julilili42/papers huggingface dataset:
Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies
2021-11-12

Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.
Under-recognition of Acute Kidney Injury after Cardiac Surgery in the ICU Impedes Early Detection and Prevention
2021-11-12

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Acute kidney injury (AKI) is associated with high morbidity and mortality; therefore, prevention is important. The aim of this study was to systematically assess AKI incidence after cardiac surgery as documented in clinical routine compared to the real incidence because AKI may be under-recognized in clinical practice. Further, its postoperative management was compared to Kidney Disease: Improving Global Outcomes (KDIGO) recommendations because recognition and adequate treatment represent the fundamental cornerstone in the prevention and management of AKI. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; This retrospective single-center study included &lt;i&gt;n&lt;/i&gt; = 100 patients who underwent cardiac surgery with cardiopulmonary bypass. The coded incidence of postoperative AKI during intensive care unit stay after surgery was compared to the real AKI incidence. Furthermore, conformity of postoperative parameters with KDIGO recommendations for AKI prevention and management was reviewed. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; We found a considerable discrepancy between coded and real incidence, and conformity with KDIGO recommendations was found to be relatively low. The coded incidence was significantly lower (&lt;i&gt;n&lt;/i&gt; = 12 vs. &lt;i&gt;n&lt;/i&gt; = 52, &lt;i&gt;p&lt;/i&gt; &amp;#x3c; 0.05), representing a coding rate of 23.1%. Regarding postoperative management, 90% of all patients had at least 1 episode with mean arterial pressure &amp;#x3c;65 mm Hg within the first 72 h. Furthermore, regarding other preventive parameters (avoiding hyperglycemia, stopping angiotensin-converting enzyme inhibitors/angiotensin receptor blockers, avoiding contrast media, and nephrotoxic drugs), only 10 patients (20.8%) in the non-AKI group and in 5 (9.6%) subjects in the AKI group had none of all the above potential AKI-promoting factors. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; AKI recognition in everyday clinical routine seems to be low, especially in lower AKI stages, and the current postoperative management still offers potential for optimization. Possibly, higher AKI awareness and stricter postoperative management could already achieve significant effects in prevention and treatment of AKI.
Level attraction and idler resonance in a strongly driven Josephson cavity
2021-11-12

&lt;p&gt;Nonlinear Josephson circuits play a crucial role in the growing landscape of quantum information and technologies. The typical circuits studied in this field consist of qubits, whose anharmonicity is much larger than their linewidth, and also of parametric amplifiers, which are engineered with linewidths of tens of MHz or more. The regime of small anharmonicity but also narrow linewidth, corresponding to the dynamics of a high-Q Duffing oscillator, has not been extensively explored using Josephson cavities. Here, we use two-tone spectroscopy to study the susceptibility of a strongly driven high-Q Josephson microwave cavity. Under blue-detuned driving, we observe a shift of the cavity susceptibility, analogous to the AC Stark effect in atomic physics. When applying a strong red-detuned drive, we observe the appearance of an additional idler mode above the bifurcation threshold with net external gain. Strong driving of the circuit leads to the appearance of two exceptional points and a level attraction between the quasimodes of the driven cavity. Our results provide insights on the physics of driven nonlinear Josephson resonators and form a starting point for exploring topological physics in strongly-driven Kerr oscillators.&lt;/p&gt;
α-hemolysin ofStaphylococcus aureusimpairs thrombus formation
2021-11-12

