Miracle-dz/UniFAR-FTUs huggingface dataset:
Absorption of light in a single vertical nanowire and a nanowire array

Both a single III–V semiconductor nanowire and an array of such nanowires have shown promise for solar cell applications. However, the correspondence between the optical properties of the single nanowire and the nanowire array has not been studied. Here, we perform electromagnetic modeling of InP nanowires to study this relationship. We find that a single nanowire can show at an absorption peak, a remarkably high absorption cross-section that is more than 50 times the geometrical cross-section. With optimization of the diameter of the single nanowire, the short-circuit current density is 30 times higher than in a bulk solar cell. With such a strong absorption, we predict an apparent efficiency >500% for the single nanowire solar cell. In contrast, we show that an efficient nanowire array solar cell cannot rely on strong absorption just through the absorption peak. Instead, the nanowires need to be packed rather closely to enhance the absorption of the full solar spectrum. At the optimum diameter for the nanowire array, neighboring nanowires compete strongly for absorption of incident photons at the absorption peak, which limits the absorption per nanowire by a factor of 18. As a result, the single InP nanowire is optimized at a diameter of 110 nm while the nanowires in the array are optimized at a considerably larger diameter of 180 nm. Importantly, we show analytically the coupling efficiency of incident light into the fundamental HE11 guided mode and consecutive absorption of the mode in the nanowires. With that analysis, we explain that a single nanowire shows two different absorption pathways—one through coupling into the guided mode and another by coupling into the nanowire through the sidewall. This analytical analysis also shows at which period the neighboring nanowires in an array start to compete for absorption of incident photons.
Moderately Neutralizing Epitopes in Nonfunctional Regions Dominate the Antibody Response to Plasmodium falciparum EBA-140

Plasmodium falciparum erythrocyte-binding antigen 140 (EBA-140) plays a role in tight junction formation during parasite invasion of red blood cells and is a potential vaccine candidate for malaria. Individuals in areas where malaria is endemic possess EBA-140-specific antibodies, and individuals with high antibody titers to this protein have a lower rate of reinfection by parasites. ABSTRACT Plasmodium falciparum erythrocyte-binding antigen 140 (EBA-140) plays a role in tight junction formation during parasite invasion of red blood cells and is a potential vaccine candidate for malaria. Individuals in areas where malaria is endemic possess EBA-140-specific antibodies, and individuals with high antibody titers to this protein have a lower rate of reinfection by parasites. The red blood cell binding segment of EBA-140 is comprised of two Duffy-binding-like domains, called F1 and F2, that together create region II. The sialic acid-binding pocket of F1 is essential for binding, whereas the sialic acid-binding pocket in F2 appears dispensable. Here, we show that immunization of mice with the complete region II results in poorly neutralizing antibodies. In contrast, immunization of mice with the functionally relevant F1 domain of region II results in antibodies that confer a 2-fold increase in parasite neutralization compared to that of the F2 domain. Epitope mapping of diverse F1 and F2 monoclonal antibodies revealed that the functionally relevant F1 sialic acid-binding pocket is a privileged site inaccessible to antibodies, that the F2 sialic acid-binding pocket contains a nonneutralizing epitope, and that two additional epitopes reside in F1 on the opposite face from the sialic acid-binding pocket. These studies indicate that focusing the immune response to the functionally important F1 sialic acid binding pocket improves the protective immune response of EBA-140. These results have implications for improving future vaccine designs and emphasize the importance of structural vaccinology for malaria.
Dynamic-range compression and contrast enhancement in infrared imaging systems

Third-generation thermal cameras have high dynamic range (up to 14 bits) and collect images that are difficult to visualize because their contrast exceeds the range of traditional display devices. Thus, sophisticated techniques are required to adapt the recorded signal to the display, maintaining, and possibly improving, objects' visibility and image contrast. The problem has already been studied in relation to images acquired in the visible spectral region, while it has been scarcely investigated in the infrared. In this work, this latter subject is addressed, and a new method is presented that combines dynamic-range compression and contrast enhancement techniques to improve the visualization of infrared images. The proposed method is designed to meet typical requirements in infrared sensor applications. The performance is studied through experimental data and compared with that yielded by three well-established algorithms. Evaluation is performed through subjective analysis, assigning each algorithm a score on the basis of the average opinion of human observers. The results demonstrate the effectiveness of the proposed technique in terms of perceptibility of details, edge sharpness, robustness against the horizon effect, and presence of very warm objects.
IQGAP-related protein IqgC suppresses Ras signaling during large-scale endocytosis

