Miracle-dz/UniFAR-FTUs huggingface dataset:
FC2 stabilizes POR and suppresses ALA formation in the tetrapyrrole biosynthesis pathway

During photoperiodic growth, the light-dependent nature of chlorophyll synthesis in angiosperms necessitates robust control of the production of 5-aminolevulinic acid (ALA), the rate-limiting step in the initial stage of tetrapyrrole biosynthesis (TBS). We are interested in dissecting the post-translational control of this process, which suppresses ALA synthesis for chlorophyll synthesis in dark-grown plants. Using biochemical approaches for analysis of wild-type and mutant lines as well as complementation lines, we show that the heme-synthesizing ferrochelatase 2 (FC2) interacts with protochlorophyllide oxidoreductase and the regulator FLU which both promote the feedback-controlled suppression of ALA synthesis by inactivation of glutamyl-tRNA reductase, thus preventing excessive accumulation of potentially deleterious tetrapyrrole intermediates. Thereby FC2 stabilizes POR by physical interaction. When the interaction between FC2 and POR is perturbed, suppression of ALA synthesis is attenuated and photoreactive protochlorophyllide accumulates. FC2 is anchored in the thylakoid membrane via its membrane-spanning CAB (chlorophyll-a-binding) domain. FC2 is one of the two isoforms of ferrochelatase catalyzing the last step of heme synthesis. Although FC2 belongs to the heme-synthesizing branch of TBS, its interaction with POR potentiates the effects of the GluTR-inactivation complex on the chlorophyll-synthesizing branch, and ensures reciprocal control of chlorophyll and heme synthesis.
Inhibition of Microbial Methane Oxidation by 2-Chloro-6-Methylpyridine

Several pyridine derivatives including the pesticide nitrapyrin [2-chloro-6-(trichloromethyl) pyridine] are strong inhibitors of methane monooxygenase, a key enzyme of aerobic methane (CH4) oxidation. In this study we examined the effects of 2-chloro-6-methylpyridine (2C6MP) concentration on aerobic CH4 oxidation and the development of populations of putative methanotrophs in sediment from Old Woman Creek, a freshwater estuary in Huron Co., Ohio. Experimental systems were prepared in serum bottles containing minimal medium with a headspace containing 20% O2 and 10% CH4. The microcosms were spiked with 2C6MP to achieve concentrations of 0, 0.1, 1, or 10 mM and inoculated with sediment. When headspace CH4 concentrations decreased from 10% to < 2%, subsamples were taken for DNA extraction and sequencing of 16S rRNA gene amplicons. There was minimal effect of 2C6MP on CH4 oxidation at concentrations of 0.1, and 1 mM, but complete inhibition for > 20 months was observed at 10 mM. ANOSIM of weighted UniFrac distances between groups of triplicate samples supported a primary distinction of the inoculum relative to the enrichments (R=0.999) and a secondary distinction between bottles containing 2C6MP versus those without (R=0.464 [0.1 mM]; R=0.894 [1 mM]). The inoculum was dominated by members of the Proteobacteria (49.9±1.5%), and to a lesser extent by Bacteroidetes (8.8±0.2%), Acidobacteria (8.9±0.4%), and Verrucomicrobia (4.4±0.3%). In enrichments with or without 2C6MP, Proteobacteria expanded to comprise 65–70% of the total. In the absence of inhibitor, members of the Methylococcaceae and Methylophilaceae increased in relative abundance from < 0.1% of the inoculum to 8.5±1.0% and 13.4±2.3%, of the total community respectively. At both 0.1 and 1 mM concentrations of the inhibitor, the Methylococcaceae were much less abundant, representing 3.3±0.5% and 2.8±3.3% respectively. No inhibition of the Methylophilaceae was seen at the lower concentration of 2C6MP, but at the higher concentration this taxon was only 7.8±1.1% of the total. In contrast, members of the Crenotrichaceae, another group of methane oxidizers, increased in relative abundance with greater amounts of inhibitor, representing 8.6±3.6% of the total at 0.1 mM and 12.0±4.5% at 1 mM, compared to only 4.1±0.4% when no inhibitor was present. These results clearly show changes in the populations of putative aerobic methanotrophs relative to the amount of 2C6MP present.
Serotonin signaling in the enteric nervous system and connection to autism spectrum disorder: a translational mathematical model