Abstract Toxins are key virulence determinants of pathogens and can impair the function of host immune cells including platelets. Insights into pathogen toxin interference with platelets will be pivotal to improve treatment of patients with bacterial bloodstream infections. In this study, we deciphered the effects of Staphylococcus aureus toxins α-hemolysin, LukAB, LukDE and LukSF on human platelets and compared the effects with the pore forming toxin pneumolysin of Streptococcus pneumoniae . In contrast to pneumolysin, α-hemolysin initially activates platelets as indicated by CD62P and αIIbβ3 integrin expression, but the resulting pores also induce alterations in the phenotype of platelets and induce apoptosis of platelets. The presence of small amounts of α-hemolysin (0.2 μg/mL) in whole blood abrogates thrombus formation indicating that in systemic infections with S. aureus the stability of formed thrombi is impaired. This might be of high clinical relevance for S. aureus induced endocarditis of the aortic valves. Stabilizing the thrombi by inhibiting α-hemolysin induced impairment of platelets likely reduces the risk for septic (micro-)embolization. However, in contrast to pneumolysin, α-hemolysin induced platelets damage could not be neutralized by intravenous immune globulins. In contrast to α-hemolysin, S. aureus bi-component pore forming leukocidins LukAB, LukED and LukSF do not bind to platelets and had no significant effect on platelet activation and viability. Main point 1: α-hemolysin forms pores in platelets, which first activate but then result in apoptosis and impairs thrombus formation and stability Main point 2: Polyvalent immunoglobulins do not neutralize the mode of action of the toxin
Does active or passive signaling support integration of text and graphs?
2021-11-12

Abstract Integrating multiple representations into a coherent mental model is one of the challenges when learning with multimedia. In this experimental study ( N = 173), we examined how highlighting corresponding information in text‐graph learning material can help higher education students to make the necessary connections and improve learning outcomes in two domains. We compared a control condition to a signaling condition with given highlights and an active signaling condition where students were asked to visually highlight corresponding text and graph information themselves. There was no overall benefit of given signals or active signaling. We discuss prior knowledge and the quality of learner‐generated signals as possible explanations. For biology learning material, prior knowledge moderated the effect of active signaling. In economics, the effect of prior knowledge was mediated by the quality of learner‐generated correspondences. Our findings suggest that different methods of supporting text‐graph integration might be useful for different students and learning material.
Indigenous and Black Confraternities in Colonial Latin America
2021-11-12

Employing a transregional and interdisciplinary approach, this volume explores indigenous and black confraternities –or lay Catholic brotherhoods– founded in colonial Spanish America and Brazil between the sixteenth and eighteenth century. It presents a varied group of cases of religious confraternities founded by subaltern subjects, both in rural and urban spaces of colonial Latin America, to understand the dynamics and relations between the peripheral and central areas of colonial society, underlying the ways in which colonialized subjects navigated the colonial domain with forms of social organization and cultural and religious practices. The book analyzes indigenous and black confraternal cultural practices as forms of negotiation and resistance shaped by local devotional identities that also transgressed imperial religious and racial hierarchies. The analysis of these practices explores the intersections between ethnic identity and ritual devotion, as well as how the establishment of black and indigenous religious confraternities carried the potential to subvert colonial discourse.
Constructing the Corpus of Chinese Textual ‘Run-on’ Sentences (CCTRS)
2021-11-12

Chinese is a discourse-oriented language. “Run-on” sentences (liushui ju) are a typical and prevalent form of discourse in Chinese. These sentences show the capacity of the Chinese language for organizing loose structures into an effective and coherent discourse. Despite their widespread use in Chinese, previous studies have only explored “run-on” sentences by using small-scale examples. In order to carry out a quantitative investigation of “run-on” sentences, we need to establish a corpus. The present study selects 500 “run-on” sentences and annotates them on the levels of discourse, syntax and semantics. We mainly adopt PDTB (Penn Discourse Treebank) styles in the discourse annotations but we also borrow some features from RST (rhetorical structure theory). We find that the distribution of the frequency of discourse relations in the data extracted from this corpus follows the power law. The preliminary results reveal that semantic leaps in “run-on” sentences are closely related to the use of the topic chain and the animacy and the span of discourse relations. This corpus can thus aid in carrying out further computational and cognitive studies of Chinese discourse.
Structural basis for diamide modulation of ryanodine receptor
2021-11-12