Significance Dictyostelium WT amoebae live in soil and feed by phagocytosis. Macropinocytosis is largely suppressed in natural strains and cannot ensure sufficient nutrient uptake for survival. On the other hand, axenic laboratory strains have strongly up-regulated macropinocytosis and can grow in nutritive liquid media. This difference is attributed to the RasGAP protein NF1 that suppresses Ras signaling, thereby down-regulating macropinocytosis in WT amoebae. Since the gene encoding NF1 is inactive in axenic strains, other GAPs must be involved in the control of bulk fluid uptake. Here, we identify IqgC as a RasGAP responsible for regulation of large-scale endocytosis in the widely used axenic laboratory strain AX2 and show that it acts as a RasG-specific GAP to suppress RasG signaling. Macropinocytosis and phagocytosis are evolutionarily conserved forms of bulk endocytosis used by cells to ingest large volumes of fluid and solid particles, respectively. Both processes are regulated by Ras signaling, which is precisely controlled by mechanisms involving Ras GTPase activating proteins (RasGAPs) responsible for terminating Ras activity on early endosomes. While regulation of Ras signaling during large-scale endocytosis in WT Dictyostelium has been, for the most part, attributed to the Dictyostelium ortholog of human RasGAP NF1, in commonly used axenic laboratory strains, this gene is mutated and inactive. Moreover, none of the RasGAPs characterized so far have been implicated in the regulation of Ras signaling in large-scale endocytosis in axenic strains. In this study, we establish, using biochemical approaches and complementation assays in live cells, that Dictyostelium IQGAP-related protein IqgC interacts with active RasG and exhibits RasGAP activity toward this GTPase. Analyses of iqgC− and IqgC-overexpressing cells further revealed participation of this GAP in the regulation of both types of large-scale endocytosis and in cytokinesis. Moreover, given the localization of IqgC to phagosomes and, most prominently, to macropinosomes, we propose IqgC acting as a RasG-specific GAP in large-scale endocytosis. The data presented here functionally distinguish IqgC from other members of the Dictyostelium IQGAP family and call for repositioning of this genuine RasGAP outside of the IQGAP group.
Infertility‐related distress following cancer for women and men: A mixed method study

Infertility‐related distress is recognised to be a long‐term effect of cancer. There have been attempts to examine predictors of such distress, but there is inconsistency in the findings. This study examined the psychological impact of infertility‐related distress in women and men cancer survivors, across age group, parity, cancer type, time since diagnosis, and relationship context; and the association of distress with acceptance of illness and relationship satisfaction.
Mediterranean versus Atlantic monk parakeets Myiopsitta monachus: towards differentiated management at the European scale.

BACKGROUND The monk parakeet Myiopsitta monachus (Boddaert), native to South America, is an invasive species in several European countries, causing crop damage and potential negative impacts on wildlife. Only Spain and Great Britain have regulations to control monk parakeets, thus fast growth and spread of populations are likely to occur on a wide scale. The aims of this research are to update information on the distribution and population size of monk parakeets in Europe, assess whether differences in population growth or spread rate exist between populations, and provide recommendations to decision-makers. RESULTS Our study estimates that there are 23 758 monk parakeets in the wild, across 179 municipalities in eight European Union (EU) countries; 84% of these municipalities hold between 1 and 100 monk parakeets. All countries with a representative historical record are experiencing exponential growth of monk parakeets. Mediterranean countries are experiencing higher exponential growth, spread rate and faster colonization of new municipalities than Atlantic countries. CONCLUSIONS We recommend that EU Mediterranean countries consider declaration of the monk parakeet as invasive alien species of regional concern, and develop coordinated efforts to monitor and manage the species, taking advantage of the low population sizes in most municipalities. © 2019 Society of Chemical Industry.
Generate an Optimum Lightweight Legs Structure Design Based on Critical Posture in A-FLoW Humanoid Robot

