Miracle-dz/UniFAR-FTUs huggingface dataset:
M3VR—A multi-stage, multi-resolution, and multi-volumes-of-interest volume registration method applied to 3D endovaginal ultrasound

Heterogeneity of echo-texture and lack of sharply delineated tissue boundaries in diagnostic ultrasound images make three-dimensional (3D) registration challenging, especially when the volumes to be registered are considerably different due to local changes. We implemented a novel computational method that optimally registers volumetric ultrasound image data containing significant and local anatomical differences. It is A Multi-stage, Multi-resolution, and Multi-volumes-of-interest Volume Registration Method. A single region registration is optimized first for a close initial alignment to avoid convergence to a locally optimal solution. Multiple sub-volumes of interest can then be selected as target alignment regions to achieve confident consistency across the volume. Finally, a multi-resolution rigid registration is performed on these sub-volumes associated with different weights in the cost function. We applied the method on 3D endovaginal ultrasound image data acquired from patients during biopsy procedure of the pelvic floor muscle. Systematic assessment of our proposed method through cross validation demonstrated its accuracy and robustness. The algorithm can also be applied on medical imaging data of other modalities for which the traditional rigid registration methods would fail.
Standardizace české verze The Confusion Assessment Method for the Intensive Care Unit (CAM-ICUcz)

Cilem studie bylo standardizovat ceskou verzi testu CAM-ICU. Stanoveni validity CAM-ICUcz v detekci přitomnosti deliria oproti expertnimu stanoveni bylo provedeno u nemocných s: A. Akutni cevni mozkovou přihodou (aCMP) n = 80; B. Umělou plicni ventilaci: n = 10; C. Demenci: n = 34; D. Depresi: n = 20; E. Schizofrenii: n = 22. Výsledky: Expertni hodnoceni zaznamenalo epizodu deliria u 37 nemocných s aCMP (46,25 %). Test CAM-ICU prokazal senzitivitu 97,3 % a specificitu testu 93,0 %. Test byl proveditelný i v podminkach uměle plicni ventilace, kde jsme zaznamenali delirium u 50 % nemocných a 100% shodu s expertnim hodnocenim. U žadneho z nemocných s demenci, depresi nebo schizofrenii nebyla dle CAM-ICUcz splněna kriteria deliria (100% specificita). Zavěr: CAM-ICUcz je vhodný skriningový test pro detekci deliria v intenzivni peci.
Persistent Mycobacterium tuberculosis infection in mice requires PerM for successful cell division

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host is central to the pathogenesis of tuberculosis, yet the underlying mechanisms remain incompletely defined. PerM, an integral membrane protein, is required for persistence of Mtb in mice. Here, we show that perM deletion caused a cell division defect specifically during the chronic phase of mouse infection, but did not affect Mtb’s cell replication during acute infection. We further demonstrate that PerM is required for cell division in chronically infected mice and in vitro under host-relevant stresses because it is part of the mycobacterial divisome and stabilizes the essential divisome protein FtsB. These data highlight the importance of sustained cell division for Mtb persistence, define condition-specific requirements for cell division and reveal that survival of Mtb during chronic infection depends on a persistence divisome.
Highlight article: Vitamin B6 deficiency in new born rats affects hepatic cardiolipin composition and oxidative phosphorylation

