Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages

Abstract CRISPR–Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR–Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli’s CRISPR–Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR–Cas systems active.
Illegitimate Tasks, Negative Affectivity, and Organizational Citizenship Behavior among Private School Teachers: A Mediated–Moderated Model

Social sustainability has gained popularity over the last decade, with a growing body of research calling for researchers to focus on the personal-level determinants of employee satisfaction and well-being in the pursuit of social sustainability. By using negative affectivity as a mediating mechanism and gender and passive leadership as moderators, this study examines a novel sequential mediation–moderation model that explores the relationship between unreasonable tasks and teachers’ Organizational Citizenship Behavior (OCB). It employs the Conservation of Resources (COR) and Stress as Offense to Self (SOS) paradigms as a comprehensive theoretical framework for organizational stressors and organizational behavior. A total of 415 matched questionnaire responses were collected from private school teachers in the UAE. Confirmatory factor analysis (CFA) is conducted using AMOS 20, hierarchical linear modeling (HLM) is utilized to verify the causal and moderation hypotheses, and the resulting moderated mediated conceptual model is evaluated by employing Hayes PROCESS analysis. Results demonstrate the effects of illegitimate tasks on OCB are indirect and statistically significant and are mediated through negative affectivity. The cumulative effect of illegitimate tasks and negative affectivity on OCB is magnified by the moderating effects of passive leadership.
Time Scales of Southern Ocean Eddy Equilibration

AbstractStratification in the Southern Ocean is determined primarily by a competition between westerly wind-driven upwelling and baroclinic eddy transport. This study investigates the time scales of equilibration of the Southern Ocean in response to changing winds through an idealized channel model. An analytical framework describing the energetic pathways between wind input, available potential energy (APE), eddy kinetic energy (EKE), and dissipation provides a simple theory of the phase and amplitude response to oscillating wind stress. The transient ocean response to variable winds lies between the two limits of Ekman response (high frequency), characterized by the isopycnal slope responding directly to wind stress, and “eddy saturation” (low frequency), wherein a large fraction of the anomalous wind work goes into mesoscale eddies. The crossover time scale is the time scale of meridional eddy diffusive transport across the Antarctic Circumpolar Current (ACC) front. For wind variability with a period o.
The Use of an Antioxidant Enables Accurate Evaluation of the Interaction of Curcumin on Organic Anion-Transporting Polypeptides 4C1 by Preventing Auto-Oxidation

Flavonoids have garnered attention because of their beneficial bioactivities. However, some flavonoids reportedly interact with drugs via transporters and may induce adverse drug reactions. This study investigated the effects of food ingredients on organic anion-transporting polypeptide (OATP) 4C1, which handles uremic toxins and some drugs, to understand the safety profile of food ingredients in renal drug excretion. Twenty-eight food ingredients, including flavonoids, were screened. We used ascorbic acid (AA) to prevent curcumin oxidative degradation in our method. Twelve compounds, including apigenin, daidzein, fisetin, genistein, isorhamnetin, kaempferol, luteolin, morin, quercetin, curcumin, resveratrol, and ellagic acid, altered OATP4C1-mediated transport. Kaempferol and curcumin strongly inhibited OATP4C1, and the Ki values of kaempferol (AA(−)), curcumin (AA(−)), and curcumin (AA(+)) were 25.1, 52.2, and 23.5 µM, respectively. The kinetic analysis revealed that these compounds affected OATP4C1 transport in a competitive manner. Antioxidant supplementation was determined to benefit transporter interaction studies investigating the effects of curcumin because the concentration-dependent curve evidently shifted in the presence of AA. In this study, we elucidated the food–drug interaction via OATP4C1 and indicated the utility of antioxidant usage. Our findings will provide essential information regarding food–drug interactions for both clinical practice and the commercial development of supplements.
Growth Hormone Receptor and PCSK9 Define a New Paradigm in the Initiation and Development of Chronic Kidney Disease as Revealed by Exome Sequencing on Illumina Platform

