Miracle-dz/UniFAR-FTUs huggingface dataset:
CRISPR-Cas9-Mediated Carbapenemase Gene and Plasmid Curing in Carbapenem-Resistant Enterobacteriaceae

Combating plasmid-mediated carbapenem resistance is essential to control and prevent the dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Here, we conducted a proof-of-concept study to demonstrate that CRISPR-Cas9-mediated resistance gene and plasmid curing can effectively resensitize CRE to carbapenems. A novel CRISPR-Cas9-mediated plasmid-curing system (pCasCure) was developed and electrotransferred into various clinical CRE isolates. The results showed that pCasCure can effectively cure blaKPC, blaNDM, and blaOXA-48 in various Enterobacteriaceae species of Klebsiella pneumoniae, Escherichia coli, Enterobacter hormaechei, Enterobacter xiangfangensis, and Serratia marcescens clinical isolates, with a >94% curing efficiency. ABSTRACT Combating plasmid-mediated carbapenem resistance is essential to control and prevent the dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Here, we conducted a proof-of-concept study to demonstrate that CRISPR-Cas9-mediated resistance gene and plasmid curing can effectively resensitize CRE to carbapenems. A novel CRISPR-Cas9-mediated plasmid-curing system (pCasCure) was developed and electrotransferred into various clinical CRE isolates. The results showed that pCasCure can effectively cure blaKPC, blaNDM, and blaOXA-48 in various Enterobacteriaceae species of Klebsiella pneumoniae, Escherichia coli, Enterobacter hormaechei, Enterobacter xiangfangensis, and Serratia marcescens clinical isolates, with a >94% curing efficiency. In addition, we also demonstrated that pCasCure can efficiently eliminate several epidemic carbapenem-resistant plasmids, including the blaKPC-harboring IncFIIK-pKpQIL and IncN pKp58_N plasmids, the blaOXA-48-harboring pOXA-48-like plasmid, and the blaNDM-harboring IncX3 plasmid, by targeting their replication and partitioning (parA in pKpQIL) genes. However, curing the blaOXA-48 gene failed to eliminate its corresponding pOXA-48-like plasmid in clinical K. pneumoniae isolate 49210, while further next-generation sequencing revealed that it was due to IS1R-mediated recombination outside the CRISPR-Cas9 cleavage site resulting in blaOXA-48 truncation and, therefore, escaped plasmid curing. Nevertheless, the curing of carbapenemase genes or plasmids, including the truncation of blaOXA-48 in 49210, successfully restore their susceptibility to carbapenems, with a >8-fold reduction of MIC values in all tested isolates. Taken together, our study confirmed the concept of using CRISPR-Cas9-mediated carbapenemase gene and plasmid curing to resensitize CRE to carbapenems. Further work is needed to integrate pCasCure in an optimal delivery system to make it applicable for clinical intervention.
Serendipity with chewing lice (Phthiraptera: Menoponidae, Philopteridae) infesting rock pigeons and mourning doves (Aves: Columbiformes: Columbidae) in Manitoba, with new records for North America and Canada