Vitamin B6 deficiency during pregnancy translates into a severe vitamin B6 deficiency (plasma levels decreased by 97%) in new-born rats. Further, hallmarks are increased (+89%) concentrations of homocysteine, gross changes in gene methylation and expression, and metabolic alterations including lipid metabolism. This study focuses on determining the effects of vitamin B6-deficiency on cardiolipin composition and oxidative phosphorylation in liver. For this purpose, hepatic cardiolipin composition was analyzed by means of LC/MS/MS, and mitochondrial oxygen consumption was determined by using a Clark-type electrode in a rat model of vitamin B6 deficiency. Liver mitochondria from new-born rats with pre-term vitamin B6 deficiency responded with substantial alterations in cardiolipin composition that include the following changes in the amounts of cardiolipin incorporated fatty acids: increase in C16, decrease in C18, decrease in saturated fatty acid, as well as increase in amount of oxidized cardiolipin species. These changes were accompanied by significantly decreased capacity of oxidative phosphorylation. In conclusion, vitamin B6 deficiency in new born rats induces massive alterations of cardiolipin composition and function of liver mitochondria. These findings support the importance of sufficient periconceptional supply of vitamin B6 to prevent vitamin B6 deficiency. Impact statement Vitamin B6 (VitB6) is an active co-enzyme for more than 150 enzymes and is required for a great diversity of biosynthesis and metabolic reactions. There is an increased need for VitB6 during pregnancy and sufficient supply of VitB6 is crucial for the prevention of cleft palate and neural tube defects. We show that liver mitochondria from new-born rats with pre-term VitB6 deficiency respond with substantial alterations in cardiolipin (CL) composition and in the amount of oxidized CL species. These changes are associated with a decrease in the efficiency of oxidative phosphorylation. The results of this study support the significance of sufficient supply of VitB6 during pregnancy (and periconceptional) for diminishing the number of early abortions and minimizing malformation. The established link between VitB6 deficiency, CL composition, and mitochondrial respiration/energy production provides mechanistic insight as to how the VitB6 deficiency translates into the known pathophysiological and clinically relevant conditions.
Behavioral Impairments and Oxidative Stress in the Brain, Muscle, and Gill Caused by Chronic Exposure of C70 Nanoparticles on Adult Zebrafish

There is an imperative need to develop efficient whole-animal-based testing assays to determine the potential toxicity of engineered nanomaterials. While previous studies have demonstrated toxicity in lung and skin cells after C70 nanoparticles (NPs) exposure, the potential detrimental role of C70 NPs in neurobehavior is largely unaddressed. Here, we evaluated the chronic effects of C70 NPs exposure on behavior and alterations in biochemical responses in adult zebrafish. Two different exposure doses were used for this experiment: low dose (0.5 ppm) and high dose (1.5 ppm). Behavioral tests were performed after two weeks of exposure of C70 NPs. We found decreased locomotion, exploration, mirror biting, social interaction, and shoaling activities, as well as anxiety elevation and circadian rhythm locomotor activity impairment after ~2 weeks in the C70 NP-exposed fish. The results of biochemical assays reveal that following exposure of zebrafish to 1.5 ppm of C70 NPs, the activity of superoxide dismutase (SOD) in the brain and muscle tissues increased significantly. In addition, the concentration of reactive oxygen species (ROS) also increased from 2.95 ± 0.12 U/ug to 8.46 ± 0.25 U/ug and from 0.90 ± 0.03 U/ug to 3.53 ± 0.64 U/ug in the muscle and brain tissues, respectively. Furthermore, an increased level of cortisol was also observed in muscle and brain tissues, ranging from 17.95 ± 0.90 pg/ug to 23.95 ± 0.66 pg/ug and from 3.47 ± 0.13 pg/ug to 4.91 ± 0.51 pg/ug, respectively. Increment of Hif1-α level was also observed in both tissues. The elevation was ranging from 11.65 ± 0.54 pg/ug to 18.45 ± 1.00 pg/ug in the muscle tissue and from 4.26 ± 0.11 pg/ug to 6.86 ± 0.37 pg/ug in the brain tissue. Moreover, the content of DNA damage and inflammatory markers such as ssDNA, TNF-α, and IL-1β were also increased substantially in the brain tissues. Significant changes in several biomarker levels, including catalase and malondialdehyde (MDA), were also observed in the gill tissues. Finally, we used a neurophenomic approach with a particular focus on environmental influences, which can also be easily adapted for other aquatic fish species, to assess the toxicity of metal and carbon-based nanoparticles. In summary, this is the first study to illustrate the adult zebrafish toxicity and the alterations in several neurobehavior parameters after zebrafish exposure to environmentally relevant amounts of C70 NPs.
Quercetin inhibits carbapenemase and efflux pump activities among carbapenem‐resistant Gram‐negative bacteria

