Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Transmittance Estimation in Heterogeneous Participating Media Using Approximated Taylor Expansions

Evaluating the transmittance between two points along a ray is a key component in solving the light transport through heterogeneous participating media and entails computing an intractable exponential of the integrated medium's extinction coefficient. While algorithms for estimating this transmittance exist, there is a lack of theoretical knowledge about their behaviour, which also prevent new theoretically sound algorithms from being developed. For this purpose, we introduce a new class of unbiased transmittance estimators based on random sampling or truncation of a Taylor expansion of the exponential function. In contrast to classical tracking algorithms, these estimators are non-analogous to the physical light transport process and directly sample the underlying extinction function without performing incremental advancement. We present several versions of the new class of estimators, based on either importance sampling or Russian roulette to provide finite unbiased estimators of the infinite Taylor series expansion. We also show that the well known ratio tracking algorithm can be seen as a special case of the new class of estimators. Lastly, we conduct performance evaluations on both the central processing unit (CPU) and the graphics processing unit (GPU), and the results demonstrate that the new algorithms outperform traditional algorithms for heterogeneous mediums.
Combining machine learning algorithms for prediction of antidepressant treatment response

Predictors for unfavorable treatment outcome in major depressive disorder (MDD) applicable for treatment selection are still lacking. The database of a longitudinal multicenter study on 1079 acutely depressed patients, performed by the German research network on depression (GRND), allows supervised and unsupervised learning to further elucidate the interplay of clinical and psycho‐sociodemographic variables and their predictive impact on treatment outcome phenotypes.
Analysis of microhabitat characteristics at roost sites of Cerulean Warblers

Little information exists on songbird roosting habits and the types of habitats that songbirds select. To better understand a species’ habitat requirements, all aspects of its biology should be studied. The Cerulean Warbler (Setophaga cerulea, Wilson) is a Nearctic-Neotropical migrant that is a species of conservation concern across its range. It is one of the fastest declining species of wood-warbler (Parulidae) in North America. Since 2007, a breeding population of Cerulean Warblers has been monitored in southern Indiana, as part of the Hardwood Ecosystem Experiment. The Hardwood Ecosystem Experiment is a 100 yr project that studies the effects of different forest management practices on plant and animal communities. During the 2017 breeding season, 10 male Cerulean Warblers were tracked to roost locations. Roost sites selected by male Cerulean Warbler were characterized with less basal area, higher canopy cover, greater grapevine (Vitis spp., L.) presence, less shrubs, steeper slopes, and less white oak (Quercus alba, L.) abundance. With this new knowledge we can incorporate additional features of habitat in the formulation of a management plan for this declining species.
Lichen-forming fungi in postindustrial habitats involve alternative photobionts

ABSTRACT Mycobionts of many lichen genera appear to demonstrate strong selectivity in the choice of algal partner. The biological properties of a photobiont and its availability in an environment significantly determine the habitat requirements of lichens. Flexibility in photobiont choice extends the ecological amplitude of lichens; therefore, it may constitute an important adaptive strategy for colonization of extreme habitats. The photobiont inventory of the three epigeic lichens most resistant to soil pollution, i.e., Cladonia cariosa, C. rei, and the hyperaccumulator Diploschistes muscorum, was examined to verify whether and to what extent algal composition depends on the type of habitat and substrate enrichment with heavy metals. Photobionts Asterochloris and Trebouxia were identified in the studied lichen species; however, the presence of Trebouxia was directly related to anthropogenic sites with technogenic substrates, and the proportion of lichen specimens with these algae clearly depended on the level of heavy-metal soil pollution and the habitat type. The total number of algal haplotypes increased with increasing soil pollution, and the richness was associated more with soil pollution than with a given lichen species. Additionally, a large number of lichen individuals bearing multiple algal genotypes at polluted sites were recorded. Although Cladonia lichens were previously thought to be restricted to Asterochloris, they are able to start the relichenization process with Trebouxia under specific habitat conditions and to establish a stable association with these algae when colonization of disturbed sites takes place. Comparative analysis of the internal transcribed spacer (ITS) rDNA sequences revealed as many as 13 haplotypes of Trebouxia, and phylogenetic analysis grouped them into two different clades. Such a high level of genetic diversity indicates that Trebouxia is well adapted to metal pollution and could be an alternative photosynthetic partner for certain lichens, especially in polluted sites.
Proteomic Adaptation of Streptococcus pneumoniae to the Antimicrobial Peptide Human Beta Defensin 3 (hBD3) in Comparison to Other Cell Surface Stresses

