Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-shot photon and electric field diagnostics using the linear array detector KALYPSO with MHz-range readout

A bottleneck for the investigation of electron beam dynamics in ring accelerators is a fast detection scheme coping with their high repetition rates in the MHz range. For example, at KARA (KArlsruhe Research Accelerator), the electron storage ring at the Karlsruhe Institute of Technology (KIT) in Germany, we showed that electro-optical methods enable single-shot detection of longitudinal electron bunch profiles by imprinting them onto chirped laser pulses. However, commercial cameras required to detect the spectra are typically limited to hundreds of kHz in readout speed. To tackle these challenges, we developed KALYPSO (KArlsruhe Linear array detector for MHz-rePetition rate SpectrOscopy), a linear detector array with a data acquisition system (DAQ) allowing high data-rates over long time scales. Due to a modular approach, various sensors (InGaAs and Si) can be used, so that KALYPSO can be adapted to different experiments with spectral regimes ranging from near-ultraviolet (NUV) to near-infrared (NIR). In this talk, we present recent results on studies of longitudinal and horizontal bunch profiles using KALYPSO. As an outlook, we give another example for MHz-range readout using KALYPSO, namely horizontal bunch profile diagnostics measuring the radiation emitted from a dispersive section in a storage ring. At the KARA visible light diagnostics (VLD) port the emitted radiation above 400 nm was previously recorded with a fast-gated camera. Here, limitations are the repetition rate in combination with the huge number of cycles during continuous measurements. To overcome these limitations, KALYPSO can repleace the fast-gated camera. Furthermore, due to the easy implementation of KALYPSO, we envision numerous applications for table-top experiments as well as for large-scale facilies.
Trajectories of kidney function and risk of mortality

Abstract Background We aimed to identify patterns within the rate of kidney function decline, determinants of these patterns and their association with all-cause mortality risk in the general population. Methods Participants aged ≥ 45 years with at least one assessment of creatinine-based estimated glomerular filtration rate (eGFR) taken between 1997 and 2018 were selected from a population-based cohort study. Analyses were performed using several distinct latent class trajectory modelling methods. Cumulative incidences were calculated with 45 years of age as the starting point. Results In 12 062 participants (85 922 eGFR assessments, mean age 67.0 years, 58.7% women, median follow-up 9.6 years), four trajectories of eGFR change with age were identified: slow eGFR decline [rate of change in mL/min/1.73 m2 per year (RC), –0.9; 95% CI, –0.9 to –0.9; reference group], intermediate eGFR decline (RC, –2.5; 95% CI, –2.7 to –2.5) and fast eGFR decline (RC, –4.3; 95% CI, –4.4 to –4.1), and an increase/stable eGFR (RC, 0.3; 95% CI, 0.3 to 0.4). Women were more likely to have an increase/stable eGFR [odds ratio (OR), 1.94; 95% CI, 1.53 to 2.46] whereas men were more likely to have a fast eGFR decline (OR, 1.86; 95% CI, 1.33 to 2.60). Participants with diabetes, cardiovascular disease (CVD) or hypertension were more likely to have an intermediate or fast eGFR decline. All-cause mortality risks (cumulative incidence at age of 70 years) were 32.3% (95% CI, 21.4 to 47.9, slow eGFR decline), 6.7% (95% CI, 3.5 to 12.4, intermediate eGFR decline), 68.8% (95% CI, 44.4 to 87.8, fast eGFR decline) and 9.5% (95% CI, 5.5 to 15.7, increase/stable eGFR). Conclusion Sex, hypertension, diabetes and CVD were identified as trajectory membership determinants. Having fast eGFR decline was associated with the highest risk of all-cause mortality, highlighting the need for extensive monitoring and prevention of kidney function decline in individuals at risk of having fast eGFR decline.
Outcomes of 4-factor Prothrombin Complex Concentrate in Patients With Liver Disease and Nonvitamin K Antagonist-Related Coagulopathy: A Retrospective Study

