of sequence-defined glycans are the most widely used approach for high-throughput studies of interactions of glycans with glycan binding proteins. Currently nitrocellulose (NC) coated or N-hydroxysuccinimide (NHS) functionalized glass slides are the two most commonly used surfaces for immobilizing glycan probes as noncovalent and covalent arrays, respectively. The mode of glycan presentation can have an influence on the microarray readouts and is an important consideration in the glycan recognition knowledgebase. Here we present the development of glycan probes, tagged with a novel type of tri-functional Fmoc-amino-azido (FAA) linker, which can be readily converted into lipid-tagged or amino-terminating glycan probes for generating neoglycolipid (NGL)-based noncovalent arrays as well as covalent arrays. The azido functionality in the FAA glycan probes provides a means to ‘light up’ the glycans via biorthogonal ‘Click’ chemistry so that they become ‘scanner-readable’ on the covalent arrays, which represents an advance in array quality control. Here analyses were carried out with a diverse set of 36 glycan binding proteins (GBPs) to compare the performance of 44 glycans presented in a liposomal formulation as noncovalent arrays on NC coated slides and on two types of NHS slides as covalent arrays. With most of anti-glycan antibodies and plant lectins investigated, there were negligible or subtle differences in the binding detected in different arrays. However, there were some striking differences observed between the covalent and noncovalent arrays. These include binding of Lotus Tetragonolobus Lectin (LTL) on the covalent but not the noncovalent arrays, and a clear preference observed for glycans on the noncovalent array in the binding of adhesins (VP1 proteins) of two human polyomaviruses JCPyV and BKPyV, and the human immune lectins Siglecs 7 and 9. Subtle yet significant differences in the binding to low affinity glycan ligands were also observed with three bacterial toxins in different arrays. These results revealed interesting insights into the binding behaviour of different GBPs on the noncovalent and covalent arrays and highlight the importance to consider different array platforms in elucidating glycan mediated interactions. The FAA glycan probes can be readily rendered fluorescent via ‘Click’ chemistry in solution, enabling the detection of GBPs at the surface of cells. Abstract Figure A new trifunctional linker can present glycans on different array surfaces for analyses of soluble glycan binding proteins or as fluorescent probes for binding by proteins at the surface of cells.
Mechanosensory feedback loops during chronic inflammation
2023-07-10

Epithelial tissues are crucial to maintaining healthy organization and compartmentalization in various organs and act as a first line of defense against infection in barrier organs such as the skin, lungs and intestine. Disruption or injury to these barriers can lead to infiltration of resident or foreign microbes, initiating local inflammation. One often overlooked aspect of this response is local changes in tissue mechanics during inflammation. In this mini-review, we summarize known molecular mechanisms linking disruption of epithelial barrier function to mechanical changes in epithelial tissues. We consider direct mechanisms, such as changes in the secretion of extracellular matrix (ECM)-modulating enzymes by immune cells as well as indirect mechanisms including local activation of fibroblasts. We discuss how these mechanical changes can modulate local immune cell activity and inflammation and perturb epithelial homeostasis, further dysregulating epithelial barrier function. We propose that this two-way relationship between loss of barrier function and altered tissue mechanics can lead to a positive feedback loop that further perpetuates inflammation. We discuss this cycle in the context of several chronic inflammatory diseases, including inflammatory bowel disease (IBD), liver disease and cancer, and we present the modulation of tissue mechanics as a new framework for combating chronic inflammation.
Recommendations for improved reproducibility of ADC derivation on behalf of the Elekta MRI-linac consortium image analysis working group
2023-07-10

Overall, calculation methods had a larger impact on ADC reproducibility compared to delineation. Based on the results, significant sources of variation were identified, which should be considered when initiating new studies, in particular multi-centre investigations.
Enhanced Image Processing Using Complex Averaging in Diffusion-Weighted Imaging of the Prostate: The Impact on Image Quality and Lesion Detectability
2023-07-10