The antimicrobial peptide human Beta defensin 3 (hBD3) is an essential part of the innate immune system and is involved in protection against respiratory pathogens by specifically permeabilizing bacterial membranes. The Gram-positive bacterium Streptococcus pneumoniae causes serious diseases including pneumonia, meningitis, and septicemia, despite being frequently exposed to human defense molecules, including hBD3 during colonization and infection. Thus, the question arises how pneumococci adapt to stress caused by antimicrobial peptides. We addressed this subject by analyzing the proteome of S. pneumoniae after treatment with hBD3 and compared our data with the proteomic changes induced by LL-37, another crucial antimicrobial peptide present in the human respiratory tract. As antimicrobial peptides usually cause membrane perturbations, the response to the membrane active cationic detergent cetyltrimethylammonium bromide (CTAB) was examined to assess the specificity of the pneumococcal response to antimicrobial peptides. In brief, hBD3 and LL-37 induce a similar response in pneumococci and especially, changes in proteins with annotated transporter and virulence function have been identified. However, LL-37 causes changes in the abundance of cell surface modification proteins that cannot be observed after treatment with hBD3. Interestingly, CTAB induces unique proteomic changes in S. pneumoniae. Though, the detergent seems to activate a two-component system that is also activated in response to antimicrobial peptide stress (TCS 05). Overall, our data represent a novel resource on pneumococcal adaptation to specific cell surface stresses on a functional level. This knowledge can potentially be used to develop strategies to circumvent pneumococcal resistance to antimicrobial peptides.
Effects of Phosphoethanolamine Supplementation on Mitochondrial Activity and Lipogenesis in a Caffeine Ingestion Caenorhabditis elegans Model

Caffeine intake is strongly linked to lipid metabolism. We previously reported the age-dependent physiological effects of caffeine intake in a Caenorhabditis elegans model. Since nutritional status can actively influence metabolism and overall health, in this study, we evaluated the effect of caffeine intake on lipid metabolism in adult-stage C. elegans. We found that, in C. elegans, fat storage and the level of phosphoethanolamine (PE) were significantly reduced with caffeine intake. In addition, mitochondrial activity decreased and mitochondrial morphology was disrupted, and the expression of oxidative stress response genes, hsp-6, gst-4, and daf-16, was induced by caffeine intake. Furthermore, the level of an energy metabolism sensor, phospho-AMP-activated protein kinase, was increased, whereas the expression of the sterol regulatory element binding protein gene and its target stearoyl-CoA desaturase genes, fat-5, -6, and -7, was decreased with caffeine intake. These findings suggest that caffeine intake causes mitochondrial dysfunction and reduces lipogenesis. Interestingly, these changes induced by caffeine intake were partially alleviated by PE supplementation, suggesting that the reduction in mitochondrial activity and lipogenesis is in part because of the low PE level, and proper dietary supplementation can improve organelle integrity.
SATMF Suppresses the Premature Senescence Phenotype of the ATM Loss-of-Function Mutant and Improves Its Fertility in Arabidopsis