Chronic kidney disease is a combination of many vascular diseases involving mutations of many genes. Hypertension diabetes and atherosclerosis are the most common causes of kidney disease, with hypertension causing just over a quarter of all cases of kidney failure and diabetes causing one-third of them. Other much less common conditions that can cause CKD include inflammation, infections, genetic factors, or longstanding blockage to the urinary system (such as enlarged prostate or kidney stones). In many cases, the causes remained unknown, albeit the manifestation of the diseases with clear phenotypes and biochemical profiles. Heredity and genetic determinants play major roles in the initiation, development, and establishment of CKD. Kidney disease phenotypes can be dissected into many underlying causing candidates’ genes and many molecular genetics approaches are striving to lift the veil on this nagging disease. Recent studies using genetic testing have demonstrated that Mendelian etiologies account for approximately 20% of cases of kidney disease of unknown etiology. CKD is known to be plagued with many genes mutations like mutation in Autosomal Dominant Polycystic Kidney Disease (ADPKD) and mutations in MYH9 and APOL1 genes, COL4A3, COL4A4, and COL4A5 genes playing important roles in the CKD picture. Genetic testing has modernized and revolutionized many areas of medical practices and diagnosis of many diseases and the field of nephrology is not an exception. The advance in Next-generation Sequencing, including whole exome sequencing has proven to be a powerful tool in personalized medicine and for potential noninvasive decryption for biomarkers in kidney disease thereby paving the way for better diagnostic purposes. In this regard, we run whole exome sequencing on whole blood genomic DNA from CKD patients. Bioinformatics analysis led us to uncover a total of more than 3000 single nucleotide polymorphisms (SNPs). To sort out these flurries of targeted SNPs, we undertook filtration using an R-algorithm in combination with the diseases association Clinvar database. This approach led us to 12 combined diagnostic missense variants scattered on different chromosomes. Combined missense reduction after FDR filtration with a Cellrate of 0.75 generated two missense variants located on PCSK9 and GHR genes on chromosomes 1 and 5 and lastly, reduction variants after Filtration by spliced region bring us to a single SNP located on the PCSK9 gene.
Sampled-Data Stabilization for a Class of Fractional-Order Switched Nonlinear Systems

This article studies sampled-data stabilization for a class of fractional-order switched nonlinear systems (FOSNSs) with arbitrary switching. The feasibility of using a fuzzy-logic system (FLS) to approximate the fractional-order systems (FOSs) is proved. Using backstepping method, the fractional-order adaptive update laws and sampled-data controller for the discussed FOSNSs are designed based on the FLS. Under the proposed sampled-data control scheme, it is proved that solutions of the studied FOSNSs are semi-globally uniformly ultimately bounded (SGUUB). Two examples are given to verify the effectiveness of the proposed sampled-data control scheme.
Deflection and natural frequency of FGM plates with porosities by using Quasi-3D seven-unknowns higher-order shear deformation theory

— This paper investigates the bending and vibration of an FGM rectangular plate with porosities under two porosity distribution patterns including even and uneven. Based on Hamilton’s principle, the governing equations of motion of novel Quasi-3D theory with seven-unknown variables are derived. By employing the Navier technique, the analytical solutions are obtained to determine the displacements, and natural frequency of simply supported rectangular plates. The comparison between the present results and the available ones in the literature is conducted to verify the accuracy of the proposed model. Moreover, numerical results are presented to examine the effects of material and geometric parameters on the deflections and natural frequency of FGP rectangular plates.
Transdiagnostic clustering of self-schema from self-referential judgements identifies subtypes of healthy personality and depression

Introduction The heterogeneity of depressive and anxiety disorders complicates clinical management as it may account for differences in trajectory and treatment response. Self-schemas, which can be determined by Self-Referential Judgements (SRJs), are heterogeneous yet stable. SRJs have been used to characterize personality in the general population and shown to be prognostic in depressive and anxiety disorders. Methods In this study, we used SRJs from a Self-Referential Encoding Task (SRET) to identify clusters from a clinical sample of 119 patients recruited from the Institute of Mental Health presenting with depressive or anxiety symptoms and a non-clinical sample of 115 healthy adults. The generated clusters were examined in terms of most endorsed words, cross-sample correspondence, association with depressive symptoms and the Depressive Experiences Questionnaire and diagnostic category. Results We identify a 5-cluster solution in each sample and a 7-cluster solution in the combined sample. When perturbed, metrics such as optimum cluster number, criterion value, likelihood, DBI and CHI remained stable and cluster centers appeared stable when using BIC or ICL as criteria. Top endorsed words in clusters were meaningful across theoretical frameworks from personality, psychodynamic concepts of relatedness and self-definition, and valence in self-referential processing. The clinical clusters were labeled “Neurotic” (C1), “Extraverted” (C2), “Anxious to please” (C3), “Self-critical” (C4), “Conscientious” (C5). The non-clinical clusters were labeled “Self-confident” (N1), “Low endorsement” (N2), “Non-neurotic” (N3), “Neurotic” (N4), “High endorsement” (N5). The combined clusters were labeled “Self-confident” (NC1), “Externalising” (NC2), “Neurotic” (NC3), “Secure” (NC4), “Low endorsement” (NC5), “High endorsement” (NC6), “Self-critical” (NC7). Cluster differences were observed in endorsement of positive and negative words, latency biases, recall biases, depressive symptoms, frequency of depressive disorders and self-criticism. Discussion Overall, clusters endorsing more negative words tended to endorse fewer positive words, showed more negative biases in reaction time and negative recall bias, reported more severe depressive symptoms and a higher frequency of depressive disorders and more self-criticism in the clinical population. SRJ-based clustering represents a novel transdiagnostic framework for subgrouping patients with depressive and anxiety symptoms that may support the future translation of the science of self-referential processing, personality and psychodynamic concepts of self-definition to clinical applications.
Edaphic Macrofauna in Areas Cultivated with Irrigated Brassica Under No-Tillage System