Diamide insecticides target insect ryanodine receptors (RYRs) and cause dysregulation of calcium signaling in insect muscles and neurons, generating worldwide sales over 2 billion US dollars annually. Several resistance mutations have been reported to reduce the efficacy of the diamides, but the exact binding sites and mechanism of resistance mutations were not clear. Recently, we solved the cryo-electron microscopy (cryo-EM) structure of RYR in complex with the anthranilic diamide chlorantraniliprole (CHL). CHL binds to the pseudo–voltage-sensor domain (pVSD) of RYR, a site in proximity to the previously identified resistance mutations. Mutagenesis studies in silico, in mutant cell lines, and in transgenic Drosophila strains revealed the key residues involved in diamide coordination and the molecular mechanism under species-selectivity and resistance mutations. We also proposed that CHL may alleviate the loss-of-function effects of some central core disease (CCD) mutations by increasing the opening probability (Po) of RYR1. In addition, we solved the crystal structures of several RYR domains from the diamondback moth and the bee, revealing insect-specific structural features which could be potentially targeted by novel insecticides. Interestingly, we found that the phosphorylation of insect RYR is temperature dependent, facilitated by the low thermal stability and dynamic structure of the insect RYR. Our structures provide a foundation for developing novel pesticides to overcome the resistance crisis.
A global survey of specialized metabolic diversity encoded in bacterial genomes
2021-11-12

Bacterial secondary metabolites have been studied for decades for their usefulness as drugs, such as antibiotics. However, the identification of new structures has been decelerating, while multi-resistant pathogens continue to emerge. It is unclear how much chemical diversity exists in Nature and whether discovery efforts should be focused on established antibiotic producers or rather on understudied taxa. Here, we surveyed around 170,000 bacterial genomes and several thousand of Metagenome Assembled Genomes (MAGs). Our results indicate that only 3% of the genomic potential for natural products has been experimentally discovered. Our analysis connects the emergence of most biosynthetic diversity in evolutionary history close to the taxonomic rank of genus, identifies <em>Streptomyces</em> as by far the most biosynthetically diverse, followed by producers from genera such as <em>Amycolatopsis</em>, <em>Kutzneria</em> and <em>Micromonospora</em>, and highlights multiple promising high-producing taxa that have thus far been less investigated, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), <em>Pleurocapsa</em>, Nostocaceae (Cyanobacteria).
Optogenetic manipulation of cGMP highlights PDE5 as the predominant cGMP-hydrolyzing PDE in megakaryocytes
2021-11-12

Abstract Cyclic guanosine monophosphate (cGMP) signalling plays a fundamental role in many cell types including platelets. cGMP has been implicated in platelet formation, but mechanistic detail about its spatiotemporal regulation in megakaryocytes (MKs) is lacking. We expressed a photo-activated guanylyl cyclase, Blastocladiella emersonii Cyclase opsin ( Be Cyclop), after viral-mediated gene transfer in bone marrow (BM)-derived MKs to precisely light-modulate cGMP levels. Be Cyclop-MKs showed a significantly increased cGMP concentration after illumination, which was strongly dependent on phosphodiesterase (PDE) 5 activity. This finding was corroborated by real-time imaging of cGMP signals which revealed that pharmacological PDE5 inhibition also potentiated nitric oxide (NO) triggered cGMP generation in BM MKs. In summary, we established for the first time optogenetics in primary MKs and identified PDE5 as the predominant PDE regulating cGMP levels in MKs. These findings also demonstrate that optogenetics allows for the precise manipulation of MK biology.
Unfamiliar Contexts Compared to Familiar Contexts Impair Learning in Humans
2021-11-12