Abstract An extensive survey of chewing lice from rock pigeon, Columba livia Gmelin, and mourning dove, Zenaida macroura (L.), carried out from 1994 to 2000 and from 2003 to 2006 in Manitoba, Canada, produced the following new records: Colocerastovornikae Tendeiro for North America; Columbicola macrourae (Wilson), Hohorstiellalata (Piaget), H. paladinella Hill and Tuff, and Physconelloides zenaidurae (McGregor) for Canada; and Bonomiella columbae Emerson, Campanulotes compar (Burmeister), Columbicola baculoides (Paine), and C. columbae (L.) for Manitoba. We collected 25 418 lice of four species (C. compar, C. columbae, H. lata, and C. tovornikae) from 322 rock pigeons. The overall prevalence of infestation was 78.9%, 52.5%, and 23.3% for C. compar, C. columbae, and H. lata, respectively. Coloceras tovornikae was not discovered until 2003, after which its prevalence was 39.9% on 114 pigeons. We collected 1116 lice of five species (P. zenaidurae, C. baculoides, C. macrourae, H. paladinella, and B. columbae) from 117 mourning doves. Physconelloides zenaidurae was encountered most often (prevalence was 36.7%), while the prevalence of the other four species was 26.3%, 18.4%, 3.5%, and 2.6%, respectively. Résumé Une étude approfondie de poux mâcheurs sur des pigeons bisets, Colomba livia Gmelin, et des tourterelles tristes, Zenaida macroura (L.), effectuée de 1994 à 2000 et de 2003 à 2006 au Manitoba, Canada, a produit les nouvelles mentions suivantes: Coloceras tovornikae Tendeiro pour l’Amérique du Nord; Columbicola macrourae (Wilson), Hohorstiella lata (Piaget), H. paladinella Hill et Tuff et Physconelloides zenaidurae (McGregor) pour le Canada; et Bonomiella columbae Emerson, Campanulotes compar (Burmeister), Columbicola baculoides (Paine) et C. columbae (L.) pour le Manitoba. Nous avons rassemblé 25 418 poux de quatre espèces (C. compar, C. columbae, H. lata et C. tovornikae) sur 322 pigeons bisets. La prédominance globale était 78,9 %, 52,5 % et 23,3 % pour C. compar, C. columbae et H. lata, respectivement. Coloceras tovornikae n’a pas été découvert avant 2003, après quoi sa prédominance de l’infestation était 39,9 % sur 114 pigeons bisets. Nous avons rassemblé 1116 poux de cinq espèces (P. zenaidurae, C. baculoides, C. macrourae, H. paladinella et B. columbae) sur 117 tourterelles tristes. Physconelloides zenaidurae a été trouvé plus fréquemment (prédominance était 36,7 %), alors que la prédominance pour les quatre autres espèces était 26,3 %, 18,4 %, 3,5 % et 2,6 %, respectivement.
Direct effects of pH and inorganic carbon on macroalgal photosynthesis and growth

Abstract The maximum final pHs reached during extended photosynthesis were 8.83 for the red algae Delesseria sanguinea and 10.19 for the brown algae Fucus vesiculosus, as long as the concentrations of exceeded 1 mmol l−1, suggesting the existence of an upper pH limit for macroalgal photosynthesis. In experiments initiated with low concentrations of inorganic carbon, the final pH decreased with reduced initial pH, indicating that inorganic carbon became limiting. Effects of high O2 concentrations could be ruled out as a contributing factor in pH drift experiments initiated at or above pH 7.5. The growth rates of both species decreased when pH exceeded 8.5. However, although the growth of D. sanguinea stopped at pH 9.1–9.3, depending on acclimation, F. vesiculosus could maintain its growth up to a pH of 9.8 in these experiments. Additional experiments carried out on F. vesiculosus at two pH levels, 8 and 9.3, and a range of dissolved inorganic carbon concentrations revealed that the growth of F. vesiculosus was reduced at pH 9.3 compared with pH 8, irrespectively of inorganic carbon concentration. The results suggest that high pH may be an important, but so far overlooked, factor in regulating coastal primary production.
Default-mode network streams for coupling to language and control systems

Significance The human brain is organized into large networks. One important brain network is the Default network, which enables cognitive functions such as social thinking, memory, and reward. In group-averaged data, this network emerges as a unitary whole, despite its involvement in multiple cognitive functions. Here, we tested whether Default networks found in individual humans, rather than group-average networks, contain organized substructure. In individuals, we consistently found nine subnetworks within the Default network. These subnetworks matched brain activity patterns during cognitive tasks. Some subnetworks resembled brain circuits involved in specific Default functions. Others linked Default network to other large networks. In summary, this study describes a set of brain circuits within the Default networks of individual humans. The human brain is organized into large-scale networks identifiable using resting-state functional connectivity (RSFC). These functional networks correspond with broad cognitive domains; for example, the Default-mode network (DMN) is engaged during internally oriented cognition. However, functional networks may contain hierarchical substructures corresponding with more specific cognitive functions. Here, we used individual-specific precision RSFC to test whether network substructures could be identified in 10 healthy human brains. Across all subjects and networks, individualized network subdivisions were more valid—more internally homogeneous and better matching spatial patterns of task activation—than canonical networks. These measures of validity were maximized at a hierarchical scale that contained ∼83 subnetworks across the brain. At this scale, nine DMN subnetworks exhibited topographical similarity across subjects, suggesting that this approach identifies homologous neurobiological circuits across individuals. Some DMN subnetworks matched known features of brain organization corresponding with cognitive functions. Other subnetworks represented separate streams by which DMN couples with other canonical large-scale networks, including language and control networks. Together, this work provides a detailed organizational framework for studying the DMN in individual humans.
Milling quality and flour strength of the grain of winter wheat grown in monoculture.