Rapid dissemination of carbapenem‐resistant Gram‐negative bacteria (CRGNB) is a global threat. Quercetin is known for its antimicrobial activity. In this study, carbapenemase and efflux pump inhibitory activities of quercetin were demonstrated against carbapenem‐resistant Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. Further, molecular docking was performed to elucidate molecular mechanisms of such inhibition. CRGNB, expressing one of the carbapenemases, demonstrated significant inhibition of carbapenemase activity when pre‐incubated with 64 µg/ml quercetin. Moreover, acrB overexpressing enterobacterial isolates exhibited significant inhibition of efflux activity upon quercetin treatment. Molecular docking studies revealed stability of quercetin‐carbapenemase complexes. (i) Virtual superimposition of quercetin onto meropenem, (ii) proximity of quercetin to attacking nucleophile and (iii) involvement of same amino acids that stabilize both meropenem and quercetin – indicated competition between quercetin and meropenem for ligand binding. Although quercetin and PAβN, a standard efflux pump inhibitor, docked at both central cavity and periplasmic drug binding sites of AcrB, they did not virtually superimpose on each other. However, sufficient release of Gibb's free energy and involvement of same set of amino acids in PAβN and quercetin stability predicted quercetin's efflux pump inhibitory potential. Hence, quercetin could be potential adjuvant therapeutics for CRGNB‐mediated infections.
Political Orientation and Belief in Science in a U.S. College Sample

Lay skepticism toward empirically supported scientific research has increased significantly in recent years. Given that part of the social contract of science is the betterment of society, it is critical for the scientific community to identify factors underlying public dismissal versus support of scientific evidence. The current study explores how individual differences in political ideology influence acceptance of factual and nonfactual information, with differences in truth-seeking values as a potential mediating variable. Participants rated their agreement with true and untrue (i.e., nonempirically supported) statements and completed self-report assessments of political ideology and personal endorsement of values associated with promoting truth. More politically, liberal individuals reported greater agreement with both scientific facts and untrue statements. Furthermore, endorsement of truth-seeking values mediated the relation between liberal ideology and agreement with facts (but not nonfactual statements). Results suggest that interventions to increase individuals’ acceptance of facts may benefit from stimulating greater support for truth-seeking values and behavior.
iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou’s 5-step rule

Among different post-translational modifications (PTMs), one of the most important one is the lysine crotonylation in proteins. Its importance cannot be undermined related to different diseases and essential biological practice. The key step for finding the hidden mechanisms of crotonylation along with their occurrence sites is to completely apprehend the mechanism behind this biological process. In previously reported studies, researchers have used different techniques, like position weighted matrix (PWM), support vector machine (SVM), k nearest neighbors (KNN), and many others. However, the maximum prediction accuracy achieved was not such high. To address this, herein, we propose an improved predictor for lysine crotonylation sites named iCrotoK-PseAAC, in which we have incorporated various position and composition relative features along with statistical moments into PseAAC. The results of self-consistency testing were 100% accurate, while the 10-fold cross validation gave 99.0% accuracy. Based on the validation and comparison of model, it is concluded that the iCrotoK-PseAAC is more accurate than the previously proposed models.
Eliminating high-intensity activity during growth reduces mechanical power capacity but not sub-maximal metabolic cost in a bipedal animal model.

Decreases in activity levels in children worldwide are feared to have long-term health repercussions. Yet, due to the difficulty of performing controlled long-term studies in humans, we do not yet understand how decreases in childhood activity influence adult functional capacity. Here we tested (in an avian bipedal model) the influence of eliminating all high-intensity activity during growth on adult performance. We evaluated three alternative hypotheses: Elimination of high-intensity activity 1) does not influence adult function, 2) results in task-specific deficits in adulthood or 3) results in deficits that generalize across locomotor tasks. We found that animals restricted from jumping and sprinting during growth, as adults showed detriments in maximal jump performance in comparison to controls, but did not require more metabolic energy during steady-state running or standing. From this, we conclude that functional deficits from elimination of high-intensity exercise are task specific and do not generalize across all locomotor function.
Comparative Proteomic Analysis Reveals Immune Competence in Hemolymph of Bombyx mori Pupa Parasitized by Silkworm Maggot Exorista sorbillans

The silkworm maggot, Exorista sorbillans, is a well-known larval endoparasitoid of the silkworm Bombyx mori that causes considerable damage to the silkworm cocoon crop. To gain insights into the response mechanism of the silkworm at the protein level, we applied a comparative proteomic approach to investigate proteomic differences in the hemolymph of the female silkworm pupae parasitized by E. sorbillans. In total, 50 differentially expressed proteins (DEPs) were successfully identified, of which 36 proteins were upregulated and 14 proteins were downregulated in response to parasitoid infection. These proteins are mainly involved in disease, energy metabolism, signaling pathways, and amino acid metabolism. Eight innate immune proteins were distinctly upregulated to resist maggot parasitism. Apoptosis-related proteins of cathepsin B and 14-3-3 zeta were significantly downregulated in E. sorbillans-parasitized silkworm pupae; their downregulation induces apoptosis. Quantitative PCR was used to further verify gene transcription of five DEPs, and the results are consistent at the transcriptional and proteomic levels. This was the first report on identification of possible proteins from the E. bombycis-parasitized silkworms at the late stage of parasitism, which contributes to furthering our understanding of the response mechanism of silkworms to parasitism and dipteran parasitoid biology.
A comparison of the bone and growth phenotype of mdx, mdx:Cmah−/− and mdx:Utrn+/− murine models with the C57BL/10 wild-type mouse