Leaf senescence is the final stage of leaf development. It is accompanied by the remobilization of nutrients from senescent leaves to developing organs. The occurrence of senescence is the consequence of integrating intrinsic and environmental signals. DNA damage triggered by stresses has been regarded as one of the reasons for senescence. To prevent DNA damage, cells have evolved elaborate DNA repair machinery. The ataxia telangiectasia mutated (ATM) functions as the chief transducer of the double-strand breaks (DSBs) signal. Our previous study suggests that ATM functions in lifespan regulation in Arabidopsis. However, ATM regulatory mechanism on plant longevity remains unclear. Here, we performed chemical mutagenesis to identify the components involved in ATM-mediated longevity and obtained three dominant mutants satmf1~3, suppressor of atm in fertility, displaying delayed senescence and restored fertility in comparison with atm mutant. Molecular cloning and functional analysis of SATMF (suppressor of atm in fertility) will help to understand the underlying regulatory mechanism of ATM in plants, and shed light on developing new treatments for the disease Ataxia-telangiectasia.
Impact of mitochondrial epistatic interactions on evolution of different human subpopulations

Studies of human mitochondrial (mt) genome variation may be undertaken to investigate the human history and natural selection. By analyzing nucleotide co-occurrence over the entire human mt-genome, we have developed a network model to describe human evolutionary patterns. Using 7,424 unique polymorphic sites, we found evidence that mutation biases at second codon position and RNA genes were critical to producing continental-level heterogeneity among human subpopulations. Further, the analysis highlighted richer comutation regions of the mt-genome and thus provided evidence of epistasis. Specifically, a large portion of COX genes co-mutate in Asian and American populations whereas, in African, European and Oceanic populations, there was greater epistasis in hypervariable regions. Very interestingly, this study demonstrated hierarchical modularity as a crucial agent for a nucleotide co-occurrence network make-up. More profoundly, our ancestry-based nucleotide module analyses showed that nucleotide co-changes cluster preferentially in known mitochondrial haplogroups. It was also conceived that contemporary human mt-genome nucleotides most closely resembled the ancestral state and very few of them were ancestral-variants. Overall, these results demonstrated that subpopulation based factors such as intra-species evolution do exert selection on mitochondrial genes by favoring specific epistatic genetic variants.
Induction of resistance against pine wilt disease caused by Bursaphelenchus xylophilus using selected pine endophytic bacteria

Pine wilt disease (PWD) is the most destructive disease threatening pine worldwide. The disease is mainly caused by the pine wood nematode, Bursaphelenchus xylophilus, which is vectored by pine sawyer longhorn-beetles, Monochamus spp. This study aimed to select resistance-inducing pine endophytic bacteria for management of PWD. To set up a defence-related genes expression pattern for screening, four chemical inducers (salicylic acid, c-aminobutyric acid (GABA), b-aminobutyric acid and a-aminobutyric acid) were tested in vitro on pine calli and in vivo on pine seedlings. Treatment with GABA had the greatest reduction in PWD severity on pine seedlings. The pattern of defence-related gene expression in calli treated with GABA was used to select potential resistance-inducing bacterial strains. In addition, 92 bacterial strains were isolated from pine tree needles and stems and were tested for expression of defencerelated genes in pine calli in vitro. Among the tested strains, 13 showed a similar pattern to GABA treatment in at least four tested defence-related genes and were selected for the seedling assay. From the seedling assay, three bacterial strains (16YSM-E48, 16YSM-P180 and 16YSM-P39) showed significant reduction in PWD severity compared to the untreated control. Moreover, among the selected strains, cell-free culture supernatant of strain 16YSM-P180 significantly reduced PWD severity in inoculated pine seedlings. The selected strains were identified based on the 16S rRNA sequence as Pseudomonas putida 16YSM-E48, Curtobacterium pusillum 16YSM-P180 and Stenotrophomonas rhizophila 16YSM-P39. These selected strains are suggested as potential alternatives for management of PWD by induction of systemic resistance.
Assessing the efficacy of two new formulations of larvicide pyriproxyfen for the control of Aedes aegypti using dissemination stations in two sites of Rio de Janeiro city