While the causes of autism spectrum disorder (ASD) remain unclear, some studies have shown that serotonin-mediated effects on enteric nervous system (ENT) correlate with ASD-like behavioral phenotype in mice. Introduced here is a mathematical model of interactions between gut serotonin and its impact on ENT. The model was used to identify three key factors that affect ENT size, namely, serotonin production, its clearance, and its ability to act as a growth factor on ENT. The model was used to reproduce experimentally reported results from a mouse model by Margolis et al. (2016), which connected serotonin-mediated ENT hypoplasia to an ASD phenotype. The proposed mathematical model was used to scale the quantified relationship from mice to humans to show how the combination of these three factors can translate to a quantifiable metric that could potentially be correlated to ASD spectrum. A detailed discussion of how ENT hypoplasia could mechanistically affect CNS activity concludes this paper.
Identification of putative GATA3 regulatory elements and comparison of GATA3 distribution in cochleae of mice, rats, macaques, and humans

The transcription factor GATA3 plays a critical role in the development of neurons and sensory epithelia of the inner ear. In mouse cochleae, GATA3 is downregulated in certain supporting cells (SCs) and in type I spiral ganglion neurons (SGNs) after development. This reduction of GATA3 in SCs severely limits Atoh1-induced hair cell (HC) regeneration and suggests that a similar downregulation in human cochleae may be limiting for regenerative therapies. However, it is unknown whether GATA3 is similarly or differentially regulated in primates versus rodents. Using CAGE-seq data, we compared over 40 putative GATA3 regulatory elements across species and found both conserved and non-conserved sequences. To assess whether cochlear GATA3 distribution is similar or different between rodents and primates, we immunostained cochleae from mice, rats, macaques, and humans using antibodies raised against highly conserved GATA3 peptide sequences. GATA3 immunostaining in the organs of Corti from all four species revealed a large degree of conservation, where SCs medial and lateral to cochlear HCs exhibited robust nuclear GATA3 immunolabeling, but pillar and Deiters cells had significantly reduced GATA3 immunoreactivity. In all four species, GATA3 was expressed in a subset of SGNs that largely co-expressed peripherin suggesting they were type II SGNs. Only one difference emerged, wherein human cochlear inner hair cells were not GATA3 immunoreactive despite being so in the other species. Overall, the pattern of GATA3 expression in primates appears similar to rodents and reinforces the notion that ATOH1 mediated regenerative therapies may be limited by reduced GATA3 expression in adult SCs.
A CATALOG OF LOW-MASS STAR-FORMING CORES OBSERVED WITH SHARC-II AT 350 μm

We present a catalog of low-mass dense cores observed with the SHARC-II instrument at 350 μm. Our observations have an effective angular resolution of 10″, approximately 2.5 times higher than observations at the same wavelength obtained with the Herschel Space Observatory, albeit with lower sensitivity, especially to extended emission. The catalog includes 81 maps covering a total of 164 detected sources. For each detected source, we tabulate basic source properties including position, peak intensity, flux density in fixed apertures, and radius. We examine the uncertainties in the pointing model applied to all SHARC-II data and conservatively find that the model corrections are good to within ∼3″, approximately 1/3 of the SHARC-II beam. We examine the differences between two array scan modes and find that the instrument calibration, beam size, and beam shape are similar between the two modes. We also show that the same flux densities are measured when sources are observed in the two different modes, indicating that there are no systematic effects introduced into our catalog by utilizing two different scan patterns during the course of taking observations. We find a detection rate of 95% for protostellar cores but only 45% for starless cores, and demonstrate the existence of a SHARC-II detection bias against all but the most massive and compact starless cores. Finally, we discuss the improvements in protostellar classification enabled by these 350 μm observations.
e-MERLIN 21 cm constraints on the mass-loss rates of OB stars in Cyg OB2

