Miracle-dz/UniFAR-FTUs huggingface dataset:
Complement C4, the Major Histocompatibility Complex, and Autoimmunity

For many autoimmune diseases, including systemic lupus erythematosus (SLE) and primary Sjögren ’ s syndrome (SS), genome-wide association analyses (GWAS) reveal that the major histocompatibility complex (MHC) is the site of the stron-gest genetic association signals. These MHC associations have long been thought to arise from HLA alleles because of the role of these molecules in antigen presentation. One HLA allele showing a consistent association with autoimmune diseases is HLA – DRB1*03:01 ( DR3 ). The DRB1*03:01 allele resides on an extended MHC haplotype, meaning that there is extensive correlation with co-inherited MHC alleles (1). The region of correlation (termed linkage disequilibrium [LD]) encompasses the entire classical MHC region from HLA class I through class III to HLA class II: speci ﬁ cally, from HLA – B8 to HLA – DQA1*05:01/ DQB1*02:01 , which incorporates a common complement C4A null gene in class III. The complement C4 locus is complex. There are 2 complement C4 genes: C4A and C4B , which are coded adjacently in genomic regions and show marked DNA sequence similarity (homology). The 2 genes are subject to common structural variation with both gene deletions and gene duplications (2). These are outlined in Figure 1. Such extensive LD and accompanying structural variation in the MHC have made identifying the causal genes very challeng-ing. The DRB1*03:01 allele (and by de ﬁ nition, all genetic varia-tions that are correlated with it) has been associated with the following conditions: SLE, SS, myositis, type I diabetes mellitus, Addison ’ s disease, Graves ’ disease, and myasthenia gravis. However, whether the causal genes on this extended region of
Tectonic Control of Groundwater Recharge and Flow in Faulted Volcanic Aquifers

Groundwater dynamics in continental rift zone settings remain poorly understood because of the spatial heterogeneity in flow, storage, and recharge dynamics. The Central Kenya Rift is an excellent example where, though groundwater is important for domestic, irrigation, and geothermal energy exploitation, its hydrogeological properties remain largely unknown. Existing conceptual groundwater models assume flow from the high‐elevation, humid rift flanks to the low‐elevation, semiarid rift floor, but the role of the faults that fracture the aquifers is commonly unaccounted for. We applied geochemical, isotopic (δ18O, δD, 87Sr/86Sr, 3H‐3He), multivariate statistical methods, and knowledge of geological structures to determine recharge sources, flow, and residence times to revise the conceptual flow model. Results show that groundwater is primarily recharged by meteoric waters, river input, and Lake recharge. The faults impart a control on the groundwater flow within four sub‐compartments. Major differences in flow patterns exist between the eastern and western rift flanks: surface and groundwater transfer from the eastern flanks to the rift floor occurs via relay ramp structures, and flow on the west side takes place laterally from the high escarpment. Although 3H‐3He dating shows that the age of groundwater ranges from a few to >>50 years, most of the groundwater in the rift‐floor area is free of 3H and was recharged before the 1960s. Hence, we propose that these areas receive episodic recharge and represent the most sensitive groundwater resources in the rift. To inform sustainable groundwater development, a robust monitoring network is required to capture the heterogeneous groundwater dynamics.
Turbulence modulation by finite-size particles of different diameters and particle–fluid density ratios in homogeneous isotropic turbulence

In this paper, the influence of particle-fluid density ratio and particle diameter on the turbulence modulation by finite-size particles in forced homogeneous isotropic turbulence is investigated. Results show that the presence of finite-size particles always attenuate the turbulence, and the attenuation is larger for particles with larger density when the particle diameter is fixed. But the attenuation is smaller for particles with larger diameter if the density is fixed, and the weaker attenuation is due to the wake fluctuation when the particle Reynolds number is large enough. The turbulence kinetic energy is attenuated at the large scales and augmented at the small scales. The radial dissipation profiles show that the region affected by the particles with same diameter is identical, but the dissipation near the particle surface is larger if the density is larger due to larger slip velocity and particle Reynolds number. For particles with same density, smaller particles have smaller dissipation near the particle surface but the influence region is larger, and the combined effect leads to the result that the contribution of dissipation in the influence region of smaller particles to the total dissipation is larger. The influence region mainly depends on the particle diameter.
All-solid-state planar on-chip micro-supercapacitors based on reduced graphene oxide with ultrahigh energy characteristics