The aim of this study was to determine the milling quality and flour strength of the grain of winter wheat -1 ) and two fungicide treatments improved kernel plumpness and grain vitreousness, in particular in winter wheat grown in monoculture. The choice of forecrops had no significant influence on the protein content of wheat grain. The quality of the protein complex, including gluten content, was higher in the grain of wheat grown after oil plants than in the grain of winter wheat grown in mo noculture. The grain of winter wheat grown after winter rapeseed was characterized by higher falling number than the grain of plants grown in short -term (2-year) monoculture. An increase in nitrogen fertilization rates (from 90 to 150 kg ha -1 ) and protecti on against fungal infections (two fungicide treatments) also increased total protein content, wet gluten concentrations, the amount of SDS - insoluble protein and falling number. The noted improvements were more pronounced in the grain of winter wheat grownin monoculture than in the grain of winter wheat grown after oil plants .
Do emotion regulation difficulties mediate the association between neuroticism, insecure attachment, and prolonged grief?

Abstract In this study, we aimed to test the mediating role of emotion regulation difficulties between prolonged grief disorder symptoms and three risk factors: neuroticism, avoidant attachment, and anxious attachment. A total sample of 203 bereaved participants was included in the study. Path analysis revealed that emotion regulation difficulties partly mediated the links between neuroticism, avoidant attachment, and prolonged grief symptoms, and mediated the link between anxious attachment and prolonged grief symptoms. The findings suggested that emotion regulation difficulties might be an important factor contributing to prolonged grief symptoms among bereaved individuals with high neuroticism and insecure attachment.
Association of Hydrophobic Carboxyl-Terminal Dendrimers with Lymph Node-Resident Lymphocytes

Delivery systems to lymph node-resident T cells around tumor tissues are essential for cancer immunotherapy, in order to boost the immune responses. We previously reported that anionic dendrimers, such as carboxyl-, sulfonyl-, and phosphate-terminal dendrimers, were efficiently accumulated in lymph nodes via the intradermal injection. Depending on the terminal structure, their cell association properties were different, and the carboxyl-terminal dendrimers did not associate with any immune cells majorly. In this study, we investigated the delivery of carboxyl-terminal dendrimers with different hydrophobicity to lymph node-resident lymphocytes. Four types of carboxyl-terminal dendrimers—succinylated (C) and 2-carboxy-cyclohexanoylated (Chex) dendrimers with and without phenylalanine (Phe)—were synthesized and named C-den, C-Phe-den, Chex-den, and Chex-Phe-den, respectively. Chex-Phe-den was well associated with lymphocytes, but others were not. Chex-Phe-den, intradermally injected at the footpads of mice, was accumulated in the lymph node, and was highly associated with the lymphocytes, including T cells. Our results suggest that Chex-Phe-den has the potential for delivery to the lymph node-resident T cells, without any specific T cell-targeted ligands.
Further Validation of the Elemental Psychopathy Assessment – Short Form (EPA-SF) in a Large University Sample