BACKGROUND Aedes aegypti is the primary transmitter of several arbovirus with great impact in human health. Controlling vector mosquitoes is an essential and complex task. One promising control method is to use mosquitoes as a vehicle to disseminate tiny particles of juvenile-killing insecticides, such as pyriproxyfen (PPF), to breeding sites. OBJECTIVES We aimed to investigate the capacity of Ae. aegypti to disseminate two new formulations of PPF in two sites of Rio de Janeiro city for assessment of the efficacy of these products. METHODS Dissemination stations impregnated with powder and liquid new formulations of PPF were installed in two test sites. Ovitraps were used in the test sites and in a control site for monitoring the presence of Ae. aegypti throughout eggs collection. FINDINGS Entomological indices indicated that the new formulations of PPF were efficient in reducing eggs abundance. Liquid formulation performed better than powder formulation. Ready-to-use formulations of PPF can be quickly applied in the field and can be replaced after a few months. MAIN CONCLUSIONS New formulations of PPF associated with mosquito dissemination approach make a valuable vector control strategy, managing to cover places of difficult access for whatever reason. New formulations application requires less labour, being economically attractive.
Quality of life of patients with nasal bone fracture after closed reduction

Background Closed reduction is the standard treatment for nasal bone fractures, which are the most common type of facial bone fractures. We investigated the effect of closed reduction on quality of life. Methods The 15-dimensional health-related quality of life survey was administered to 120 patients who underwent closed reduction under general anesthesia for nasal bone fractures from February 2018 to December 2019, on both the day after surgery and 3 months after surgery. Three months postoperatively, the presence or absence of five nasal symptoms (nose obstruction, snoring, pain, nasal secretions, and aesthetic dissatisfaction) was also evaluated. Results The quality of life items that showed significant changes between immediately after surgery and 3 months postoperatively were breathing, sleeping, speech, excretion, and discomfort. Low scores were found at 3 months for breathing, sleeping, and distress. There were 31 patients (25.83%) with nose obstruction, 25 (20.83%) with snoring, 12 (10.00%), with pain, 11 (9.17%) with nasal secretions, and 29 (24.17%) with aesthetic dissatisfaction. Conclusion Closed reduction affected patients’ quality of life, although most aspects improved significantly after 3 months. However, it was not possible to rule out deterioration of quality of life due to complications and dissatisfaction after surgery.
Ab Initio Computational Chemical Studies of Molecular Processes and Decomposition in Ammonium Perchlorate

Abstract : Ammonium perchlorate is widely used as an oxidiser in composite propellants for rocket motors. Its decomposition is of interest in stability, sensitivity and combustion studies for rocket motor safety and performance analysis and prediction. This document presents some theoretical studies conducted to yield insights into the mechanisms and kinetics of ammonium perchlorate decomposition.
Changing Prevalence of Potential Mediators of Aminoquinoline, Antifolate, and Artemisinin Resistance Across Uganda.

BACKGROUND In Uganda artemether-lumefantrine is recommended for malaria treatment and sulfadoxine-pyrimethamine (SP) for chemoprevention during pregnancy, but drug resistance may limit efficacies. METHODS Genetic polymorphisms associated with sensitivities to key drugs were characterized in samples collected from 16 sites across Uganda in 2018 and 2019 by ligase detection reaction fluorescent microsphere, molecular inversion probe, dideoxy sequencing, and qPCR assays. RESULTS Considering transporter polymorphisms associated with resistance to aminoquinolines, the prevalence of PfCRT 76T decreased, but varied markedly between sites (0-48% in 2018; 0-22% in 2019); additional PfCRT polymorphisms and plasmepsin-2/3 amplifications associated elsewhere with resistance to piperaquine were not seen. For PfMDR1, in 2019 the 86Y mutation was absent at all sites, the 1246Y mutation had prevalence ≤20% at 14/16 sites, and gene amplification was not seen. Considering mutations associated with high level SP resistance, prevalences of PfDHFR 164L (up to 80%) and PfDHPS 581G (up to 67%) were high at multiple sites. Considering PfK13 propeller domain mutations associated with artemisinin delayed clearance, prevalence of the 469Y and 675V mutations has increased at multiple sites in northern Uganda (up to 23% and 40%, respectively). CONCLUSIONS We demonstrate concerning spread of mutations that may limit efficacies of key antimalarial drugs.
IPEM topical report: current molecular radiotherapy service provision and guidance on the implications of setting up a dosimetry service