The administration of 4-factor prothrombin complex concentrate (4F-PCC) has expanded beyond its Food and Drug Administration (FDA)-approved indication for the emergent reversal of vitamin K antagonists (VKAs). Therefore, this study aimed to evaluate the risks and benefits associated with the expanded use of 4F-PCC. We conducted a single-center retrospective review of 4F-PCC administrations at our university hospital. Of the 159 patients who received 4F-PCC, 76% (n = 121) and 24% (n = 38) received it for the FDA-approved indication in the vitamin K-related coagulopathy (VKA) group and for expanded use in the nonvitamin K-related coagulopathy (nVKA) group, respectively. The expanded use of 4F-PCC was associated with a less robust reduction in the international normalized ratio (INR) (INR of −0.7 ± 1.3 vs INR of −1.6 ± 1.8, P = .002), and fewer patients in the nVKA group achieved a postadministration INR of less than1.5 (11% vs 79%, P = .001) than those in the VKA group. Furthermore, the 30-day mortality rate was significantly higher in the nVKA cohort than in the VKA cohort (42% vs 20%, P = .04). Notably, based on our data, underlying differences in the patient’s comorbidities, particularly advanced liver disease, may have contributed to the observed outcome variations, including mortality rate. Therefore, factors, including comorbidities and the underlying etiology of coagulopathy, should be considered when deciding on the expanded use of 4F-PCC. Further research is needed to better understand the potential risks and benefits of 4F-PCC in expanded use scenarios, and the clinical decision to use 4F-PCC outside its FDA-approved indication should be made carefully, considering this information.
The added value of ferritin levels and genetic markers for the prediction of haemoglobin deferral

On‐site haemoglobin deferral for blood donors is sometimes necessary for donor health but demotivating for donors and inefficient for the blood bank. Deferral rates could be reduced by accurately predicting donors' haemoglobin status before they visit the blood bank. Although such predictive models have been published, there is ample room for improvement in predictive performance. We aim to assess the added value of ferritin levels or genetic markers as predictor variables in haemoglobin deferral prediction models.
Effectiveness of Violence Prevention Interventions: Umbrella Review of Research in the General Population

To address the societal harms of violence, many violence prevention interventions have been developed, tested, and implemented in the general population. These have been reported in systematic reviews and meta-analyses, which have typically focused on one type of intervention or outcome. We aimed to provide a comprehensive overview of the current evidence regarding the effectiveness of different psychosocial interventions in reducing all forms of violence toward others. We have conducted an umbrella review of previous meta-analyses using standard approaches and converted findings on effectiveness into odds ratios. We tested for the underlying quality of the meta-analytic evidence by examining heterogeneity, excess statistical significance, prediction intervals, and small study effects. We identified 16 meta-analyses, including nine investigating psychosocial interventions, and five legislative and policy changes. Most meta-analyses reported positive effects of tested interventions. The strongest effects were found for sports-based initiatives, and the weakest for general population programs aimed at early childhood, youth development, and reducing sexual assault perpetration by men. Legislative changes had varying effectiveness. We conclude that simple, scalable, and cost-efficient programs, such as sport-based initiatives, have the clearest empirical support as population-based approaches to violence prevention.
Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits

Understanding differences in adipose gene expression between individuals with different levels of clinical traits may reveal the genes and mechanisms leading to cardiometabolic diseases. However, adipose is a heterogeneous tissue. To account for cell-type heterogeneity, we estimated cell-type proportions in 859 subcutaneous adipose tissue samples with bulk RNA sequencing (RNA-seq) using a reference single-nuclear RNA-seq data set. Cell-type proportions were associated with cardiometabolic traits; for example, higher macrophage and adipocyte proportions were associated with higher and lower BMI, respectively. We evaluated cell-type proportions and BMI as covariates in tests of association between >25,000 gene expression levels and 22 cardiometabolic traits. For >95% of genes, the optimal, or best-fit, models included BMI as a covariate, and for 79% of associations, the optimal models also included cell type. After adjusting for the optimal covariates, we identified 2,664 significant associations (P ≤ 2e−6) for 1,252 genes and 14 traits. Among genes proposed to affect cardiometabolic traits based on colocalized genome-wide association study and adipose expression quantitative trait locus signals, 25 showed a corresponding association between trait and gene expression levels. Overall, these results suggest the importance of modeling cell-type proportion when identifying gene expression associations with cardiometabolic traits. Article Highlights Our goal was to create a resource of trait-gene expression associations on a genome-wide scale across several cardiometabolic traits that accounts for cell-type heterogeneity. We aimed to determine whether cell-type composition affects trait-gene associations. We found that adjusting for both BMI and cell-type proportion is the best-fitting model for most trait-gene expression associations in adipose tissue. We identified 2,664 significant associations for 1,252 genes and 14 traits using a linear model that accounts for cell-type composition and BMI. Our findings suggest that cell-type composition should be considered when assessing the association between adipose gene expression and cardiometabolic traits.
Changes of Optic Disc and Macular Vessel Perfusion Density in Primary Angle Closure Glaucoma: A Quantitative Study Using Optical Coherence Tomography Angiograph

Introduction: This study aims to investigate the changes of retinal vascular system in primary angle closure glaucoma (PACG) and acute primary angle closure (APAC) by optical coherence tomography (OCT) angiograph (OCTA) and to evaluate the diagnostic ability of changes of vessel density (VD) in different sectors and layers of optic disc and macular area in APAC and PACG. Methods: In this cross-sectional, observational study, 21 APAC patients (22 eyes) and 21 PACG patients (27 eyes) along with 17 healthy people were enrolled from August 2018 to March 2019. Optic disc region and macular region were imaged using swept-source OCTA system. VD of the macular region was quantified by Image J (1.52a, USA) and Matlab 2018a. The circumpapillary retinal nerve fiber layer (cpRNFL) thickness and ganglion cell complex thickness were obtained by spectral-domain OCT. Results: Compared with the healthy group, the cpRNFL thickness in superior sector was thicker in the APAC group, and this area had the most diffuse microvascular dropout as well. The difference in the macular superficial capillary plexus (SCP) VD between APAC and the control group was not statistically significant. The area under the ROC curves (AUC) of the total optic disc VD in the radial peripapillary capillary (RPC) layer was higher than the AUC of the papillary VD in the optic nerve head (ONH) layer. Compared to the control group, the total optic disc VD, peripapillary VD, and each quadrant of peripapillary VD were decreased in PACG (p < 0.01). In PACG macular region, SCP VD, and deep capillary plexus (DCP) VD, parafovea VD (except temporal sectors) decreased (p < 0.01). The PACG eyes had a greater decrease percentage of VD in total ONH than total macula. The diagnostic value of the VD in the ONH layer and the RPC layer was similar. The diagnostic value of the SCP VD in the macula was greater than the DCP VD in the macula. The AUC was no significant difference between cpRNFL thickness and the total optic disc VD AUC. Conclusion: Elevated intraocular pressure preferentially affects vascular perfusion in the optic disc region more than the macular region in APAC and PACG. In the APAC eyes, there was a perfusion defect in the optic disc region and an increase in RNFL thickness. In this study, the OCTA vascular parameters have similar performance to the OCT structural parameters for glaucoma diagnosis in PACG.
Temporal dynamics and genomic programming of plasma cell fates

Affinity-matured plasma cells (PCs) of varying lifespans are generated through a germinal center (GC) response. The developmental dynamics and genomic programs of antigen-specific PC precursors remain to be elucidated. Using a model antigen, we demonstrate biphasic generation of PC precursors, with those generating long-lived bone marrow PCs preferentially produced in the late phase of GC response. Clonal tracing using scRNA-seq+BCR-seq in spleen and bone marrow compartments, coupled with adoptive transfer experiments, reveal a novel PC transition state that gives rise to functionally competent PC precursors. The latter undergo clonal expansion, dependent on inducible expression of TIGIT. We propose a model for the proliferation and programming of precursors of long-lived PCs, based on extended antigen encounters followed by reduced antigen availability.
Profitability of Vanilla Intercropping in Pine Forests in West Java, Indonesia