Abstract Planar on-chip micro-supercapacitors are recognized as one of the most competitive energy sources for electronics. Here, we showed ultrahigh performance all-solid-state planar on-chip micro-supercapacitors with photolithographic interdigital electrodes based on modified liquid-air interface self-assembly technique. The electrode width which is narrower than other existing lithography is only on the order of 10° μm (electrode width is 4 μm and the gap width is 4 μm). Planar on-chip micro-supercapacitors prepared with reduced graphene oxide films as electrodes had the energy density of 124.4 mWh cm−3, the corresponding time constant of 2.15 μs and the displayed stack capacitance of 895.74 F cm−3. In addition, it exhibited excellent cycle stability with a capacitance retention of 98.9% after 10,000 cycles. The demonstrated planar on-chip micro-supercapacitors have a good application foreground in the preparation of high-performance integrated micro-devices.
The double exponential sinc collocation method for singular Sturm-Liouville problems

Sturm-Liouville problems are abundant in the numerical treatment of scientific and engineering problems. In the present contribution, we present an efficient and highly accurate method for computing eigenvalues of singular Sturm-Liouville boundary value problems. The proposed method uses the double exponential formula coupled with sinc collocation method. This method produces a symmetric positive-definite generalized eigenvalue system and has exponential convergence rate. Numerical examples are presented and comparisons with single exponential sinc collocation method clearly illustrate the advantage of using the double exponential formula.
Residual Dense Autoencoder Network for Nonlinear Hyperspectral Unmixing

Hyperspectral unmixing is a popular research topic in hyperspectral processing, aiming at obtaining the ground features contained in the mixed pixels and their proportion. Recently, nonlinear mixing models have received particular attention in hyperspectral decomposition since the linear mixing model cannot suitably apply in the situation that exists in multiple scattering. In this article, we constructed a residual dense autoencoder network (RDAE) for nonlinear hyperspectral unmixing in multiple scattering scenarios. First, an encoder was built based on the residual dense network (RDN) and attention layer. The RDN is employed to characterize multiscale representations, which are further transformed with the attention layer to estimate the abundance maps. Second, we designed a decoder based on the unfolding of a generalized bilinear model to extract endmembers and estimate their second-order scattering interactions. Comparative experiments between the RDAE and six other state-of-the-art methods under synthetic and real hyperspectral datasets demonstrate that the proposed method achieved a better performance in terms of endmember extraction and abundance estimation.
Semisimple degree of symmetry of manifold with the homotopy type of product $(S\sp1)\spr\times (S\sp2)\sps\times (S\sp3)\spt$

In this note, we shall consider the topological semisimple degree of symmetry of manifold with the homotopy type of a product (S)' X (S) X (S)* of spheres. Here the topological semisimple degere of symmetry is, by definition, the maximum of dimension of compact connected semisimple Lie group which acts on the manifold topologically and almost effectively. This note is motivated by works on the degree of symmetry of manifold with large low homotopy groups as K(π, l)-manifolds or product of 2-sρheres (see [1], [S], [6], [9], [14] or [15]). We shall prove the following
$\Lambda$-modules and holomorphic Lie algebroid connections

Let $X$ be a complex smooth projective variety, and $\mathcal{G}$ a locally free sheaf on $X$. We show that there is a 1-to-1 correspondence between pairs $(\Lambda,\Xi)$, where $\Lambda$ is a sheaf of almost polynomial filtered algebras over $X$ satisfying Simpson's axioms and $\Xi: \Gr\Lambda \rightarrow \Sym^\bullet_{\corO_X} \mathcal{G}$ is an isomorphism, and pairs $(\mathcal{L},\Sigma)$, where $\mathcal{L}$ is a holomorphic Lie algebroid structure on $\mathcal{G}$ and $\Sigma$ is a class in $F^1H^2(\mathcal{L},\C)$, the first Hodge filtration piece of the second cohomology of $\bella$. As an application, we construct moduli spaces of semistable flat $\mathcal{L}$-connections for any holomorphic Lie algebroid $\mathcal{L}$. Particular examples of these are given by generalized holomorphic bundles for any generalized complex structure associated to a holomorphic Poisson manifold.
Structured Set Variable Domains in Bayesian Network Structure Learning

Constraint programming is a state of the art technique for learning the structure of Bayesian Networks from data (Bayesian Network Structure Learning – BNSL). However, scalability both for CP and other combinatorial optimization techniques for this problem is limited by the fact that the basic decision variables are set variables with domain sizes that may grow super polynomially with the number of random variables. Usual techniques for handling set variables in CP are not useful, as they lead to poor bounds. In this paper, we propose using decision trees as a data structure for storing sets of sets to represent set variable domains. We show that relatively simple operations are sufficient to implement all propagation and bounding algorithms, and that the use of these data structures improves scalability of a state of the art CP-based solver for BNSL
COVID-19 preventive measures coincided with a marked decline in other infectious diseases in Denmark, spring 2020