Despite a growth in molecular radiotherapy treatment (MRT) and an increase in interest, centres still rarely perform MRT dosimetry. The aims of this report were to assess the main reasons why centres are not performing MRT dosimetry and provide advice on the resources required to set-up such a service. A survey based in the United Kingdom was developed to establish how many centres provide an MRT dosimetry service and the main reasons why it is not commonly performed. Twenty-eight per cent of the centres who responded to the survey performed some form of dosimetry, with 88% of those centres performing internal dosimetry. The survey showed that a ‘lack of clinical evidence’, a ‘lack of guidelines’ and ‘not current UK practice’ were the largest obstacles to setting up an MRT dosimetry service. More practical considerations, such as ‘lack of software’ and ‘lack of staff training/expertise’, were considered to be of lower significance by the respondents. Following on from the survey, this report gives an overview of the current guidelines, and the evidence available demonstrating the benefits of performing MRT dosimetry. The resources required to perform such techniques are detailed with reference to guidelines, training resources and currently available software. It is hoped that the information presented in this report will allow MRT dosimetry to be performed more frequently and in more centres, both in routine clinical practice and in multicentre trials. Such trials are required to harmonise dosimetry techniques between centres, build on the current evidence base, and provide the data necessary to establish the dose–response relationship for MRT.
Structural Insights into β-arrestin/CB1 Receptor Interaction: NMR and CD Studies on Model Peptides

Activation of the cannabinoid CB1 receptor induces different cellular signaling cascades through coupling to different effector proteins (G-proteins and β-arrestins), triggering numerous therapeutic effects. Conformational changes and rearrangements at the intracellular domain of this GPCR receptor that accompany ligand binding dictate the signaling pathways. The GPCR-binding interface for G proteins has been extensively studied, whereas β-arrestin/GPCR complexes are still poorly understood. To gain knowledge in this direction, we designed peptides that mimic the motifs involved in the putative interacting region: β-arrestin1 finger loop and the transmembrane helix 7-helix 8 (TMH7-H8) elbow located at the intracellular side of the CB1 receptor. According to circular dichroism and NMR data, these peptides form a native-like, helical conformation and interact with each other in aqueous solution, in the presence of trifluoroethanol, and using zwitterionic detergent micelles as membrane mimics. These results increase our understanding of the binding mode of β-arrestin and CB1 receptor and validate minimalist approaches to structurally comprehend complex protein systems.
Emotional distraction in working memory: Bayesian-based evidence of the equivalent effect of positive and neutral interference

ABSTRACT Evidence has shown that negative distracting stimuli are most difficult to control when we are focused in a relevant task, while positive and neutral distractors might be equally overcome. Still, recent meta-analytic evidence has pointed out that differences in the ability to cope with positive or neutral distractors may be difficult to detect in healthy people and in laboratory sets. Here we re-analyse memory performance in four already published working memory experiments in which affective and non-affective distractors were used. We focused on the positive versus neutral contrast, which did not reveal differences in the original analysis, with the aim of quantifying evidence for the null hypothesis using a Bayesian approach. Bayes factor (BF) estimates show substantial evidence in favour to the absence of differences in three out of four datasets. Further, BF aggregated from the four studies shows stronger evidence for the null hypothesis. Results from this analysis show that WM performance after positive and neutral interference can be considered equivalent, suggesting that positive distractors can be overcome to the same extent as neutral ones.