Diffusion-weighted images of the prostate can suffer from a “hazy” background in low signal-intensity areas. We hypothesize that enhanced image processing (EIP) using complex averaging reduces artifacts, noise, and distortion in conventionally acquired diffusion-weighted images and synthesized high b-value images, thus leading to higher image quality and better detection of potentially malignant lesions. Conventional DWI trace images with a b-value of 1000 s/mm2 (b1000), calculated images with a b-value of 2000 s/mm2 (cb2000), and ADC maps of 3T multiparametric prostate MRIs in 53 patients (age 68.8 ± 10 years) were retrospectively evaluated. Standard images were compared to images using EIP. In the standard images, 36 lesions were detected in the peripheral zone and 20 in the transition zone. In 13 patients, EIP led to the detection of 8 additional lesions and the upgrading of 6 lesions; 6 of these patients were diagnosed with prostate carcinoma Gleason 7 or 8. EIP improved qualitative ratings for overall image quality and lesion detectability. Artifacts were significantly reduced in the cb2000 images. Quantitative measurements for lesion detectability expressed as an SI ratio were significantly improved. EIP using complex averaging led to image quality improvements in acquired and synthesized DWI, potentially resulting in elevated diagnostic accuracy and management changes.
Contextualising flexible nonlinear periodization as a person-adaptive behavioral model for exercise maintenance
2023-07-10

There is a growing focus on developing person-adaptive strategies to support sustained exercise behaviour, necessitating conceptual models to guide future research and applications. This paper introduces Flexible nonlinear periodisation (FNLP) - a proposed, but underdeveloped person-adaptive model originating in sport-specific conditioning - that, pending empirical refinement and evaluation, may be applied in health promotion and disease prevention settings. To initiate such efforts, the procedures of FNLP (i.e., acutely and dynamically matching exercise demand to individual assessments of mental and physical readiness) are integrated with contemporary health behaviour evidence and theory to propose a modified FNLP model and to show hypothesised pathways by which FNLP may support exercise adherence (e.g., flexible goal setting, management of affective responses, and provision of autonomy/variety-support). Considerations for future research are also provided to guide iterative, evidence-based efforts for further development, acceptability, implementation, and evaluation.
Effects of isolation and confinement on gastrointestinal microbiota–a systematic review
2023-07-10

Purpose The gastrointestinal (GI) microbiota is a complex and dynamic ecosystem whose composition and function are influenced by many internal and external factors. Overall, the individual GI microbiota composition appears to be rather stable but can be influenced by extreme shifts in environmental exposures. To date, there is no systematic literature review that examines the effects of extreme environmental conditions, such as strict isolation and confinement, on the GI microbiota. Methods We conducted a systematic review to examine the effects of isolated and confined environments on the human GI microbiota. The literature search was conducted according to PRISMA criteria using PubMed, Web of Science and Cochrane Library. Relevant studies were identified based on exposure to isolated and confined environments, generally being also antigen-limited, for a minimum of 28 days and classified according to the microbiota analysis method (cultivation- or molecular based approaches) and the isolation habitat (space, space- or microgravity simulation such as MARS-500 or natural isolation such as Antarctica). Microbial shifts in abundance, alpha diversity and community structure in response to isolation were assessed. Results Regardless of the study habitat, inconsistent shifts in abundance of 40 different genera, mainly in the phylum Bacillota (formerly Firmicutes) were reported. Overall, the heterogeneity of studies was high. Reducing heterogeneity was neither possible by differentiating the microbiota analysis methods nor by subgrouping according to the isolation habitat. Alpha diversity evolved non-specifically, whereas the microbial community structure remained dissimilar despite partial convergence. The GI ecosystem returned to baseline levels following exposure, showing resilience irrespective of the experiment length. Conclusion An isolated and confined environment has a considerable impact on the GI microbiota composition in terms of diversity and relative abundances of dominant taxa. However, due to a limited number of studies with rather small sample sizes, it is important to approach an in-depth conclusion with caution, and results should be considered as a preliminary trend. The risk of dysbiosis and associated diseases should be considered when planning future projects in extreme environments. Systematic review registration https://www.crd.york.ac.uk/prospero/ , identifier CRD42022357589.
What the Attentional-SNARC and its (null) replications can and cannot tell us
2023-07-10

