Miracle-dz/UniFAR-FTUs huggingface dataset:
Description of the predictability assessment methodology Deliverable D3.2

This report describes the methodology that will be used to produce information about wind predictability in the European wind atlas. A review of the state-of-the-art in predictability assessment is reported at different scales, from day ahead (short-term) to sub-seasonal (medium-term predictability), seasonal and decadal (long-term predictability). The report provides an overview of the potential applications of wind predictability, the sources of predictability, the available prediction systems and the methods to evaluate them.
Effect of Growth Regulators, Selenium and Potassium Fertilizers on Downy Mildew and Purple Blotch Diseases and Yield of Onion

oliar application of indol acetic acid (IAA) and/or indol butyric acid (IBA) to onion cv. Giza 20 under field conditions, significantly reduced the incidence of either downy mildew or purple blotch diseases than the control. Selenium and potassium hydrogen carbonate (KHCO 3 ), also affected the incidence of both diseases. However, spraying potassium hydrogen phosphate (K 2 HPO 4 ) showed high efficacy in reducing downy mildew and purple blotch diseases. Yield of bulbs was increased by 93.5 and 53.3% than the control in response to the application of IAA (400 ppm) at 2010 and 2011 growing seasons, respectively. In the same respect, selenium (50 ppm) resulted 85.5 and 45.3% yield increase than control. Phenolic compounds were increased as compared to the control in response to the different tested treatments. The highest increment was noticed when IBA was applied. This was also recorded in total sugars, while KHCO 3 gave the least increase of the total sugars than the control. Galben-Mancozeb was more effective than other treatments in reducing both diseases.
Towards the Automated Identiﬁcation of Orphan Diseases From Case Descriptions

—Orphan diseases are very rare diseases that are not well-known to many medical doctors. Patients suffering from them often remain without the correct diagnosis. Yet, there is a potential that advice-seeking doctors, posting medical case descriptions in web forums, may be automatically given a hint to matching orphan diseases. In this work-in-progress paper, we investigate opportunities and issues for an automated identiﬁcation of orphan diseases in medical case descriptions through text mining and data analytics.
Systemic Viral Infection Optimal Expansion of CD8 T Cells During a Complement Component 3 Is Required for

In addition to its established role in innate immune mechanisms, complement component C3 is also of critical importance in B cell activation and T cell-dependent Ab responses. In this study, we have examined the requirement for C3 in the generation of primary CD8 T cell responses to an acute systemic viral infection. We compared Ag-speciﬁc CD8 T cell responses to lymphocytic choriomeningitis virus (LCMV) between wild-type ( (cid:1) / (cid:1) ) and C3-deﬁcient (C3 (cid:2) / (cid:2) ) mice on both 129/B6 and B6 backgrounds. These studies revealed that C3 activity is required for optimal expansion of LCMV-speciﬁc effector CD8 T cells in an epitope-dependent fashion, which is inﬂuenced by the genetic background of the mice. Studies in complement receptor 1/2 (CR1/CR2)-deﬁcient mice showed that regulation of LCMV-speciﬁc CD8 T cell responses by C3 is not dependent upon CR1/CR2. These ﬁndings may have implications in vaccine development, therapy of autoimmune diseases, and prevention of graft rejection. The Journal of Immunology, 2003, 170: 788–794. anti-CR1/2 anti-CR3 (Mac-1), anti-C5aR analyzed by cytometry. To determine the expression of MHC I on macrophages and B lymphocytes, splenocytes anti-CD8 CA), Macrophages
Modeling and determination of the regulation of gene expression: The binary switch model

The levels of expression of the genes are controlled by certain genes and by other factors. There exist many different models for these gene regulations. Most of these models only consider the case where the regulators are measured. We propose here a modification of the Boolean network model of gene regulation which permits to describe the case where the regulators are not measured. In our model, the state of the genes is not determined by values found inside the network, but by external switches. The evolution of the profiles of expression can be reduced to those switches, which are expected to represent a biological reality. A technique permitting to infer the values of the switches from the data is presented. This technique is applied to two real sets of data. The switches recovered offer a simple explanation of the behavior of the cells and permit to identify a large part of the regulatory network.
The principle of minimized iterations in the solution of the matrix eigenvalue problem