We present e-MERLIN 21 cm (L-band) observations of single luminous OB stars in the Cygnus OB2 association, from the Cyg OB2 Radio Survey Legacy programme. The radio observations potentially offer the most straightforward, least model-dependent, determinations of mass-loss rates, and can be used to help resolve current discrepancies in mass-loss rates via clumped and structured hot star winds. We report here that the 21 cm flux densities of O3 to O6 supergiant and giant stars are less than ∼70 μJy. These fluxes may be translated to ‘smooth’ wind mass-loss upper limits of ∼4.4–4.8 × 10−6 M⊙ yr −1 for O3 supergiants and ≲2.9 × 10−6 M⊙ yr −1 for B0 to B1 supergiants. The first ever resolved 21 cm detections of the hypergiant (and luminous blue variable candidate) Cyg OB2 #12 are discussed; for multiple observations separated by 14 d, we detect an ∼69 per cent increase in its flux density. Our constraints on the upper limits for the mass-loss rates of evolved OB stars in Cyg OB2 support the model that the inner wind region close to the stellar surface (where Hα forms) is more clumped than the very extended geometric region sampled by our radio observations.
Sloppiness: Fundamental study, new formalism and its application in model assessment

Computational modelling of biological processes poses multiple challenges in each stage of the modelling exercise. Some significant challenges include identifiability, precisely estimating parameters from limited data, informative experiments and anisotropic sensitivity in the parameter space. One of these challenges’ crucial but inconspicuous sources is the possible presence of large regions in the parameter space over which model predictions are nearly identical. This property, known as sloppiness, has been reasonably well-addressed in the past decade, studying its possible impacts and remedies. However, certain critical unanswered questions concerning sloppiness, particularly related to its quantification and practical implications in various stages of system identification, still prevail. In this work, we systematically examine sloppiness at a fundamental level and formalise two new theoretical definitions of sloppiness. Using the proposed definitions, we establish a mathematical relationship between the parameter estimates’ precision and sloppiness in linear predictors. Further, we develop a novel computational method and a visual tool to assess the goodness of a model around a point in parameter space by identifying local structural identifiability and sloppiness and finding the most sensitive and least sensitive parameters for non-infinitesimal perturbations. We demonstrate the working of our method in benchmark systems biology models of various complexities. The pharmacokinetic HIV infection model analysis identified a new set of biologically relevant parameters that can be used to control the free virus in an active HIV infection. Author summary
Enhancing the tribological characteristics of Jatropha oil using graphene nanoflakes

Graphene is one of the contemporary nano-additives employed to boost the tribological characteristics of the lubricants. It has remarkable lubricating capabilities due to its peculiar properties and structure. This paper investigates the influence of graphene nanoflakes on the tribological properties of Jatropha oil (JO). Ball-on-flat tribological tests were conducted on a steel-steel tribo-pair with different concentrations (by wt.) of graphene mixed in the lubricant and the deviations with load and speed were noted. The wear scars were analyzed on Scanning Electron Microscope, Optical Microscope, and 3D Profilometer. The results indicated that the addition of graphene to JO substantially reduced the friction and wear rate between the tribo-pair. The best tribological performance was found at 0.5% graphene which reduced the coefficient of friction by 44% and wear rate by 43.7% as compared to base JO. This outcome was attributed to the formation of tribo-layer on the surface as characterized by Raman analysis which detected the presence of graphene nanoflakes in the wear scar. Finally, it was concluded that JO added with 0.5% graphene can be a promising lubricant option for industries in terms of energy-saving and environmental concerns. The graphene doped JO can be a viable substitute for depleting petroleum resources.
Searching for cosmological signatures of the Einstein equivalence principle breaking

Modifications of gravity generated by a multiplicative coupling of a scalar field to the electromagnetic Lagrangian lead to a breaking of the Einstein equivalence principle (EEPB), as well as to variations of fundamental constants. In these theoretical frameworks, deviations of standard values of the fine structure constant, $\mathrm{\ensuremath{\Delta}}\ensuremath{\alpha}/\ensuremath{\alpha}=\ensuremath{\phi}$, and of the cosmic distance duality relation, ${D}_{L}(1+z{)}^{\ensuremath{-}2}/{D}_{A}=\ensuremath{\eta}=1$, where ${D}_{L}$ and ${D}_{A}$ are the luminosity and angular diameter distances, respectively, are unequivocally linked. In this paper, we search for cosmological signatures of the EEPB by using angular diameter distance from galaxy clusters, obtained via their Sunyaev-Zel'dovich effect (SZE) and x-ray observations, and distance modulus of type Ia supernovae (SNe Ia). The crucial point here is that we take into account the dependence of the SZE/x-ray technique with $\ensuremath{\phi}$ and $\ensuremath{\eta}$. Our new results show no indication of the EEPB.
Preliminary Assessment of As-Built Design Characteristics for the Transformational Challenge Reactor