Abstract We aimed to descriptively analyse the possible impact of the national COVID-19 interventions on the incidence of common infectious diseases in Denmark during spring and summer 2020. This observational study focused on national register data on infections caused by 16 different bacterial and viral pathogens. We included new cases registered between 1 January 2016 and 31 July 2020. The weekly number of new cases were analysed with respect to the COVID-19-related interventions introduced during 2020. We found a marked decrease in infections associated with droplet transmission coinciding with the COVID-19 interventions in spring and summer 2020. These included decreases in both viral and bacterial airway infections and also decreases in invasive infections caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis. There was also a reduction in cases associated with foodborne transmission during the COVID-19 lockdown period. We found no effect of the lockdown on infections by invasive beta-haemolytic streptococci group B, C and G, Staphylococcus aureus bacteraemia, Neisseria gonorrhoeae or Clostridioides difficile. In conclusion, we found that the widespread interventions such as physical distancing, less travel, hygiene measures and lockdown of schools, restaurants and workplaces together coincided with a marked decline in respiratory infections and, to a smaller extent, some foodborne-transmitted infections.
A brief course of digitally delivered cognitive behavioural therapy for the treatment of blood contamination-based obsessive-compulsive disorder: a structured case report

Abstract The lifetime prevalence of OCD in the UK is estimated to be between 1 in 100 and 1 in every 50 people. It is therefore necessary to explore innovations in practice to expand the reach of the gold standard therapeutic approaches of exposure with response prevention (ERP) and cognitive behavioural therapy (CBT). The COVID-19 pandemic has facilitated such innovations with several services accommodating changes to routine practice by utilising digital platforms to provide videoconference-delivered therapy. Despite a growing evidence base demonstrating efficacy and scope for the use of videoconference-delivered CBT for obsessive-compulsive disorder (OCD), there remains qualitative research collated from clinicians which suggests that a lack of practitioner confidence and a low belief in positive outcomes are barriers to adopting remote therapy practices for clinicians. Therefore, this structured case report describes the assessment, formulation, intervention and outcome of an 11-week videoconference-delivered therapeutic intervention. Reflections are made regarding the use of the digital platform throughout the intervention, alongside the strengths and difficulties of applying videoconference-delivered CBT for OCD. Key learning aims (1) To illustrate a digital treatment of OCD through flexible application of the current evidence base. (2) To gain an understanding of the strengths and weaknesses of delivering digital out-patient CBT for OCD. (3) To consider the utility of structured case reports in routine practice when delivering digital therapy.
Characteristics, Effect of Histological Grade and Localization on the Prognosis of Colorectal Cancer. A retrospective Study.

Background: Colorectal cancer is the third most deadly cancer and the fourth most frequent in the world according to GLOBOCAN 2018. The number of new cases is growing up, which may also be related to lifestyle. Many studies have shown a difference in the number of males and females, correlation of localization, stage, and grade with prognosis. Material and Methods: In our study were included operated cases with colorectal cancer in University Hospital Center “Mother Theresa” during the period from January 1, 2016, to December 31, 2017. In our study, the total number of patients enrolled is 334. In the end was evaluated the correlation between histological grade, stage, and localization with prognosis. Results: From the study resulted that males were affected more than females by colorectal cancer. The average age of diagnosis of colorectal cancer is 63.9 (±12.4) years. Moderately differentiated adenocarcinoma, histological grade II and pathological stage pT3N0Mx after TNM are predominant. The commonest localization is the rectum. Disease-free survival is better in stages I and IIa than in other stages, least favorable in poorly differentiated adenocarcinoma. Conclusion: In Albania, patients diagnosed with CRC showed a low survival rate specific to cancer. The type of histology, the stage of cancer, the level of CEA at diagnosis, and the type of treatment a patient received significantly determine the mortality rate. Therefore, cancer screening programs can help to detect the disease at an early stage and initiate timely available treatments in order to extend the life expectancy of CRC patients.
Band offset measurements of the Si3N4/GaN (0001) interface

