Miracle-dz/UniFAR-FTUs huggingface dataset:
A framework for exhaustive modelling of genetic interaction patterns using Petri nets

MOTIVATION Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases, and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs. RESULTS In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest ∼5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets. AVAILABILITY The framework is available at http://www.ibi. vu.nl/programs/ExhMod. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Sleep deprivation‐induced impairment of memory consolidation is not mediated by glucocorticoid stress hormones

The general consensus is that sleep promotes neuronal recovery and plasticity, whereas sleep deprivation (SD) impairs brain function, including cognitive processes. Indeed, a wealth of data has shown a negative impact of SD on learning and memory processes, particularly those that involve the hippocampus. The mechanisms underlying these negative effects of sleep loss are only partly understood, but a reoccurring question is whether they are in part caused by stress hormones that may be released during SD. The purpose of the present study is therefore to examine the role of glucocorticoid stress hormones in SD‐induced memory impairment. Male C57BL/6J mice were trained in an object‐location memory paradigm, followed by 6 hr of SD by mild stimulation. At the beginning of the SD mice were injected with the corticosterone synthesis inhibitor metyrapone. Memory was tested 24 hr after training. Blood samples taken in a separate group of mice showed that SD resulted in a mild but significant increase in plasma corticosterone levels, which was prevented by metyrapone. However, the SD‐induced impairment in object‐location memory was not prevented by metyrapone treatment. This indicates that glucocorticoids play no role in causing the memory impairments seen after a short period of SD.
Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures

Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system. Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur. We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles. Trichuris trichiura infection intensity also had the strongest association with blood transcriptional profiles. By characterizing paired longitudinal samples collected before and after deworming treatment, we determined that changes in serum zinc and iron levels among the Orang Asli were driven by changes in helminth infection status, independent of dietary metal intake. Serum zinc and iron levels were associated with changes in the abundance of several microbial taxa. Hence, there is considerable interplay between helminths, micronutrients and the microbiota on the regulation of immune responses in humans.
The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes

Genome-wide association studies have identified 25 germline genetic loci that increase the risk of glioma. The somatic tumor molecular alterations, including IDH-mutation status and 1p/19q co-deletion, have been included into the WHO 2016 classification system for glioma. To investigate how the germline genetic risk variants correlate with the somatic molecular subtypes put forward by WHO, we performed a meta-analysis that combined findings from 330 Swedish cases and 876 controls with two other recent studies. In total, 5,103 cases and 10,915 controls were included. Three categories of associations were found. First, variants in TERT and TP53 were associated with increased risk of all glioma subtypes. Second, variants in CDKN2B-AS1, EGFR, and RTEL1 were associated with IDH-wildtype glioma. Third, variants in CCDC26 (the 8q24 locus), C2orf80 (close to IDH), LRIG1, PHLDB1, ETFA, MAML2 and ZBTB16 were associated with IDH-mutant glioma. We therefore propose three etiopathological pathways in gliomagenesis based on germline variants for future guidance of diagnosis and potential functional targets for therapies. Future prospective clinical trials of patients with suspicion of glioma diagnoses, using the genetic variants as biomarkers, are necessary to disentangle how strongly they can predict glioma diagnosis.
Dentinal tubule penetration and root canal cleanliness following ultrasonic activation of intracanal-heated sodium hypochlorite.

This study investigated the effect of ultrasonic activation of intracanal-heated sodium hypochlorite (NaOCl) on its dentinal tubular penetration and root canal cleanliness in vitro. In experiment 1, mandibular premolars were randomly allocated to three groups (n = 8): group A, ultrasonic activation; group B, ultrasonic activation of intracanal-heated NaOCl and group C, syringe-and-needle irrigation. Penetration of the fluorescent-labelled NaOCl was investigated using light microscopy. In experiment 2, mandibular premolars were randomly allocated to group B or C (n = 10), for histological analysis of the remaining pulp tissue and debris. Data were statistically analysed using Kruskal-Wallis and Mann-Whitney tests (P = 0.05). The highest penetration of NaOCl was observed in group B, followed by group A (P < 0.05). Group B showed significantly less amount of debris than group C (P < 0.05). Dentinal tubule penetration of NaOCl and root canal cleanliness were significantly improved by ultrasonic activation of intracanal-heated NaOCl.
Most Relevant Spectral Bands Identification for Brain Cancer Detection Using Hyperspectral Imaging