ABSTRACT The muscular dystrophy X-linked (mdx) mouse is commonly used as a mouse model of Duchenne muscular dystrophy (DMD). Its phenotype is, however, mild, and other mouse models have been explored. The mdx:Cmah−/− mouse carries a human-like mutation in the Cmah gene and has a severe muscle phenotype, but its growth and bone development are unknown. In this study, we compared male mdx, mdx:Utrn+/−, mdx:Cmah−/− and wild-type (WT) mice at 3, 5 and 7 weeks of age to determine the suitability of the mdx:Cmah−/− mouse as a model for assessing growth and skeletal development in DMD. The mdx:Cmah−/− mice were lighter than WT mice at 3 weeks, but heavier at 7 weeks, and showed an increased growth rate at 5 weeks. Cortical bone fraction as assessed by micro-computed tomography was greater in both mdx and mdx:Cmah−/− mice versus WT mice at 7 weeks. Tissue mineral density was also higher in mdx:Cmah−/− mice at 3 and 7 weeks. Gene profiling of mdx:Cmah−/− bone identified increased expression of Igf1, Igf1r and Vegfa. Both the mdx and mdx:Cmah−/− mice showed an increased proportion of regulated bone marrow adipose tissue (BMAT) but a reduction in constitutive BMAT. The mdx:Cmah−/− mice show evidence of catch-up growth and more rapid bone development. This pattern does not mimic the typical DMD growth trajectory and therefore the utility of the mdx:Cmah−/− mouse for studying growth and skeletal development in DMD is limited. Further studies of this model may, however, shed light on the phenomenon of catch-up growth. This article has an associated First Person interview with the first author of the paper. Editors' choice: Unlike boys with DMD, the mdx:Cmah−/− mouse shows increased weight gain and more rapid bone development; therefore, its utility for studying growth and skeletal development in DMD is limited.
Effectiveness of steam sterilization of reusable medical devices in primary and secondary care public hospitals in Nepal and factors associated with ineffective sterilization: A nation-wide cross-sectional study

Background Inadequate sterilization of reusable medical devices can lead to healthcare associated infections (HAIs) through person-to-person or environmental transmission of pathogens. Autoclaving (steam sterilization) is most commonly used for sterilizing medical devices in healthcare facilities. We conducted a nation-wide cross-sectional study to evaluate the effectiveness of steam sterilization practices in primary and secondary care public hospitals in Nepal and to identify factors associated with ineffective sterilization. Methods Using a stratified clustered random sampling, 13 primary- and secondary-care public hospitals in Nepal were selected. 189 steam sterilization cycles from these hospitals were evaluated for their effectiveness using self-contained biological indicators, class-5 chemical indicators, autoclave indicator tape and physical parameters. Information about the hospitals and the types of autoclaves being used was also collected. Data were analysed to estimate the proportion of ineffective steam sterilization cycles. Logistic regression was used to identify factors associated with ineffective sterilization. Findings In primary and secondary care public hospitals in Nepal, 71.0% (95% CI 46.8% - 87.2%) of the autoclave cycles were ineffective (i.e. showed positive results) when tested with biological indicators and 69.8% (95% CI 44.4% - 87.0%) showed ‘reject’ results with class 5 chemical indicators. There was no statistically significant difference in proportions showing positive or reject results by hospital types for either biological (p = 0.51) or class 5 chemical (p = 0.87) indicators. Autoclave type and pressure achieved during sterilization were statistically significantly associated with steam sterilization failures, adjusted for holding period, evenness of pressure and barrier system used. Conclusion Primary and secondary care hospitals in Nepal have a high proportion of steam sterilization failure, indicating a risk of person-to-person transmission of pathogens through reusable medical devices. There is an urgent need to improve steam sterilization processes in these hospitals.
RNAi-Mediated Gene Silencing of Trcot1 Induces a Hyperbranching Phenotype in Trichoderma reesei