Lightweight construction and energy efficiency play an important role in humanoid robot development. The application of computer-aided engineering (CAE) in the development process is one of the possibilities to achieve the appropriate reduction of the weight. This paper describes a method to generate an optimum lightweight legs structure design based on critical posture during walking locomotion in A-FLoW Humanoid robot.The criticalposture can be obtained from the highest forces and moments in each joint of the robot body during walking locomotion. From the finite element analysis (FEA) result can be realized leg structure design of A-FLoW humanoid robot with a maximum displacement value of 0.05 mmand weight reduction about 0.598 Kg from the thigh structure and a maximum displacement value of 0,13 mmand weight reduction about 0.57 kg from the shin structure.
The Kindlin Family of Adapter Proteins.

A half century of research and >75 000 publications have cemented the foundational role of integrins as major conduits of communication between the extracellular environment and the interior of cells. By serving as cell-surface receptors for numerous extracellular ligands, integrin α and β heterodimers are integrally involved in the physiological and pathophysiological responses of virtually all cell types. Excessive or suppressed ligand binding to integrins is implicated in many diseases, including cancer, inflammation, and cardiovascular diseases.
Structural and Functional Insights into PpgL, a Metal-Independent β-Propeller Gluconolactonase That Contributes to Pseudomonas aeruginosa Virulence

Biofilm formation is a critical determinant in the pathopoiesis of Pseudomonas aeruginosa. It could significantly increase bacterial resistance to drugs and host defense. ABSTRACT Biofilm formation is a critical determinant in the pathopoiesis of Pseudomonas aeruginosa. It could significantly increase bacterial resistance to drugs and host defense. Thus, inhibition of biofilm matrix production could be regarded as a promising attempt to prevent colonization of P. aeruginosa and the subsequent infection. PpgL, a periplasmic gluconolactonase, has been reported to be involved in P. aeruginosa quorum-sensing (QS) system regulation. However, the detailed function and catalysis mechanism remain elusive. Here, the crystal structure of PpgL is described in the current study, along with biochemical analysis, revealing that PpgL is a typical β-propeller enzyme with unique metal-independent lactone hydrolysis activity. Consequently, comparative analysis of seven-bladed propeller lactone-catalyzing enzymes and mutagenesis studies identify the critical sites which contribute to the diverse catalytic and substrate recognition functions. In addition, the reduced biofilm formation and attenuated invasion phenotype resulting from deletion of ppgL confirm the importance of PpgL in P. aeruginosa pathogenesis. These results suggest that PpgL is a potential target for developing new agents against the diseases caused by P. aeruginosa.
sRNA‐FISH: versatile fluorescent in situ detection of small RNAs in plants

Localization of mRNA and small RNAs (sRNAs) is important for understanding their function. Fluorescent in situ hybridization (FISH) has been used extensively in animal systems to study the localization and expression of sRNAs. However, current methods for fluorescent in situ detection of sRNA in plant tissues are less developed. Here we report a protocol (sRNA-FISH) for efficient fluorescent detection of sRNAs in plants. This protocol is suitable for application in diverse plant species and tissue types. The use of locked nucleic acid probes and antibodies conjugated with different fluorophores allows the detection of two sRNAs in the same sample. Using this method, we have successfully detected the co-localization of miR2275 and a 24-nucleotide phased small interfering RNA in maize anther tapetal and archesporial cells. We describe how to overcome the common problem of the wide range of autofluorescence in embedded plant tissue using linear spectral unmixing on a laser scanning confocal microscope. For highly autofluorescent samples, we show that multi-photon fluorescence excitation microscopy can be used to separate the target sRNA-FISH signal from background autofluorescence. In contrast to colorimetric in situ hybridization, sRNA-FISH signals can be imaged using super-resolution microscopy to examine the subcellular localization of sRNAs. We detected maize miR2275 by super-resolution structured illumination microscopy and direct stochastic optical reconstruction microscopy. In this study, we describe how we overcame the challenges of adapting FISH for imaging in plant tissue and provide a step-by-step sRNA-FISH protocol for studying sRNAs at the cellular and even subcellular level.
High‐flow nasal oxygen vs. standard flow‐rate facemask pre‐oxygenation in pregnant patients: a randomised physiological study