Hyperspectral imaging (HSI) is a non-ionizing and non-contact imaging technique capable of obtaining more information than conventional RGB (red green blue) imaging. In the medical field, HSI has commonly been investigated due to its great potential for diagnostic and surgical guidance purposes. However, the large amount of information provided by HSI normally contains redundant or non-relevant information, and it is extremely important to identify the most relevant wavelengths for a certain application in order to improve the accuracy of the predictions and reduce the execution time of the classification algorithm. Additionally, some wavelengths can contain noise and removing such bands can improve the classification stage. The work presented in this paper aims to identify such relevant spectral ranges in the visual-and-near-infrared (VNIR) region for an accurate detection of brain cancer using in vivo hyperspectral images. A methodology based on optimization algorithms has been proposed for this task, identifying the relevant wavelengths to achieve the best accuracy in the classification results obtained by a supervised classifier (support vector machines), and employing the lowest possible number of spectral bands. The results demonstrate that the proposed methodology based on the genetic algorithm optimization slightly improves the accuracy of the tumor identification in ~5%, using only 48 bands, with respect to the reference results obtained with 128 bands, offering the possibility of developing customized acquisition sensors that could provide real-time HS imaging. The most relevant spectral ranges found comprise between 440.5–465.96 nm, 498.71–509.62 nm, 556.91–575.1 nm, 593.29–615.12 nm, 636.94–666.05 nm, 698.79–731.53 nm and 884.32–902.51 nm.
Contribution of income and job strain to the association between education and cardiovascular disease in 1.6 million Danish employees

Abstract Aims We examined the extent to which associations between education and cardiovascular disease (CVD) morbidity and mortality are attributable to income and work stress. Methods and results We included all employed Danish residents aged 30–59 years in 2000. Cardiovascular disease morbidity analyses included 1 638 270 individuals, free of cardiometabolic disease (CVD or diabetes). Mortality analyses included 41 944 individuals with cardiometabolic disease. We assessed education and income annually from population registers and work stress, defined as job strain, with a job-exposure matrix. Outcomes were ascertained until 2014 from health registers and risk was estimated using Cox regression. During 10 957 399 (men) and 10 776 516 person-years (women), we identified 51 585 and 24 075 incident CVD cases, respectively. For men with low education, risk of CVD was 1.62 [95% confidence interval (CI) 1.58–1.66] before and 1.46 (95% CI 1.42–1.50) after adjustment for income and job strain (25% reduction). In women, estimates were 1.66 (95% CI 1.61–1.72) and 1.53 (95% CI 1.47–1.58) (21% reduction). Of individuals with cardiometabolic disease, 1736 men (362 234 person-years) and 341 women (179 402 person-years) died from CVD. Education predicted CVD mortality in both sexes. Estimates were reduced with 54% (men) and 33% (women) after adjustment for income and job strain. Conclusion Low education predicted incident CVD in initially healthy individuals and CVD mortality in individuals with prevalent cardiometabolic disease. In men with cardiometabolic disease, income and job strain explained half of the higher CVD mortality in the low education group. In healthy men and in women regardless of cardiometabolic disease, these factors explained 21–33% of the higher CVD morbidity and mortality.
SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLα to MutSα on damaged chromatin induces apoptosis in human cells

The mismatch repair (MMR) complex is composed of MutSα (MSH2-MSH6) and MutLα (MLH1-PMS2) and specifically recognizes mismatched bases during DNA replication. O6-Methylguanine is produced by treatment with alkylating agents, such as N-methyl-N-nitrosourea (MNU), and during DNA replication forms a DNA mismatch (i.e. an O6-methylguanine/thymine pair) and induces a G/C to A/T transition mutation. To prevent this outcome, cells carrying this DNA mismatch are eliminated by MMR-dependent apoptosis, but the underlying molecular mechanism is unclear. In this study, we provide evidence that the chromatin-regulatory and ATP-dependent nucleosome-remodeling protein SMARCAD1 is involved in the induction of MMR-dependent apoptosis in human cells. Unlike control cells, SMARCAD1-knockout cells (ΔSMARCAD1) were MNU-resistant, and the appearance of a sub-G1 population and caspase-9 activation were significantly suppressed in the ΔSMARCAD1 cells. Furthermore, the MNU-induced mutation frequencies were increased in these cells. Immunoprecipitation analyses revealed that the recruitment of MutLα to chromatin-bound MutSα, observed in SMARCAD1-proficient cells, is suppressed in ΔSMARCAD1 cells. Of note, the effect of SMARCAD1 on the recruitment of MutLα exclusively depended on the ATPase activity of the protein. On the basis of these findings, we propose that SMARCAD1 induces apoptosis via its chromatin-remodeling activity, which helps recruit MutLα to MutSα on damaged chromatin.
Generation of Lamprey Monoclonal Antibodies (Lampribodies) Using the Phage Display System