An interpretation of Dr. Cornelius Lanczos' iteration method, which he has named "minimized iterations", is discussed in this article, expounding the method as applied to the solution of the characteristic matrix equations both in homogeneous and nonhomogeneous form. This interpretation leads to a variation of the Lanczos procedure which may frequently be advantageous by virtue of reducing the volume of numerical work in practical applications. Both methods employ essentially the same algorithm, requiring the generation of a series of orthogonal functions through which a simple matrix equation of reduced order is established. The reduced matrix equation may be solved directly in terms of certain polynomial functions obtained in conjunction with the generated orthogonal functions, and the convergence of the solution may be observed as the order of the reduced matrix is successively increased with the order of the original matrix as a limit. The method of minimized iterations is recommended as a rapid means for determining a small number of the larger eigenvalues and modal columns of a large matrix and as a desirable alternative for various series expansions of the Fredholm problem. 1. The conventional iterative procedures. It is frequently required that real latent roots, or eigenvalues, and modal columns be determined for a real numerical matrix, u, of order, n, in the characteristic homogeneous equation,*
Human B Cell to Plasma Cell Differentiation Preplasmablast Population in the Process of Characterization of a Transitional

The early steps of differentiation of human B cells into plasma cells are poorly known. We report a transitional population of CD20 low/ 2 CD38 2 preplasmablasts along differentiation of human memory B cells into plasma cells in vitro. Preplasmablasts lack documented B cell or plasma cell (CD20, CD38, and CD138) markers, express CD30 and IL-6R, and secrete Igs at a weaker level than do plasmablasts or plasma cells. These preplasmablasts further differentiate into CD20 2 CD38 high CD138 2 plasmablasts and then CD20 2 CD38 high CD138 + plasma cells. Preplasmablasts were fully characterized in terms of whole genome transcriptome proﬁling and phenotype. Preplasmablasts coexpress B and plasma cell transcription factors, but at a reduced level compared with B cells, plasmablasts, or plasma cells. They express the unspliced form of XBP1 mRNA mainly, whereas plasmablasts and plasma cells express essentially the spliced form. An in vivo counterpart (CD19 + CD20 low/ 2 CD38 2 IL-6R + cells) of in vitro-generated preplasmablasts could be detected in human lymph nodes (0.06% of CD19 + cells) and tonsils (0.05% of CD19 + cells). An open access “B to Plasma Cell Atlas,” which makes it possible to interrogate gene expression in the process of B cell to plasma cell differentiation, is provided. Taken together, our ﬁndings show
Optical lattice clock

Precision spectroscopy was performed for the 5s 2 1 So (F=9/2)-5s5p 3 P 0 (F=9/2) clock transition of 87 Sr atoms trapped in a one-dimensional optical lattice. The transition frequency for the Sr lattice clock was measured to be 429,228,004,229,952(15) Hz by an optical frequency comb referenced to the S1 second.
Edinburgh Research Explorer Personality and risk of frailty

Background There is evidence that the personality traits conscientiousness, extraversion and neuroticism are associated with health behaviours and with risk of various health outcomes. We hypothesised that people who are lower in conscientiousness or extraversion or higher in neuroticism may be at greater risk of frailty in later life. Methods We used general linear models to examine the prospective relation between personality, assessed using the Midlife Development Inventory, and change in frailty, modelled by a frailty index, in 5314 men and women aged 60 to over 90 years from the English Longitudinal Study of Ageing. Results Men and women with higher levels of neuroticism or lower levels of extraversion or conscientiousness had an increased frailty index score at follow-up. After adjustment for potential confounding or mediating variables, including frailty index score at baseline, the frailty index score at follow-up — which potentially ranges from 0 to 1 — was higher by 0.035 (95 % confidence interval 0.018, 0.052) for a standard deviation increase in neuroticism and lower by 0.061 (0.031, 0.091) or 0.045 (0.020, 0.071) for a standard deviation increase in extraversion or conscientiousness, respectively. There was some evidence that the association between extraversion and frailty may be due to reverse causation whereby poorer health affected responses to items in the personality inventory. Conclusions Higher levels of neuroticism or lower levels of conscientiousness or extraversion may be risk factors for the onset or progression of frailty. Future studies need to replicate these observations in other populations and explore the mechanisms underlying these associations.
Parallel Block Preconditioning for Multi-Physics Problems