Intercropping in timber plantations is a common practice in Indonesia. However, intercropping in steep slope areas causes severe soil erosion. Therefore, the local government in West Java has implemented a new policy prohibiting intercropping in steep slope areas. A timber plantation company which restored the Community-based Forest Management Program recommended that farmers grow vanilla in steep areas in West Java. However, the profitability of vanilla cultivation has not been studied. Therefore, interviews with farmers and managers were conducted in the Sumedang District, West Java. The profitability of intercropping with vanilla was slightly higher than that of intercropping with either cash crops or banana. The income level of the farmers was positively correlated with the size of the vanilla-intercropped areas, but negatively correlated with the size of paddy fields. The present study showed that vanilla cultivation is effective for increasing the income level of the farmers who own few or do not own paddy fields.
Removal of site effects and enhancement of signal using dual projection independent component analysis for pooling multi‐site MRI data

Combining magnetic resonance imaging (MRI) data from multi‐site studies is a popular approach for constructing larger datasets to greatly enhance the reliability and reproducibility of neuroscience research. However, the scanner/site variability is a significant confound that complicates the interpretation of the results, so effective and complete removal of the scanner/site variability is necessary to realise the full advantages of pooling multi‐site datasets. Independent component analysis (ICA) and general linear model (GLM) based harmonisation methods are the two primary methods used to eliminate scanner/site effects. Unfortunately, there are challenges with both ICA‐based and GLM‐based harmonisation methods to remove site effects completely when the signals of interest and scanner/site effects‐related variables are correlated, which may occur in neuroscience studies. In this study, we propose an effective and powerful harmonisation strategy that implements dual projection (DP) theory based on ICA to remove the scanner/site effects more completely. This method can separate the signal effects correlated with site variables from the identified site effects for removal without losing signals of interest. Both simulations and vivo structural MRI datasets, including a dataset from Autism Brain Imaging Data Exchange II and a travelling subject dataset from the Strategic Research Program for Brain Sciences, were used to test the performance of a DP‐based ICA harmonisation method. Results show that DP‐based ICA harmonisation has superior performance for removing site effects and enhancing the sensitivity to detect signals of interest as compared with GLM‐based and conventional ICA harmonisation methods.
Chloramphenicol reduces phage resistance evolution by suppressing bacterial cell surface mutants

Bacteriophages infect Gram-negative bacteria by attaching to molecules present on the bacterial outer membrane, often lipopolysaccharides (LPS). Modification of the LPS can lead to phage resistance. LPS modifications also impact antibiotic susceptibility, allowing for phage-antibiotic synergism. The mechanism for these synergistic interactions is unclear. Here, we show that antibiotics affect the evolution of phage resistance using phage ΦX174 and Escherichia coli C wildtype. We use a collection of E. coli C LPS mutants, each of which is resistant to ΦX174, and has either a “rough” or “deep-rough” LPS phenotype. Growth of deep rough mutants is inhibited at subinhibitory chloramphenicol concentrations. In contrast, gentamicin has no major effect on growth. Treating E. coli C wildtype with ΦX174 and chloramphenicol eliminates deep rough mutants, and reduces phage resistance evolution. Our results show that differential survival of phage resistant mutants with antibiotics explains phage-antibiotic synergism in our model system.
Effects of Elevated Intraocular Pressure on Retinal Ganglion Cell Density and Expression and Interaction of Retinal Aquaporin 9 and Monocarboxylate Transporters