The variable lymphocyte receptors (VLRs) consist of leucine rich repeats (LRRs) and comprise the humoral antibodies produced by lampreys and hagfishes. The diversity of the molecules is generated by stepwise genomic rearrangements of LRR cassettes dispersed throughout the VLRB locus. Previously, target-specific monovalent VLRB antibodies were isolated from sea lamprey larvae after immunization with model antigens. Further, the cloned VLR cDNAs from activated lamprey leukocytes were transfected into human cell lines or yeast to select best binders. Here, we expand on the overall utility of the VLRB technology by introducing it into a filamentous phage display system. We first tested the efficacy of isolating phage into which known VLRB molecules were cloned after a series of dilutions. These experiments showed that targeted VLRB clones could easily be recovered even after extensive dilutions (1 to 109). We further utilized the system to isolate target-specific “lampribodies” from phage display libraries from immunized animals and observed an amplification of binders with relative high affinities by competitive binding. The lampribodies can be individually purified and ostensibly utilized for applications for which conventional monoclonal antibodies are employed.
Effects of Primary Aldosteronism and Different Therapeutic Modalities on Glucose Metabolism

Despite findings that aldosterone impairs glucose metabolism, studies concerning the effect of primary aldosteronism (PA) and its treatment on glucose metabolism are controversial. We aimed to determine glucose metabolism in PA and the effect of the treatment modality. We compared glucose metabolism between PA patients (N = 286) and age-, sex-, and body mass index-matched controls (N = 816), and the changes in glucose metabolism depending on the treatment modality (adrenalectomy vs. spironolactone treatment). Hyperglycemia including diabetes mellitus (DM; 19.6% vs. 13.1%, p = 0.011) was more frequent in PA patients. Hyperglycemia was also more frequent in PA patients without subclinical hypercortisolism (SH: p < 0.001) and in those regardless of hypokalemia (p < 0.001–0.001). PA patients and PA patients without SH had higher DM risk (odds ratio (OR); 95% confidence interval (CI): 1.63; 1.11–2.39 and 1.65; 1.08–2.51, respectively) after adjusting confounders. In PA patients, there was significant decrease in the DM prevalence (21.3% to 16.7%, p = 0.004) and fasting plasma glucose (p = 0.006) after adrenalectomy. However, there was no significant change in them after spironolactone treatment. Adrenalectomy was associated with more improved glucose status than spironolactone treatment (OR; 95% CI: 2.07; 1.10–3.90). Glucose metabolism was impaired in PA, regardless of hypokalemia and SH status, and was improved by adrenalectomy, but not spironolactone treatment.
Loss of Dmrt5 Affects the Formation of the Subplate and Early Corticogenesis

Abstract Dmrt5 (Dmrta2) and Dmrt3 are key regulators of cortical patterning and progenitor proliferation and differentiation. In this study, we show an altered apical to intermediate progenitor transition, with a delay in SP neurogenesis and premature birth of Ctip2+ cortical neurons in Dmrt5−/− mice. In addition to the cortical progenitors, DMRT5 protein appears present in postmitotic subplate (SP) and marginal zone neurons together with some migrating cortical neurons. We observed the altered split of preplate and the reduced SP and disturbed radial migration of cortical neurons into cortical plate in Dmrt5−/− brains and demonstrated an increase in the proportion of multipolar cells in primary neuronal cultures from Dmrt5−/− embryonic brains. Dmrt5 affects cortical development with specific time sensitivity that we described in two conditional mice with slightly different deletion time. We only observed a transient SP phenotype at E15.5, but not by E18.5 after early (Dmrt5lox/lox;Emx1Cre), but not late (Dmrt5lox/lox;NestinCre) deletion of Dmrt5. SP was less disturbed in Dmrt5lox/lox;Emx1Cre and Dmrt3−/− brains than in Dmrt5−/− and affects dorsomedial cortex more than lateral and caudal cortex. Our study demonstrates a novel function of Dmrt5 in the regulation of early SP formation and radial cortical neuron migration. Summary Statement Our study demonstrates a novel function of Dmrt5 in regulating marginal zone and subplate formation and migration of cortical neurons to cortical plate.
Low Energy Pulsed Laser Excitation in UV Enhances the Gas Sensing Capacity of Photoluminescent ZnO Nanohybrids

Nanohybrids, composed of luminescent zinc oxide (ZnO) nanoparticles dispersed in an inert polydimethylsiloxane (PDMS) matrix, exhibit an excellent ability to follow changes in the type and composition of their surrounding atmosphere. These changes are found to affect the UV photoluminescence (PL) emission of the ZnO-PDMS hybrids measured at room temperature. The influence of irradiation parameters, such as excitation intensity and wavelength, on the response of the ZnO-PDMS sensor against ethanol and oxygen, have been systematically investigated in a comparative study performed employing pulsed excitation at 248 and 355 nm. This study represents the first demonstration that the sensing performance of the PL-based ZnO sensors can be optimized by tuning the excitation parameters and it particularly illustrates that maintaining a low pump energy density is crucial for enhancing the sensitivity of the sensor achieving response values approaching 100%.
The transcriptome analysis of the Arabidopsis thaliana in response to the Vibrio vulnificus by RNA-sequencing