Trichoderma reesei is the major filamentous fungus used to produce cellulase and there is huge interest in promoting its ability to produce higher titers of cellulase. Among the many factors affecting cellulase production in T. reesei, the mycelial phenotype is important but seldom studied. Herein, a close homolog of the Neurospora crassa COT1 kinase was discovered in T. reesei and designated TrCOT1, which is of 83.3% amino acid sequence identity. Functional disruption of Trcot1 in T. reesei by RNAi-mediated gene silencing resulted in retarded sporulation on potato dextrose agar and dwarfed colonies on minimal medium agar plates containing glucose, xylan, lactose, xylose, or glycerol as the sole carbon source. The representative mutant strain, SUS2/Trcot1i, also displayed reduced mycelia accumulation but hyperbranching in the MM glucose liquid medium, with hyphal growth unit length values decreased to 73.0 μm/tip compared to 239.8 μm/tip for the parent strain SUS2. The hyperbranching phenotype led to slightly but significantly increased cellulase secretion from 24 to 72 h in a batch culture. However, the cellulase production per unit of mycelial biomass was much more profoundly improved from 24 to 96 h.
A Novel ‘Candidatus Liberibacter asiaticus’-Encoded Sec-Dependent Secretory Protein Suppresses Programmed Cell Death in Nicotiana benthamiana

‘Candidatus Liberibacter asiaticus’ (CLas) is one of the causal agents of citrus Huanglongbing (HLB), a bacterial disease of citrus trees that greatly reduces fruit yield and quality. CLas strains produce an array of currently uncharacterized Sec-dependent secretory proteins. In this study, the conserved chromosomally encoded protein CLIBASIA_03875 was identified as a novel Sec-dependent secreted protein. We show that CLIBASIA_03875 contains a putative Sec- secretion signal peptide (SP), a 29 amino acid residue located at the N-terminus, with a mature protein (m3875) of 22 amino acids found to localize in multiple subcellular components of the leaf epidermal cells of Nicotiana benthamiana. When overexpressed via a Potato virus X (PVX)-based expression vector in N. benthamiana, m3875 suppressed programmed cell death (PCD) and the H2O2 accumulation triggered by the pro-apoptotic mouse protein BAX and the Phytophthora infestans elicitin INF1. Overexpression also resulted in a phenotype of dwarfing, leaf deformation and mosaics, suggesting that m3875 has roles in plant immune response, growth, and development. Substitution mutagenesis of the charged amino acid (D7, R9, R11, and K22) with alanine within m3875 did not recover the phenotypes for PCD and normal growth. In addition, the transiently overexpressed m3875 regulated the transcriptional levels of N. benthamiana orthologs of CNGCs (cyclic nucleotide-gated channels), BI-1 (Bax-inhibitor 1), and WRKY33 that are involved in plant defense mechanisms. To our knowledge, m3875 is the first PCD suppressor identified from CLas. Studying the function of this protein provides insight as to how CLas attenuates the host immune responses to proliferate and cause Huanglongbing disease in citrus plants.
Basic Neuroanatomical Methods

This unit covers some basic procedures that are common to a wide range of neuroanatomical protocols for brain tissue. Procedures are provided for preparation of unfixed fresh brain tissue as well as for perfusion fixation of animals to obtain fixed neural tissue. A variety of methods for sectioning are described, including frozen sectioning using a cryostat or microtome and sectioning with a vibratome. The choice of sectioning method depends on how the brain has been prepared and what histochemical method is to be used. A fluorescent immunohistochemical method to localize endogenous molecules as well as induced markers such as green fluorescent protein and red fluorescent protein is also provided. Additionally, three post‐sectioning procedures are described: defatting of slide‐mounted sections, fluorescent Nissl staining, and thionin staining of sections. Finally, support protocols are provided, describing a method for maintaining the correct order of cut tissue, whether rostral to caudal or lateral to medial; a procedure for subbing slides with gelatin, which is necessary in some protocols in order for sections to adhere to slides; and preparation of custom 3D‐printed 10‐ or 20‐well tissue plates and trays for subsequent immunostaining. Published 2019. U.S. Government.