In this thesis we study efficient parallel iterative solution algorithms for multi-physics problems. In particular, we consider fluid structure interaction (FSI) problems, a type of multi-physics problem in which a fluid and a deformable solid interact.All computations were performed in Oomph-Lib, a finite element library for the simulation of multi-physics problems. In Oomph-Lib, the constituent problems in a multi-physics problem are coupled monolithically, and the resulting system of non-linear equations solved with Newton's method. This requires the solution of sequences of large, sparse linear systems, for which optimal solvers are essential. The linear systems arising from the monolithic discretisation of multi-physics problems are natural candidates for solution with block-preconditioned Krylov subspace methods.We developed a generic framework for the implementation of block preconditioners within Oomph-Lib. Furthermore the framework is parallelised to facilitate the efficient solution of very large problems. This framework enables the reuse of all of Oomph-Lib's existing linear algebra infrastructure and preconditioners (including block preconditioners). We will demonstrate that a wide range of block preconditioners can be seamlessly implemented in this framework, leading to optimal iterative solvers with good parallel scaling.We concentrate on the development of an effective preconditioner for a FSI problem formulated in an arbitrary Lagrangian Eulerian (ALE) framework with pseudo-solid node updates (for the deforming fluid mesh). We begin by considering the pseudo-solid subsidiary problem; the deformation of a solid governed by equations of large displacement elasticity, subject to a prescribed boundary displacement imposed with Lagrange multiplier. We present a robust, optimal, augmented-Lagrangian type preconditioner for the resulting saddle-point linear system and prove analytically tight bounds for the spectrum of the preconditioned operator with respect to the discrete problem size.This pseudo-solid preconditioner is incorporated into a block preconditioner for the full FSI problem. One key feature of the FSI preconditioner is that existing optimal single physics preconditioners (such as the well known Navier-Stokes Least Squares Commutator preconditioner) can be employed to approximately solve the linear systems associated with the constituent sub-problems. We evaluate its performance on selected 2D and 3D problems. The preconditioner is optimal for most problems considered. In cases when sub-optimality is detected, we explain the reasons for such behavior and suggest potential improvements.
Perforin-Dependent Effector Function on the Tumor Cells for Optimal Intercellular Adhesion Molecule-1 Expression Renal Cancer (Renca), yet Require NK Cells Use NKG2D to Recognize a Mouse

The NKG2D receptor on NK cells can recognize a variety of ligands on the tumor cell surface. Using a mouse renal cancer (Renca), we show that NKG2D recognition by NK cells was crucial for their ability to limit tumor metastases in vivo in both liver and lungs using perforin-dependent effector mechanisms. However, for the R331 cell line established from Renca, NKG2D recognition and perforin-dependent lysis played no role in controlling liver metastases. R331 cells were also more resistant to perforin-dependent lysis by NK cells in vitro. We therefore used these phenotypic differences between Renca and R331 to further investigate the crucial receptor:ligand interactions required for triggering lytic effector functions of NK cells. Reconstitution of R331 cells with ICAM-1, but not Rae-1 (cid:1) , restored NKG2D-mediated, perforin-dependent lysis. Interestingly, R331 cells were efﬁciently lysed by NK cells using death ligand-mediated apoptosis. This death ligand-mediated killing did not depend on NKG2D recognition of its ligands on tumor cells. This result suggests that the intracellular signaling in NK cells required for perforin and death ligand-mediated lysis of tumor target cell are quite distinct, and activation of both of these antitumor lytic effector functions of NK cells could improve therapeutic beneﬁts for certain tumors. The Journal of Immunology, 2006, 177: 2575–2583.
A deep survey of the 5C2 area at 4850 MHz

On presente les resultats de l'observation a 4850 MHz d'une zone de 6,60•10 −3 sterad couvrant la region 5C2. Le programme inclut 106 sources au-dessus de la densite de flux limite de 17 mJy. On discute des distributions a deux points de l'indice spectral pour des sources selectionnees a trois frequences differentes
Tibial metaphyseal cones combined with short stems perform as well as long stems in revision total knee arthroplasty

There is uncertainty around optimal tibial stem length in revision total knee arthroplasty (rTKA) utilizing a tibial trabecular metal (TM) cone. The purpose of this study was to compare: (1) functional outcomes, (2) radiographic outcomes and (3) implant survivorship in rTKA utilizing TM cones combined with either short stems (SS) or long stems (LS) at minimum 2 years follow‐up.
Retracted: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency

MOTIVATION CRISPR/Cas9 technology has been revolutionizing the field of gene editing in recent years. Guide RNAs (gRNAs) enable Cas9 proteins to target specific genomic loci for editing. However, editing efficiency varies between gRNAs. Thus, computational methods were developed to predict editing efficiency for any gRNA of interest. High-throughput datasets of Cas9 editing efficiencies were produced to train machine-learning models to predict editing efficiency. However, these high-throughput datasets have low correlation with functional and endogenous editing. Another difficulty arises from the fact that functional and endogenous editing efficiency is more difficult to measure, and as a result, functional and endogenous datasets are too small to train accurate machine-learning models on. RESULTS We developed DeepCRISTL, a deep-learning model to predict the on-target efficiency given a gRNA sequence. DeepCRISTL takes advantage of high-throughput datasets to learn general patterns of gRNA on-target editing efficiency, and then uses transfer learning (TL) to fine-tune the model and fit it to the functional and endogenous prediction task. We pre-trained the DeepCRISTL model on more than 150 000 gRNAs, produced through the DeepHF study as a high-throughput dataset of three Cas9 enzymes. We improved the DeepHF model by multi-task and ensemble techniques and achieved state-of-the-art results over each of the three enzymes: up to 0.89 in Spearman correlation between predicted and measured on-target efficiencies. To fine-tune model weights to predict on-target efficiency of functional or endogenous datasets, we tested several TL approaches, with gradual learning being the overall best performer, both when pre-trained on DeepHF and when pre-trained on CRISPROn, another high-throughput dataset. DeepCRISTL outperformed state-of-the-art methods on all functional and endogenous datasets. Using saliency maps, we identified and compared the important features learned by the model in each dataset. We believe DeepCRISTL will improve prediction performance in many other CRISPR/Cas9 editing contexts by leveraging TL to utilize both high-throughput datasets, and smaller and more biologically relevant datasets, such as functional and endogenous datasets. AVAILABILITY AND IMPLEMENTATION DeepCRISTL is available via github.com/OrensteinLab/DeepCRISTL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Oxygen uptake kinetics and ventilatory and metabolic parameters do not differ between moderate‐intensity front crawl and breaststroke swimming