Context plays a key role in learning and memory processes. Re-exposure to the context that information was learned in facilitates memory retrieval of this information. However, it is currently unclear whether context changes also influence the ability to learn new information, which the present work investigated in two experiments with healthy participants (n = 40 per experiment; 20 female). In experiment 1, participants learned a list of word-pairs (A-B) in the morning and a second non-overlapping list (C-D) in the evening, either in the same context or in a different context than the first list (between-subjects). We confirmed that new learning is enhanced if it takes place in the same context, putatively driven by context-dependent retrieval of meta-learning processes. In addition, new learning in the other context was significantly decreased compared to baseline. In experiment 2, participants were exposed to both contexts in the morning, but only learned word-pairs in one of them. Familiarity with the other context abolished differences between the same and other context group. These data point to the novelty of the context interfering with new learning rather than the familiarity of the context enhancing it. Importantly, the reduction of new learning in the other context in the first experiment, where the context was unfamiliar in both learning sessions, suggests mechanisms beyond attention processes that are bound by the novelty of the other context. Rather, the old context impairs the processing of the new context, possibly by biasing pattern completion and pattern separation trade-offs within the hippocampus.
Raman Imaging and Fluorescence Lifetime Imaging Microscopy for Diagnosis of Cancer State and Metabolic Monitoring
2021-11-13

Hurdles for effective tumor therapy are delayed detection and limited effectiveness of systemic drug therapies by patient-specific multidrug resistance. Non-invasive bioimaging tools such as fluorescence lifetime imaging microscopy (FLIM) and Raman-microspectroscopy have evolved over the last decade, providing the potential to be translated into clinics for early-stage disease detection, in vitro drug screening, and drug efficacy studies in personalized medicine. Accessing tissue- and cell-specific spectral signatures, Raman microspectroscopy has emerged as a diagnostic tool to identify precancerous lesions, cancer stages, or cell malignancy. In vivo Raman measurements have been enabled by recent technological advances in Raman endoscopy and signal-enhancing setups such as coherent anti-stokes Raman spectroscopy or surface-enhanced Raman spectroscopy. FLIM enables in situ investigations of metabolic processes such as glycolysis, oxidative stress, or mitochondrial activity by using the autofluorescence of co-enzymes NADH and FAD, which are associated with intrinsic proteins as a direct measure of tumor metabolism, cell death stages and drug efficacy. The combination of non-invasive and molecular-sensitive in situ techniques and advanced 3D tumor models such as patient-derived organoids or microtumors allows the recapitulation of tumor physiology and metabolism in vitro and facilitates the screening for patient-individualized drug treatment options.
A non‐inferiority comparative analysis of micro‐ultrasonography and MRI‐targeted biopsy in men at risk of prostate cancer
2021-11-13

Objective To compare the efficacy of multiparametric magnetic resonance imaging (mpMRI)‐directed and micro‐ultrasonography (micro‐US)‐directed biopsy for detecting clinically significant (Grade Group &gt;1) prostate cancer (csPCa). Materials and Methods A total of 203 patients were prospectively enrolled at three institutions across Germany and Austria in the period from January 2019 to December 2019. During each biopsy, the urologist was blinded to the mpMRI report until after the micro‐US targets had been assessed. After unblinding, targets were then sampled using software‐assisted fusion, followed by systematic samples. The primary outcome measure was non‐inferiority of micro‐US to detect csPCa, with a detection ratio of at least 80% that of mpMRI. Results A total of 79 csPCa cases were detected overall (39%). Micro‐US‐targeted biopsy detected 58/79 cases (73%), while mpMRI‐targeted biopsy detected 60/79 (76%) and non‐targeted (completion sampling) samples detected 45/79 cases (57%). mpMRI‐targeted samples alone detected 7/79 (9%) csPCa cases which were missed by micro‐US‐targeted and non‐targeted samples. Three of these seven were anterior lesions with 2/7 in the transition zone. Micro‐US‐targeted samples alone detected 5/79 (6%) and completion sampling alone detected 4/79 cases (5%). Micro‐US was non‐inferior to mpMRI and detected 97% of the csPCa cases detected by mpMRI‐targeted biopsy (95% CI 80–116%; P = 0.023). Conclusions This is the first multicentre prospective study comparing micro‐US‐targeted biopsy with mpMRI‐targeted biopsy. The study provides further evidence that micro‐US can reliably detect cancer lesions and suggests that micro‐US biopsy might be as effective as mpMRI for detection of csPCA. This result has significant implications for increasing accessibility, reducing costs and expediting diagnosis.
Pentamethylcyclopentadienyl Complexes of Cerium(IV): Synthesis, Reactivity, and Electrochemistry
2021-11-13