Objective: Quantify and qualify the soil macrofauna present in areas cultivated with brassicas under the No-till system vegetable (NTSV) in different phases. Method/design/approach: The study was conducted in three different areas: 1-NTSV with one year (NTSV1), 2-NTSV with three years (NTSV3), 3-Native Forest (In natural regeneration for 20 years (NF20)); At depths: 0-10; 10-20 and 20-30 cm, with 5 repetitions. Litter was collected in an area of 0.50x0. 50 cm and soil samples were collected with an iron square measuring 25x25x30 cm in each plot, where the number of individuals (ind m-2) was quantified and the total richness and diversity and equitability indexes of the macrofauna were qualified. Result and conclusion: The management in areas NTSV1, NTSV3 and NF20 favored the development of the population of the Formicidae and Isoptera groups; The NTSV3 area at a depth of 20 to 30 cm provided the best conditions for the highest relative frequency of the Oligochaeta group. Research implications: The assessment of vertical distribution favored a broader knowledge of the macrofauna community in the systems; The adoption time of the one- or three-cycle no-tillage system did not affect the density and diversity of macrofauna. Originality/value: Most studies soil macrofauna have been carried out in areas under conventional or no-tillage of grains or in forests, few studies are carried out in areas with irrigated vegetables, where processes involving organic matter reach be three times faster, where the diversity of this macrofauna is higher and needs to be evaluated.
The variation of labile organic matter content following the application of industrial compost in maize production

This study examined the influence of compost application on alterations in soil organic matter levels and the content of labile organic matter fractions in soil during maize sowing. Due to the lack of organic fertilizers, industrial compost is being investigated as an alternative. The research aims to identify relevant soil quality and fertility indicators and their effects on agricultural production. Short-term compost application as an organic fertilizer may increase the content of labile organic matter fractions in the soil, especially in less fertile plots. The results indicate a significant influence of compost application on soil quality, confirming its role as a nutrient source and enhancer of soil physical, chemical, and biological properties. This highlights its potential for preserving soil quality and supporting agricultural production.
Simple Shear Mechanism to Revealing Geological Complexity of Geosite Assessment in the Bukit Duabelas National Park Jambi Province, Indonesia

Bukit Duabelas National Park (BDNP) Jambi Province is a national protected area that has geodiversity. BDNP forms northwest – southeast oriented, morphologically connected to the Barisan Mountains by the Bangko Basin. Digital elevation model observations show that the morphological orientation of these hills is surrounded by valleys and plains occupied by Paleogene-Neogene sedimentary rocks. The presence of Schist Terantam Formation provides interesting information about the exposed basement. This research uses remote sensing, field observations and stratigraphic analysis, as well as assessing geological complexity. The BDNP Territory is geologically influenced by geological structures such as faults and folds as a result of the simple shear deformation mechanism. Schist from the Terantam Formation and Granite and Pegmatite Intrusions are a consequence of simple shear mechanisms and tectonic orogenesis. Geological complexity of geosite assessment based on the criteria of petrological features, landscape, age of formation, fossil appear, tectonic basement, basement group, cultural diversity, other geological information. The proposed geosite is Terantam Inselberg which is composed of the Terantam Formation of Carboniferous and Jurassic-age of Granite and Pegmatite. The uniqueness of this proposed geosite is that the rocks exposed are the oldest basement rocks on the Sumatra Island. The landscape with Inselberg morphology, of course, is unique and is very rarely found in other areas, then the presence of ethnic groups from the Inner Child Tribe who inhabit the area characterizes cultural diversity. Comparing this proposed geosite with geosites of national and international value in the MJUGGp Territory, it can be concluded that the Terantam Inselberg Geosite is in between the two positions.
Aspects that constitute citizens’ trust in e-government - A review and framework development

The extent of citizens' trust in government determines the success or failure of e-government initiatives. Nevertheless, the idiosyncrasies of the concept and the broad spectrum of its approach still present relevant challenges. This work presents a systematic literature review on e-government trust while elaborating and summarizing a conceptual analysis of trust, introducing evaluation methods for government trust, and compiling relevant research on e-government trust and intentional behavior. A total of 26 key factors that constitute trust have been identified and classified into six categories: Government trust, Trust in Internet and technology (TiIT), Trust in e-government (TiEG), Personal Beliefs, Trustworthiness, and Trust of intermediary (ToI). The value added of this work consists of developing a conceptual framework of TiEG to provide a significant reference for future in-depth studies and research on e-government trust.
Effect of Anode Configuration on Ionization Characteristic in Miniature Ion Thrusters