In response to a point raised by Fischer et al. (2020), we discuss the theoretical implications of both the original Attentional SNARC (Att-SNARC) and its recent failed multi-laboratory replication. In our view, the theoretical importance of the original Att-SNARC can be summarized in two points: (1) there is a conceptual link between numbers and space, which can be observed as Spatial-Numerical Associations, and (2) Spatial-Numerical Associations are involuntary and automatic. We conclude that convergent evidence from other paradigms saves the first point from being challenged in light of the failed replication; but, on the other hand, empirical evidence for the second point no longer holds.
Adsorption Structures Affecting the Electronic Properties and Photoinduced Charge Transfer at Perylene‐Based Molecular Interfaces
2023-07-10

Abstract Perylene‐based organic semiconductors are widely used in organic electronic devices. Here, we studied the ultrafast excited state dynamics after optical excitation at interfaces between the electron donor (D) diindenoperylene (DIP) and the electron acceptor (A) dicyano‐perylene‐bis(dicarboximide) (PDIR‐CN 2 ) using femtosecond time‐resolved second harmonic generation (SHG) in combination with large scale quantum chemical calculations. Thereby, we varied in bilayer structures of DIP and PDIR‐CN 2 the interfacial molecular geometry. For an interfacial configuration which contains a edge‐on geometry but also additional face‐on domains an optically induced charge transfer (CT) is observed, which leads to a pronounced increase of the SHG signal intensity due to electric field induced second harmonic generation. The interfacial CT state decays within 7.5±0.7 ps, while the creation of hot CT states leads to a faster decay (5.3±0.2 ps). For the bilayer structures with mainly edge‐on geometries interfacial CT formation is suppressed since π ‐ π overlap perpendicular to the interface is missing. Our combined experimental and theoretical study provides important insights into D/A charge transfer properties, which is needed for the understanding of the interfacial photophysics of these molecules.
Impact of A-Scan Rate on Image Quality and Acquisition Time in OCT
2023-07-10

An A-scan rate of 20 kHz resulted in a significantly higher scan quality but also a significantly longer acquisition time compared to scan rates of 85 kHz and 125 kHz. Differences between an A-scan rate of 85 kHz and 125 kHz were marginal.
Annihilating dark matter search with 12 years of Fermi LAT data in nearby galaxy clusters
2023-07-10

Galaxy clusters contain an abundance of dark matter making them attractive laboratories for indirect DM searches. This work details a search for signals of pair annihilation from WIMP dark matter in the GeV gamma ray regime. We perform this search in five low z <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>z</mml:mi></mml:math> and high galactic latitude galaxy clusters (Centaurus, Coma, Virgo, Perseus and Fornax); using nearly 12 years of Fermi/LAT data. Through the non-detection of this characteristic signal, we derive constraints on the annihilation cross-section of DM pair annihilation into the b\\overline{b} <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>b</mml:mi><mml:mover><mml:mi>b</mml:mi><mml:mo accent="true"> ̅</mml:mo></mml:mover></mml:mrow></mml:math> , W^+W^- <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mi>W</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msup><mml:mi>W</mml:mi><mml:mo>−</mml:mo></mml:msup></mml:mrow></mml:math> and \\gamma\\gamma <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>γ</mml:mi><mml:mi>γ</mml:mi></mml:mrow></mml:math> channels. The limits obtained are of a comparable magnitude to those of recently derived from Fermi/LAT observations of dwarf spheroidal galaxies.
A Dataset for Violence Trends in the Ancient Middle East between 12,000 and 400 BCE
2023-07-10

Thsi archive provides all data generated and analysed and the custom codes produced for the study which will be published in <em>Nature Human Behaviour</em> with the title "<strong>Violence Trends in the Ancient Middle East between 12,000 and 400 BCE</strong>"<strong>. </strong>In this paper we study violence trends in the very long run by exploiting a novel dataset on cranial trauma and weapon-related wounds from skeletons excavated across the Middle East, spanning the whole pre-Classical period (ca. 12,000-400 BCE). The data set includes more than 3,500 individuals. These data have been collected from existing online digital archives, electronic and print original publications, and from unpublished field reports.