Treatment of Cp*<sub>2</sub>CeCl<sub>2</sub>K(THF) with alkali-metal alkoxides and siloxides in the presence of hexachloroethane generates the monomeric bis(pentamethylcyclopentadienyl) cerium(IV) complexes Cp*<sub>2</sub>Ce(OR)<sub>2</sub> (Cp* = C<sub>5</sub>Me<sub>5</sub>; R = Et, <i>i</i>Pr, CH<sub>2</sub><i>t</i>Bu, <i>t</i>Bu, SiMe<sub>3</sub>, or SiPh<sub>3</sub>). Large substituents R trigger ligand scrambling to half-sandwich complexes Cp*Ce(OR)<sub>3</sub>, which could be isolated for R = <i>t</i>Bu and SiPh<sub>3</sub>. Similar reactions with sodium aryloxide NaOAr (OAr = OC<sub>6</sub>H<sub>3</sub><i>i</i>Pr<sub>2</sub>-2,6) led to Cp*<sub>2</sub>Ce(OAr)Cl. Treatment of tris(cyclopentadienyl) complexes Cp<sup>R</sup><sub>3</sub>CeCl (Cp<sup>H</sup> = Cp = C<sub>5</sub>H<sub>5</sub>; Cp<sup>Me</sup> = C<sub>5</sub>H<sub>4</sub>Me) with NaOAr afforded Cp<sup>Me</sup><sub>2</sub>Ce(OAr)<sub>2</sub> and Cp<sub>3</sub>Ce(OAr). The cerium(IV) complexes display a pseudotetrahedral geometry in the solid state. Cyclic voltammetry revealed mostly chemically reversible as well as electrochemically quasi-reversible redox processes with potentials ranging from -0.84 to -1.61 V versus Fc/Fc<sup>+</sup>. Switching from sandwich to half-sandwich complexes decreased the electrochemical potentials drastically, showing better stabilization of the cerium(IV) center in the case of Cp*Ce(OR)<sub>3</sub> than in the case of Cp*<sub>2</sub>Ce(OR)<sub>2</sub>. Enhanced stabilization of the cerium +IV oxidation state could be further demonstrated in the series alkoxy > siloxy > aryloxy as well as C<sub>5</sub>Me<sub>5</sub> > C<sub>5</sub>HMe<sub>4</sub>.
Multimodal Engagement Analysis From Facial Videos in the Classroom
2021-11-13

Student engagement is a key construct for learning and teaching. While most of the literature explored the student engagement analysis on computer-based settings, this paper extends that focus to classroom instruction. To best examine student visual engagement in the classroom, we conducted a study utilizing the audiovisual recordings of classes at a secondary school over one and a half month's time, acquired continuous engagement labeling per student (N=15) in repeated sessions, and explored computer vision methods to classify engagement levels from faces in the classroom. We trained deep embeddings for attentional and emotional features, training Attention-Net for head pose estimation and Affect-Net for facial expression recognition. We additionally trained different engagement classifiers, consisting of Support Vector Machines, Random Forest, Multilayer Perceptron, and Long Short-Term Memory, for both features. The best performing engagement classifiers achieved AUCs of .620 and .720 in Grades 8 and 12, respectively. We further investigated fusion strategies and found score-level fusion either improves the engagement classifiers or is on par with the best performing modality. We also investigated the effect of personalization and found that using only 60-seconds of person-specific data selected by margin uncertainty of the base classifier yielded an average AUC improvement of .084. 4.Our main aim with this work is to provide the technical means to facilitate the manual data analysis of classroom videos in research on teaching quality and in the context of teacher training.