Introduction: Astrocyte-to-neuron lactate shuttle (ANLS) plays an important role in the energy metabolism of neurons, including retinal ganglion cells (RGCs). Aquaporin 9 (AQP9), which is an aquaglyceroporin that can transport lactate, may be involved in ANLS together with monocarboxylate transporters (MCTs) to maintain RGC function and survival. This study aimed to investigate the impact of elevated intraocular pressure (IOP) on AQP9-MCT interaction and RGC survival. Methods: IOP was elevated in Aqp9 knock-out (KO) mice and wild-type (WT) littermates by anterior chamber microbead injection. RGC density was measured by TUBB3 immunostaining on retinal flat mounts. Immunolabeling, immunoblot, and immunoprecipitation were conducted to identify and quantitate expressions of AQP9, MCT1, MCT2, and MCT4 in whole retinas and ganglion cell layer (GCL). Results: Aqp9 KO and WT mice had similar RGC density at baseline. Microbead injection increased cumulative IOP by approximately 32% up to 4 weeks, resulting in RGC density loss of 42% and 34% in WT and Aqp9 KO mice, respectively, with no statistical difference. In the retina of WT mice, elevated IOP decreased the amount of AQP9, MCT1, and MCT2 protein and changed the AQP9 immunoreactivity and reduced MCT1 and MCT2 immunoreactivities in GCL. Meanwhile, it decreased MCT1 and increased MCT2 that interact with AQP9, without affecting MCT4 expression. Aqp9 gene deletion increased baseline MCT2 expression in the GCL and counteracted IOP elevation regarding MCT1 and MCT2 expressions. Conclusion: The compensatory upregulation of MCT1 and MCT2 with Aqp9 gene deletion and ocular hypertension may reflect the need to maintain lactate transport in the retina for RGC survival.
A DFT and Monte Carlo studies of physical properties of the Fe2N compound

Abstract In this paper, we studied the magnetism of Fe2N, using the ab initio and Monte Carlo studies. The magnetic moment and the exchange couplings are deduced by ab initio calculations. The obtained density of states is not symmetrical with respect to the axis of energy proving the ferromagnetic character of this compound. Any gap energy, at the Fermi level, is found confirming the metallic character of this compound. The Hamiltonian of this system consists of several physical parameters. Both the magnetic entropy and the maximum magnetic entropy are obtained. The relative cooling power and the magnetic hysteresis cycle are illustrated. The transition temperature TC value has been deduced and found to be about 252.01 K. This value is in good agreement with the experimental results presented. Also, we found that the magnetizations decrease rapidly to zero with increasing temperature. This is due to the ferromagnetic-paramagnetic phase transition caused by thermal energy.
Lidar multispectral pour la caractérisation des aérosols

Cette these vise a montrer rapport d'un lidar multispectral, en particulier en ajoutant des longueurs d'onde dans le proche infrarouge proche, pour la caracterisation des aerosols. En effet par rapport a un lidar mono-longueur d'onde, l'information contenue dans les profils multispectraux permet de remonter aux proprietes microphysiques des aerosols (distribution en aille et composition). Pour cela un simulateur de signaux lidar multispectraux a ete adapte a notre etude afin de pouvoir developper et tester deux methodes permettant de retrouver les proprietes microphysiques des aerosols le long de la ligne e visee a partir de signaux lidar synthetiques. La premiere methode, basee sur l'inversion des signaux lidar, permet de retrouver la repartition en taille des aerosols et donc d'en deduire notamment leur concentration et leur rayon modal. Cette methode necessite des informations a priori sur les aerosols. Un bilan d'erreur a ete realise en introduisant des incertitudes sur ces parametres a priori et montre que les resultats obtenus sur la concentration et le rayon modal sont precis (respectivement 16% et 17% d'erreur). Cette methode presente l'avantage de ne pas necessiter d'etalonnage absolu de l'instrument. La deuxieme methode est basee sur la minimisation de l'ecart entre des signaux simules et les signaux que l'on etudie. Meme si la precision obtenue sur la repartition en taille retrouvee est plus faible (35% et 40 % d'erreur sur la concentration t le rayon modal) et que la constante d'etalonnage de l'instrument doit etre connue, cette methode a l'avantage de retrouver la composition des aerosols dans 74 % des cas.
Demo: Sonic Catalog of Rare Diseases

This 15-20 minute demo presents our work in progress, a sonic catalog of rare diseases, along with prior work of data- driven music based on genetic sequences from SARS CoV-2. These data-driven compositions are created from spread- sheets, imported into Max and Kyma, and mapped to musical sound.