The Transformational Challenge Reactor design effort in 2021 included constructing a full-core mock-up of the reactor in-core components. This effort was undertaken to ascertain differences between the as-designed and as-built individual components and determine impacts of assembly of the as-built components into a full-scale core assembly. Through this effort, several deviations from as-designed components were observed. Some of these deviations were related to the additive manufacturing processes, and others were related to deviations in traditionally manufactured components. The tolerance stack-up of these minor deviations was evaluated and quantified. A new layered geometry capability in Shift (CAD + combinatorial) was used to model variations in the placement of YH moderator rods, and the effects of this variation on k eff and power distribution are analyzed in this paper. Bison was used to model the thermomechanical effect of contact between adjacent fuel elements.
Assistive Video Filters for People with Parkinson's Disease to Remove Tremors and Adjust Voice

COVID ushered in the widespread use of videoconferencing and it's here to stay. In virtual communication, we can alter everything from our appearance, voice and backgrounds. Most of these changes are fun gimmicks, but what if we could leverage these filtering technologies to a life-changing assistive technology? We propose the idea of developing assistive video filters for people with Parkinson's disease (PwP) that will remove involuntary tremors and smooth the stuttering in their voice. We surveyed 177 PwP and 107 people from the general public, and we personally interviewed 52 PwP as well as 3 health care professionals. We find overwhelming statistical evidence that these filters would fulfill a demonstrated communication need for PwP and that the general public also approves of a video filter that could assist with communication for PwP. To test the feasibility of our concept, we developed a filter prototype to remove physical tremors and tested it on two PwP. Although this paper focuses on PwP as a use case, we hope this work encourages others to ethically develop filtering technologies to help individuals with other movement disorders, eye-contact impairment and stuttering in computer-mediated conversations.
New Aspects of Geometrical Calculus With Invariants

In this paper, we show how to treat projective con gurations of points in an invariant way. By this, we mean that we do not want to take any basis, but compute directly with these geometric objects and with coe cients which are invariant by a change of basis. We show, in a rst part, how to de ne two operations \sums" and \intersection" in the exterior algebra ^E of a linear space E. These generalization of the Cayley algebra operators are achieved by extending the coe cients to the ring S(^E) (symmetric algebra of ^E). It allows us to transform two projective conditions on a point in a single one equivalent to the rst. In a second part, we apply these techniques to show how a special irreducible component (called the generic component) of the variety asssociated to a triangular projective con guration of points can be described by rules and characterized by the dimension of its projections. This leads to an algorithm which reduces an element of a \formal" space ^SF to zero if and only if the corresponding geometric property is true on the generic component. It can be used to test properties of non-degenerated con gurations as shown on examples, whatever the dimension of the ambiant space may be.
Lipid Profile and IL-1β Levels in Wistar Rats with Atherogenic Diet