Because of the recent increase in the demand for fresh produce, contamination of raw food products has become an issue. Foodborne diseases are frequently caused by the infection of leguminous plants by human bacterial pathogens. Moreover, contamination by Vibrio cholerae, closely related with Vibrio vulnificus, has been reported in plants and vegetables. Here, we investigated the possibility of Vibrio vulnificus 96-11-17M, an opportunistic human pathogen, to infect and colonize Arabidopsis thaliana plants, resulting in typical disease symptoms at 5 and 7 days post-inoculation in vitro and in planta under artificial and favorable conditions, respectively. RNA-Seq analysis revealed 5,360, 4,204, 4,916 and 3,741 differentially expressed genes (DEGs) at 12, 24, 48 and 72 h post-inoculation, respectively, compared with the 0 h time point. Gene Ontology analysis revealed that these DEGs act in pathways responsive to chemical and hormone stimuli and plant defense. The expression of genes involved in salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)-dependent pathways was altered following V. vulnificus inoculation. Genetic analyses of Arabidopsis mutant lines verified that common pathogen-associated molecular pattern (PAMP) receptors perceive the V. vulnificus infection, thus activating JA and ET signaling pathways. Our data indicate that the human bacterial pathogen V. vulnificus 96-11-17M modulates defense-related genes and host defense machinery in Arabidopsis thaliana under favorable conditions.
1q21 gain but not t(4;14) indicates inferior outcomes in multiple myeloma treated with bortezomib

Abstract Chromosome 1q21 aberrations in multiple myeloma have attracted much attention for a long time, however, the prognostic value is still under investigation. We confirmed the independent prognostic impact of 1q21 aberrations in this non-randomized clinical study. Our study noted that additional copies and larger clonal size of 1q21 gain did not worsen the outcome. We discovered that 1q21 gain was associated with the acquisition of new chromosome abnormalities and genomic instability, evidenced by the strong correlation between 1q21 gain and complex karyotypes or the acquisition of more than two cytogenetic aberrations. Moreover, 1q21 gain and/or del(17p) were powerful enough to discriminate high-risk patients. Furthermore, 1q21 gain retained unfavorable even when stratified by concurrent presence of t(4;14), especially in the bortezomib arm. Finally, although bortezomib might benefit patients with 1q21 gain, it could not completely overcome its adverse effects, suggesting the necessity of more effective therapies for these patients.
Rapid DNA template preparation directly from a rice sample without purification for loop-mediated isothermal amplification (LAMP) of rice genes

ABSTRACT Rapid DNA template preparation directly from a single rice (Oryza sativa) grain or rice flour of its equivalent weight was developed for loop-mediated isothermal amplification (LAMP). LAMP efficiency using DNA extract obtained from consecutive addition of alkaline lysis reagent (25 mM NaOH, 0.2 mM EDTA) and neutralizing reagent (40 mM Tris–HCl [pH 5]) was comparable to that using an equivalent amount of purified DNA as template. The stability of the prepared DNA extract was confirmed for up to six-day storage at room temperature. Without using any special laboratory devices, the developed method enabled a rapid, simple, and low-cost DNA template preparation method for reliable LAMP testing to detect rice genes. GRAPHICAL ABSTRACT A novel improved LAMP method for a single rice grain or rice flour from DNA extraction to visual detection of amplicon without laborious DNA purification and special laboratory devises.
Mutant C9orf72 human iPSC‐derived astrocytes cause non‐cell autonomous motor neuron pathophysiology

Mutations in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS). Accumulating evidence implicates astrocytes as important non‐cell autonomous contributors to ALS pathogenesis, although the potential deleterious effects of astrocytes on the function of motor neurons remains to be determined in a completely humanized model of C9orf72‐mediated ALS. Here, we use a human iPSC‐based model to study the cell autonomous and non‐autonomous consequences of mutant C9orf72 expression by astrocytes. We show that mutant astrocytes both recapitulate key aspects of C9orf72‐related ALS pathology and, upon co‐culture, cause motor neurons to undergo a progressive loss of action potential output due to decreases in the magnitude of voltage‐activated Na+ and K+ currents. Importantly, CRISPR/Cas‐9 mediated excision of the C9orf72 repeat expansion reverses these phenotypes, confirming that the C9orf72 mutation is responsible for both cell‐autonomous astrocyte pathology and non‐cell autonomous motor neuron pathophysiology.
Dalton's pseudo‐isochromatic plates and congenital colour vision deficiency

Diagnosing colour vision deficiency is vital, owing to its impact on the choice of career and activities of daily living. Conventional screening methods require frequent replacement due to soiling of the materials, and hence are expensive and not feasible for large‐scale community screening. This study aims to construct and validate a new screening tool, Dalton's pseudo‐isochromatic plates (PIP), addressing the disadvantages of the conventional methods.