Abstract The purpose of the current study was to provide further validation of the short form of the Elemental Psychopathy Assessment (EPA-SF), which was developed on the basis of a general personality model, the Five Factor Model (FFM) of personality. This study evaluated the internal structure of the EPA-SF trait scales, and examined the EPA-SF scales against two other psychopathy measures, the Triarchic Psychopathy Measure (TriPM) and the Expanded Leveson Self-Report Psychopathy Scales (E-LSRP), as well as a general FFM measure, in a sample of 924 university students. Exploratory Structural Equation Modeling generally supported internal structure for EPA-SF scales, in that the 18 EPA-SF traits generally loaded onto their four respective domain scales: Antagonism, Emotional Stability, Inhibition and Narcissism. Tucker’s congruence coefficients (.95-.99) indicated excellent replicability of the original structure. The EPA-SF total and domain scale scores also showed moderate to large correlations with TriPM, E-LSRP and FFM domain scales in a manner mostly consistent with conceptual expectations. Finally, EPA-SF trait scales were also mostly associated with their corresponding FFM trait scale counterparts. Overall, the EPA-SF scale scores showed evidence for good convergent and discriminant validity.
Effect of Different Implant Designs on Strain and Stress Distribution under Non-Axial Loading: A Three-Dimensional Finite Element Analysis

Implant design evolved alongside the development of implant therapy. The purpose of this finite element analysis (FEA) study was to analyze the influence of different implant designs on the stress and strain distribution to the implants and surrounding bone. Three implant designs with the same length and diameter were used. The three-dimensional geometry of the bone was simulated with a cortical bone of three different thicknesses and two medullar bone densities: low density (150 Hounsfield units) and high density (850 Hounsfield units). A 30° oblique load of 150 N was applied to the implant restoration. Displacement and stress (von Mises) results were obtained for bone and dental implants. The strain and stress distributions to the bone were higher for the tissue-level implant for all types of bone. The maximum principal strain and stress decreased with an increase in cortical bone thickness for both cancellous bone densities. The distribution of the load was concentrated at the coronal portion of the bone and implants. All implants showed a good distribution of forces for non-axial loads, with higher forces concentrated at the crestal region of the bone–implant interface. Decrease in medullar bone density negatively affects the strain and stress produced by the implants.
Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance

Plastid gene expression (PGE) must adequately respond to changes in both development and environmental cues. The transcriptional machinery of plastids in land plants is far more complex than that of prokaryotes. Two types of DNA-dependent RNA polymerases transcribe the plastid genome: a multimeric plastid-encoded polymerase (PEP), and a monomeric nuclear-encoded polymerase (NEP). A single NEP in monocots (RPOTp, RNA polymerase of the T3/T7 phage-type) and two NEPs in dicots (plastid-targeted RPOTp, and plastid- and mitochondrial-targeted RPOTmp) have been hitherto identified. To unravel the role of PGE in plant responses to abiotic stress, we investigated if Arabidopsis RPOTp could function in plant salt tolerance. To this end, we studied the sensitivity of T-DNA mutants scabra3-2 (sca3-2) and sca3-3, defective in the RPOTp gene, to salinity, osmotic stress and the phytohormone abscisic acid (ABA) required for plants to adapt to abiotic stress. sca3 mutants were hypersensitive to NaCl, mannitol and ABA during germination and seedling establishment. Later in development, sca3 plants displayed reduced sensitivity to salt stress. A gene ontology (GO) analysis of the nuclear genes differentially expressed in the sca3-2 mutant (301) revealed that many significantly enriched GO terms were related to chloroplast function, and also to the response to several abiotic stresses. By quantitative RT-PCR (qRT-PCR), we found that genes LHCB1 (LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING1) and AOX1A (ALTERNATIVE OXIDASE 1A) were respectively down- and up-regulated in the Columbia-0 (Col-0) salt-stressed plants, which suggests the activation of plastid and mitochondria-to-nucleus retrograde signaling. The transcript levels of genes RPOTp, RPOTmp and RPOTm significantly increased in these salt-stressed seedlings, but this enhanced expression did not lead to the up-regulation of the plastid genes solely transcribed by NEP. Similar to salinity, carotenoid inhibitor norflurazon (NF) also enhanced the RPOTp transcript levels in Col-0 seedlings. This shows that besides salinity, inhibition of chloroplast biogenesis also induces RPOTp expression. Unlike salt and NF, the NEP genes were significantly down-regulated in the Col-0 seedlings grown in ABA-supplemented media. Together, our findings demonstrate that RPOTp functions in abiotic stress tolerance, and RPOTp is likely regulated positively by plastid-to-nucleus retrograde signaling, which is triggered when chloroplast functionality is perturbed by environmental stresses, e.g., salinity or NF. This suggests the existence of a compensatory mechanism, elicited by impaired chloroplast function. To our knowledge, this is the first study to suggest the role of a nuclear-encoded plastid-RNA polymerase in salt stress tolerance in plants.
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation

Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N‐α‐acetylation (NTA) and ε‐lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5‐related N‐acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid‐localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.
Co-Design of Dynamic Event-Triggered Communication Scheme and Resilient Observer-Based Control Under Aperiodic DoS Attacks

This article is concerned with the problem of observer-based dynamic event-triggered control for a networked control system (NCS) under a class of power-constrained denial-of-service (DoS) attacks that aim at impeding the network communication from time to time. First, by carefully modeling such DoS attacks as aperiodic pulse-width-modulated (PWM) jamming signals, a switching observer, adapting to the DoS attacks, is delicately constructed to deal with the unavailability of full-state information. Second, to economize the limited bandwidth resources, a dynamic event-triggered communication scheme is designed under the aperiodic DoS jamming attacks, whose duration and frequency are assumed to be restricted. Third, a switching system model with artificial state delay is formulated, which characterizes the effects of the aperiodic DoS attacks and event-triggered communication scheme in a unified framework. Then, the asymptotic stability analysis and controller/observer synthesis conditions of the resulting switching system are obtained by using a piecewise Lyapunov–Krasovskii functional approach. Furthermore, a co-design method of the dynamic triggering parameters, controller, and observer gains is presented. Finally, an example is employed to verify the effectiveness of the obtained results.
Effects of single or combined dietary supplementation of boric acid and plant extract mixture on egg production, egg quality and blood cholesterolemia in laying hens.

Summary This experiment was conducted to determine the effects of boric acid (BA) (60 mg/kg of feed) and plant extract mixture (Fitococci, F) (0.75 g/kg of feed), individually or in combination, on egg production, egg quality parameters and blood cholesterol concentration of laying hens in 23 wk of age. After wk 7 of the trial the level of boric acid in feeds were increased to 180 mg/kg. The feeding period lasted 14 wk. One hundred ninety-two pullets (Hyline) were randomly divided into control and 3 treatment groups each containing 48 birds and 6 replicates (each with 8 birds). At the end of the experiment there were no significant effects of dietary boric acid and plant extract mixture inclusion on feed efficiency, egg weights and egg production, egg quality parameters (shell thickness, breaking strength, and shape index) compared with control. But feed intake of hens which were supplemented with plant extract mixture and boric acid were increased (P<0.01). It was also determined that there were no effects of treatments on blood cholesterol levels. As a result, since hens which were fed with basal diet plus plant extract mixture showed better feed conversion ratio at 9-10 wks, this combination of feed additives can be added to diets without any adverse effect on laying hens. But inclusion of 60 mg/kg boric acid is considered better than 180 mg/kg with regard to feed efficiency in laying hens.
Functional magnetic resonance imaging multivoxel pattern analysis reveals neuronal substrates for collaboration and competition with myopic and predictive strategic reasoning

Competition and collaboration are strategies that can be used to optimize the outcomes of social interactions. Research into the neuronal substrates underlying these aspects of social behavior has been limited due to the difficulty in distinguishing complex activation via univariate analysis. Therefore, we employed multivoxel pattern analysis of functional magnetic resonance imaging to reveal the neuronal activations underlying competitive and collaborative processes when the collaborator/opponent used myopic/predictive reasoning. Twenty‐four healthy subjects participated in 2 × 2 matrix‐based sequential‐move games. Searchlight‐based multivoxel patterns were used as input for a support vector machine using nested cross‐validation to distinguish game conditions, and identified voxels were validated via the regression of the behavioral data with bootstrapping. The left anterior insula (accuracy = 78.5%) was associated with competition, and middle frontal gyrus (75.1%) was associated with predictive reasoning. The inferior/superior parietal lobules (84.8%) and middle frontal gyrus (84.7%) were associated with competition, particularly in trials with a predictive opponent. The visual/motor areas were related to response time as a proxy for visual attention and task difficulty. Our results suggest that multivoxel patterns better represent the neuronal substrates underlying the social cognition of collaboration and competition intermixed with myopic and predictive reasoning than do univariate features.