: Background: Atherosclerosis is a pathological condition characterized by active, chronic, progressive inflammation and plaque in the artery walls. High cholesterol diet is one of the factors that can initiate inflammation and the production of proinflammatory cytokines such as IL-1β to cause atherosclerosis. This study aims to determine the value of lipid profile and IL-1β as a marker of atherosclerosis in male wistar rats fed atherogenic diet. As a positive control, a statin group atorvastatin 7.2 mg/kg, was used. Methods: The design of this research is a true post test control study laboratory experimental. Wistar male rats aged 10 weeks with body weight 150-200 grams were divided into 3 groups, normal, atherogenic (high cholesterol) and atorvastatin groups. Induction was carried out for 60 days and the administration of atorvastatin for 30 days. After 90 days of treatment, serum total cholesterol and IL-1β levels were measured. Results: There were significant differences in total cholesterol levels in the atherogenic group, normal group, and atorvastatin group (331.793 ±19.118 vs 113.864±6.615 vs. 144.132±35.214 mg/dL; P<0.001). Triglyceride levels showed significant differences in the atherogenic group, normal group, and atorvastatin group (133.335±20.080 vs. 65.38475±4.098 vs. 73.077±3.854 mg/dL; P<0.001). LDL cholesterol levels in the atherogenic group, normal group, and atorvastatin group showed significant differences (263,887±19,032 vs 22,369±17,1901 vs 68,192±24.947 mg/dL; P<0.001). HDL cholesterol levels also showed significant differences in the atherogenic group, the normal group, and the atorvastatin group (41.239±1.894 vs. 78.419±10.683 vs. 61.324±10.241 mg/dL; P<0.001). IL-1β showed significant differences in levels in the atherogenic group, normal group, and atorvastatin group (11,733±2,217 vs 4,348±0,273 vs 4,860±1,766 pg/mL; P<0.001). Pearson correlation showed that IL-1β was positively correlated with increasing levels of total cholesterol (r = 0.940; P<0.001), triglycerides (r = 0.910; P<0.001), and LDL cholesterol (r = 0.936; P<0.001). Conclusion: There were significant differences in lipid profiles in the atherogenic group against the normal control group and the atorvastatin group against the atherogenic group. The levels of IL-1β as a proinflammatory cytokine in atherosclerosis showed high values and were significantly different in the atherogenic group. Atorvastatin showed significantly lower IL-1β levels (P<0.05) compared to the atherogenic group. Based on the correlation test, total cholesterol, LDL, and triglyceride levels were significantly positively correlated with IL-1β secretion (P<0.05). So that in the future lipid profile and IL-1β can be used as markers of the severity of atherosclerosis.
Physics of Leap Second

The physical origin of the leap second is discussed in terms of the new gravity model. The calculated time shift of the earth rotation around the sun for one year amounts to $\displaystyle{\Delta T \simeq 0.621 s/ year}$. According to the data, the leap second correction for one year corresponds to $\Delta T \simeq 0.63 \pm 0.03 s/ year $, which is in perfect agreement with the prediction. This shows that the leap second is not originated from the rotation of the earth in its own axis. Instead, it is the same physics as the Mercury perihelion shift. We propose a novel dating method (Leap Second Dating) which enables to determine the construction date of some archaeological objects such as Stonehenge.
ThirdEye: Attention Maps for Safe Autonomous Driving Systems

Automated online recognition of unexpected conditions is an indispensable component of autonomous vehicles to ensure safety even in unknown and uncertain situations. In this paper we propose a runtime monitoring technique rooted in the attention maps computed by explainable artificial intelligence techniques. Our approach, implemented in a tool called ThirdEye, turns attention maps into confidence scores that are used to discriminate safe from unsafe driving behaviours. The intuition is that uncommon attention maps are associated with unexpected runtime conditions. In our empirical study, we evaluated the effectiveness of different configurations of ThirdEye at predicting simulation-based injected failures induced by both unknown conditions (adverse weather and lighting) and unsafe/uncertain conditions created with mutation testing. Results show that, overall, ThirdEye can predict 98% misbehaviours, up to three seconds in advance, outperforming a state-of-the-art failure predictor for autonomous vehicles.
Association between Smartphone Addiction and the Impact of Headaches Among Medical Students

— Smartphone addiction may be considered one of the most prevalent habits in Saudi Arabia, with users ranging between 41 and 44 million. This addiction has andebilitating impact, including increase in headaches. We aim to determine the relationship between smartphone addiction and headaches among medical students at King Abdulaziz University, Jeddah, Saudi Arabia. This cross-sectional study involved 429 medical students of the faculty of Medicine at King Abdulaziz University. Data were collected by an electronic self-reported questionnaire containing demographic questions and scales for smartphone addiction (SAS-SV), headache impact on participants’ lives (HIT-6), and headache assessment questions. Data were entered into Microsoft Excel and analyzed using SPSS version 21. Pearson’s chi-square was used to determine the significance of the relationships. The results showed that more than half of the participants were addicted to using smartphones.Statistical analysis found no significant relation between smartphone addiction and headache frequency throughout students’ lives. However, there is a significant relationship between headache impact and addiction. Furthermore, there is also asignificant relationship between avoidanceof activities and addiction.Smartphone addiction negatively affects medical students by increasing the impact of headaches on their lives, which is worse than addiction by nature.An alternative for the excessive use of smartphones, should be introduced, or proper counseling for students who overuse smartphones should be considered. These may decrease the impact of the headaches and increase students’ productivity.