High‐flow nasal oxygen has been shown to provide effective pre‐oxygenation and prolong apnoeic time during intubation attempts in non‐pregnant patients. We aimed to compare pre‐oxygenation using high‐flow nasal oxygen (30–70 l.min−1 oxygen flow) via nasal prongs with standard 15 l.min−1 oxygen breathing via a tight‐fitting facemask. Forty healthy parturients were randomly allocated to these two groups, and furthermore each patient underwent the selected pre‐oxygenation method with both 3‐min tidal volume breathing and 30s tidal breathing followed by eight vital capacity breaths. With 3‐min tidal volume breathing, the respective estimated marginal means for high‐flow nasal oxygen and standard flow rate facemask pre‐oxygenation were 87.4% (95%CI 85.5–89.2%) and 91.0% (95%CI 89.3–92.7%), p = 0.02; with eight vital capacity breaths the estimated marginal means were 85.9% (95%CI 84.1–87.7%) and 91.8% (95%CI 90.1–93.4%, p < 0.0001). Furthermore, high‐flow nasal oxygen did not reliably achieve a mean end‐tidal oxygen concentration ≥ 90% compared with the standard flow rate facemask. In this physiological study, high‐flow nasal oxygen pre‐oxygenation performed worse than standard flow rate facemask pre‐oxygenation in healthy term parturients.
Bariatric Surgery Reduces Elevated Urinary Mitochondrial DNA Copy Number in Patients With Obesity.

OBJECTIVE Obesity is an independent risk factor for chronic kidney disease. Recently, urinary mitochondrial DNA (mtDNA) has been used as a surrogate marker of mitochondrial damage in various kidney diseases. However, there are no data regarding its use in patients with obesity or the change in urinary mtDNA copy number after surgery. DESIGN We prospectively recruited age- and sex-matched healthy volunteers and patients with obesity (n = 22 in each group: nine men and 13 women). The copy number of urinary and serum mtDNA nicotinamide adenine dinucleotide dehydrogenase subunit-1 (mtND-1) and cytochrome-c oxidase 3 (mtCOX-3) was measured using quantitative PCR. We measured urinary mtDNA and body weight and carried out laboratory tests, 6 months after surgery. RESULTS Urinary mtND-1 copy number was significantly higher in the obese group than in healthy volunteers. However, urinary mtCOX-3 and serum ND-1 copy numbers in the obese group did not differ from that in the healthy volunteers. When patients with obesity were divided into two groups, according to their baseline mtND-1 copy number, bariatric surgery reduced the mtND-1 copy number (P = 0.006) in the high baseline mtDNA copy-number group. The change in urinary mtND-1 copy number was correlated with a change in urinary albumin (r = 0.478, P = 0.025). CONCLUSIONS Obesity is associated with elevated urinary mtND-1 copy number. Bariatric surgery reduces the elevated urinary mtND-1 copy number in patients with obesity. This suggests that bariatric surgery could attenuate mitochondrial damage in the kidney cells of patients with obesity.
The metabolome as a biomarker of mortality risk in the common marmoset