In this study, a particle-in-cell model of a discharge chamber was developed to simulate the ionization characteristics of miniature ion thrusters by replacing the anode at the magnetic cusp with an insulator. The results show that replacing the anode with an insulator guides the electrons to move along the magnetic field lines to other cusps, which expands the radial range of the downstream electron group, produces a high-density plasma group over a larger radial range, and improves the plasma density in the discharge chamber. However, an insulator that is too long causes electrons to move toward the bottom cusp and gather upstream of the discharge chamber, weakening the ionization effect downstream. In summary, a better ionization effect can be obtained by choosing a reasonable insulator length, which can be used to regulate the degrees of freedom to improve the ionization performance.
Impact of Spiritual Intelligence on Job Satisfaction of Social Welfare Officers in Pakistan

The core purpose of the present research is to examine the spiritual intelligence and job satisfaction of Social Welfare Officers in Pakistan. Spiritual intelligence is one of the many types of intelligence that can be developed relatively independently. Spiritual intelligence is a way of knowing and connecting the inner life of the mind and soul with the outer life. Job satisfaction is a sense of accomplishment that a person gets from his work. It is a measure of workers' satisfaction with their jobs. It can be measured in terms of knowledge, motivation, and behavior. For this study, a sample of three hundred seventy-four Social Welfare Officers has been taken through a proportionate random sample technique from all the provinces of Pakistan, namely, Punjab, KPK, Sindh, Balochistan, ICT, GB, and AJK. A cross-sectional survey has been conducted and a well-structured questionnaire was used for the study. The Uni-variate, bi-variate, and multi-variate analyses have been performed to draw results and conclusions. The study findings show that spiritual intelligence, directly and indirectly, causes impacts on job satisfaction among Social Welfare Officers in Pakistan. The study findings also report that spiritual intelligence has positively contributed to Social Welfare Officer's pay and promotion, job security, workload status, relationship with co-workers, work environment, and feedback and support.
Vulnerability and Livelihoods on MT. Kilmanjaro

Livelihoods in Tanzania are constructed through a diverse range of practices. This paper draws on the Livelihoods Approach alongside the ‘double exposure’ framework in order to explore how households on Mount Kilimanjaro construct their livelihoods, and are constrained by the local and wider political economy. Specifically, it uses these frameworks in order to explore how people may in future adapt to an increasingly changing climate. Most households in the case study region are found to be highly reliant on the natural base of the area, and are liable to be highly vulnerable to future climate change. Means by which households can reduce vulnerability are explored, and the most feasible are found to be those that involve a reduction in reliance on direct production from nature. The paper concludes with a discussion of the appropriateness of the research framework, and argues that a dialectical approach may enable more appropriate questions to be posed and engaged with.
Sectarian conflict and sunni Islamic radicalization in Tripoli, Lebanon. (c2015)

Since the outbreak of the Syrian crisis in early 2011, Lebanon has seen a drastic deterioration in security: domestic supporters and opponents of the Syrian government have confronted each other in armed clashes and Lebanese groups also got involved in the war in Syria. The extremist groups that emerged in Syria also found supporters in Lebanon and a series of suicide bombings rocked civilian areas. Violent conflict affected several regions in Lebanon, but Tripoli, in particular, was called “little Syria” because it seemed to mirror the hostilities in the neighboring country. Many authors have pointed at the Syrian crisis spillover in order to explain the conflict in Tripoli. The thesis aims at explaining the mechanisms that led to polarization and radicalization in the Sunni community in Tripoli. It looks at the conflict through the lens of sectarian identity, explaining how the already existing political polarization turned to sectarian conflict in the presence of the catalysts provided by the Syrian crisis.
‘Serpent stones’: myth and medical application

Abstract ‘Serpent stones’ have been credited with medical efficacy since antiquity. Likely having their root in ancient traditions from India, accounts are now widespread across much of the world. Serpent stones are known by many names and descriptions of their appearance and medical uses are diverse; however, they commonly have a legendary association with serpents and are most frequently considered efficacious in the alexipharmic treatment of snakebite. This work presents and details five broad categories of serpent stone: a round white stone (thought to be extracted from the head of a dragon), a smooth lens-shaped black stone (purported to be taken from the head of a snake, but artificially manufactured of burnt bone or horn), ammonites (the fossilized shells of extinct cephalopods), glass or vitreous paste in the form of rings or beads, and serpentinite.