Pulmonary oxygen uptake ( V̇O2 ) kinetics have been well studied during land‐based exercise. However, less is known about V̇O2 kinetics during swimming exercise and comparisons between strokes is non‐existent. We aimed to characterize and compare the V̇O2 kinetics, ventilatory,e and metabolic response to constant velocity moderate‐intensity freely breathing front crawl (FC) and breaststroke (BR) swimming in a swimming flume. These two strokes reflect predominantly upper body versus lower body modes of swimming locomotion, respectively. Eight trained swimmers (4 females, 20 ± 1 years, 1.74 ± 0.06 m; 66.8 ± 6.3 kg) attended 5–6 laboratory‐based swimming sessions. The first two trials determined FC and BR V̇O2max and the ventilatory threshold (VT), respectively, during progressive intensity swimming to the limit of tolerance. Subsequent trials involved counterbalanced FC and BR transitions from prone floating to constant velocity moderate‐intensity swimming at 80% of the velocity at VT (vVT), separated by 30‐min recovery. Breath‐by‐breath changes in pulmonary gas exchange and ventilation were measured continuously using a snorkel and aquatic metabolic cart system. The ventilatory and metabolic responses were similar (p > 0.05) between strokes during maximal velocity swimming, however, vVT and maximal velocity were slower (p < 0.05) during BR . During moderate‐intensity swimming, V̇O2 kinetics, ventilatory and metabolic parameters were similar (p > 0.05) between strokes. In conclusion, when breathing ad libitum, V̇O2 kinetics during moderate‐intensity constant velocity swimming, and ventilatory and metabolic responses during moderate‐intensity and maximal velocity swimming, are similar between FC and BR strokes.
An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related sarbecoviruses enter host cells by receptor-recognition and membrane-fusion. An indispensable step in fusion is the formation of 6-helix bundle by viral spike heptad repeats 1 and 2 (HR1 and HR2). Here, we report the construction of 5-helix bundle (5HB) proteins for virus infection inhibition. The optimal construct inhibits SARS-CoV-2 pseudovirus entry with sub-micromolar IC50. Unlike HR2-based peptides that cannot bind spike in the pre-fusion conformation, 5HB features with the capability of binding to pre-fusion spike. Furthermore, 5HB binds viral HR2 at both serological- and endosomal-pH, highlighting its entry-inhibition capacity when SARS-CoV-2 enters via either cell membrane fusion or endosomal route. Finally, we show that 5HB could neutralize S-mediated entry of the predominant SARS-CoV-2 variants and a wide spectrum of sarbecoviruses. These data provide proof-of-concept evidence that 5HB might be developed for the prevention and treatment of SARS-CoV-2 and other emerging sarbecovirus infections.
Evaluating Social Determinants of Health Domains and Their Predictive Validity Within Black/African American and White Older Adults From the ACTIVE Trial

Objective To assess domains of social determinants of health (SDoH) and their associations with cognition and quality of life. Method This investigation uses baseline data from individuals participating in the ACTIVE trial (n = 2505) to reproduce the SDoH domains described in Healthy People 2030 (economic stability, health care, education, neighborhood and built environment, and social and community context). Results: Results support using data from the ACTIVE trial to assess all five SDoH domains, and the ability of the composites to predict baseline performance on measures of cognition and self-reported quality of life within a sample of older adults. Additionally, higher SDoH domain scores were associated with better functioning on composite measures of cognition and higher scores for mental and general health-related quality of life with Access to Healthcare associated with all outcomes. Discussion: These findings can inform investigators interested in assessing multiple domains of SDoH and highlight the importance of access to health care within older Black/African American and White older adults.
Sub-exponential mixing rate for a class of Markov processes 1

A system is disclosed in which an input binary address is transformed into a set of module select signals and a set of address signals whereby an aggregate of memory modules, each of which may contain a different number of storage cells, are combined to form a memory assembly which has a fixed number of storage cells. The address transformation system uses signals taken from the individual modules which represent the number of memory cells contained therein.