Recently, the common marmoset has been proposed as a non‐human primate model of aging. Their short lifespan coupled with pathologies that are similar to humans make them an ideal model to understand the genetic, metabolic, and environmental factors that influence aging and longevity. However, many of the underlying physiological changes that occur with age in the marmoset are unknown. Here, we attempt to determine if individual metabolites are predictive of future death and to recapitulate past metabolomic results after a change in environment (move across the country) was imposed on a colony of marmosets. We first determined that low levels of tryptophan metabolism metabolites were associated with risk of death in a 2‐year follow‐up in the animals, suggesting these metabolites may be used as future biomarkers of mortality. We also discovered that betaine metabolism and methionine metabolism are associated with aging regardless of environment for the animals, or of metabolomic assay technique. These two metabolic pathways are therefore of particular interest to examine as future targets for health and lifespan extending interventions. Many of the pathways associated with age in our first study of marmoset metabolomics were not found to have significant age effects in our second study, suggesting more work is needed to understand the reproducibility of large scale metabolomic studies in mammalian models. Overall, we were able to show that while several metabolomics markers show promise in understanding health and lifespan relationships with aging, it is possible that choice of technique for assay and reproducibility in these types of studies are still issues that need to be examined further.
LUBAC determines chemotherapy resistance in squamous cell lung cancer

Lung squamous cell carcinoma (LSCC) and adenocarcinoma (LADC) are the most common lung cancer subtypes. Molecular targeted treatments have improved LADC patient survival but are largely ineffective in LSCC. The tumor suppressor FBW7 is commonly mutated or down-regulated in human LSCC, and oncogenic KRasG12D activation combined with Fbxw7 inactivation in mice (KF model) caused both LSCC and LADC. Lineage-tracing experiments showed that CC10+, but not basal, cells are the cells of origin of LSCC in KF mice. KF LSCC tumors recapitulated human LSCC resistance to cisplatin-based chemotherapy, and we identified LUBAC-mediated NF-&kgr;B signaling as a determinant of chemotherapy resistance in human and mouse. Inhibition of NF-&kgr;B activation using TAK1 or LUBAC inhibitors resensitized LSCC tumors to cisplatin, suggesting a future avenue for LSCC patient treatment.
Repeat‐associated non‐AUG translation in C9orf72‐ALS/FTD is driven by neuronal excitation and stress

Nucleotide repeat expansions (NREs) are prevalent mutations in a multitude of neurodegenerative diseases. Repeat‐associated non‐AUG (RAN) translation of these repeat regions produces mono or dipeptides that contribute to the pathogenesis of these diseases. However, the mechanisms and drivers of RAN translation are not well understood. Here we analyzed whether different cellular stressors promote RAN translation of dipeptide repeats (DPRs) associated with the G4C2 hexanucleotide expansions in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We found that activating glutamate receptors or optogenetically increasing neuronal activity by repetitive trains of depolarization induced DPR formation in primary cortical neurons and patient derived spinal motor neurons. Increases in the integrated stress response (ISR) were concomitant with increased RAN translation of DPRs, both in neurons and different cell lines. Targeting phosphorylated‐PERK and the phosphorylated‐eif2α complex reduces DPR levels revealing a potential therapeutic strategy to attenuate DPR‐dependent disease pathogenesis in NRE‐linked diseases.
Cognitive impairment in substance use disorders

Cognitive impairments in substance use disorders have been extensively researched, especially since the advent of cognitive and computational neuroscience and neuroimaging methods in the last 20 years. Conceptually, altered cognitive function can be viewed as a hallmark feature of substance use disorders, with documented alterations in the well-known “executive” domains of attention, inhibition/regulation, working memory, and decision-making. Poor cognitive (sometimes referred to as “top-down”) regulation of downstream motivational processes—whether appetitive (reward, incentive salience) or aversive (stress, negative affect)—is recognized as a fundamental impairment in addiction and a potentially important target for intervention. As addressed in this special issue, cognitive impairment is a transdiagnostic domain; thus, advances in the characterization and treatment of cognitive dysfunction in substance use disorders could have benefit across multiple psychiatric disorders. Toward this general goal, we summarize current findings in the abovementioned cognitive domains of substance use disorders, while suggesting a potentially useful expansion to include processes that both precede (precognition) and supersede (social cognition) what is usually thought of as strictly cognition. These additional two areas have received relatively less attention but phenomenologically and otherwise are important features of substance use disorders. The review concludes with suggestions for research and potential therapeutic targeting of both the familiar and this more comprehensive version of cognitive domains related to substance use disorders.