X-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy were used to measure electronic states as Si3N4 was deposited on clean GaN (0001) surfaces. The n-type (2×1018) and p-type (1×1017) GaN surfaces were atomically cleaned in NH3 at 860 °C, and the n-and p-type surfaces showed upward band bending of ∼0.2±0.1 eV and downward band bending of 1.1±0.1 eV, respectively, both with an electron affinity of 3.1±0.1 eV. Layers of Si (∼0.2 nm) were deposited on the clean GaN and nitrided using an electron cyclotron resonance N2 plasma at 300 °C and subsequently annealed at 650 °C for densification into a Si3N4 film. Surface analysis was performed after each step in the process, and yielded a valence band offset of 0.5±0.1 eV. Both interfaces exhibited type II band alignment where the valence band maximum of GaN lies below that of the Si3N4 valence band. The conduction band offset was deduced to be 2.4±0.1 eV, and a change of the interface dipole of 1.1±0.1 eV was observed for Si3N4/GaN interfac.
Department of Earth Sciences at the University of Rome Radiocarbon Dates III

This is a partial list of archaeological samples processed between May 1990 and December 1992 at the Department of Earth Sciences Radiocarbon Dating Laboratory of the University of Rome. Most of the samples in the list, both from Italy and other countries, were related to excavations carried out by researchers at the University of Rome, Department of Scienze dell'Antichità. Although primarily measured for archaeological studies, some of these dates also have geological and paleoenvironmental relevance.
Group Actions on Real Cubings and Limit Groups over Partially Commutative Groups

We introduce a class of spaces, called real cubings, and study the stucture of groups acting nicely on these spaces. Just as cubings are a natural generalisation of simplicial trees, real cubings can be regarded as a natural generalisation of real trees. Our main result states that a finitely generated group $G$ acts nicely (essentially freely and co-specially) on a real cubing if and only if it is a subgroup of a graph tower (a higher dimensional generalisation of $\omega$-residually free towers and NTQ-groups). It follows that $G$ acts freely, essentially freely and co-specially on a real cubing if and only if $G$ is a subgroup of the graph product of cyclic and (non-exceptional) surface groups. In the particular case when the real cubing is a tree, it follows that $G$ acts freely, essentially freely and co-specially on the real cubing if and only if it is a subgroup of the free product of abelian and surface groups. Hence, our main result can be regarded as a generalisation of the Rips' theorem on free actions on real trees. We apply our results to obtain a characterisation of limit groups over partially commutative groups as subgroups of graph towers. This result generalises the work of Kharlampovich-Miasnikov, \cite{KhMNull}, Sela, \cite{Sela1} and Champetier-Guirardel, \cite{CG} on limit groups over free groups.
Unwrapped continuation invariance in Lagrangian Floer theory: energy and $C^0$ estimates

We consider pairs of Lagrangian submanifolds $(L_0,L), (L_1, L)$ belonging to the class of Lagrangian submanifolds with \emph{conic} ends on \emph{Weinstein manifolds}. The main purpose of the present paper is to define a canonical chain map $h_\CL: CF(L_0,L) \to CF(L_1,L)$ of Lagrangian Floer complex inducing an isomorphism in homology, under the Hamiltonian isotopy $\CL=\{L_s\}_{0 \leq s\leq 1}$ generated by \emph{conic} Hamiltonian functions such that the intersections $L \cap L_s$ do not escape to infinity. The main ingredients of the proof is an a priori bound for general isotopy of the energy \emph{quadratic} at infinity and a $C^0$-bound for the \emph{$C^1$-small} isotopy $\CL = \{L_s\}$, for the associated pseudo-holomorphic map equations with \emph{moving} Lagrangian boundary induced by a conic Hamiltonian isotopy. For the Lagrangian submanifolds with \emph{asymptotically conic} ends, we construct a natural homomorphism $h_\LL: HF(L_0,L) \to HF(L_1,L)$ for which the corresponding chain map may \emph{not} necessarily exist. This provides a more conventional construction of the chain isomorphism which replaces the sophisticated method using the Lagrangian cobordism via the machinery of \cite{kasturi-oh1,kasturi-oh2} whose details were only outlined in \cite{oh:gokova}.
Broadband study of hard X-ray selected absorbed AGN

[Abridged]We report on the broadband X-ray properties of a complete sample of absorbed Seyfert galaxies hard X-ray selected with INTEGRAL. The sample is composed of 33 sources: 15 are newly discovered above 20 keV while 18 are already known AGN. For 17 sources we have performed a broadband analysis with XMM and INTEGRAL data. We have complemented the analysis of the 16 remaining sources with existing broadband studies. The spectra are well reproduced with an absorbed primary emission with a high energy cutoff and its scattered fraction below 2-3 keV, plus the Compton reflection features. A high energy cut-off is found in 30% of the sample, with an average value below 150 keV. The hard X-ray selection favours the detection of more obscured sources, with the log NH average value of 23.15. The diagnostic plot NH vs F(corr)(2-10keV)/F(20-100keV) allowed the isolation of the Compton thick objects and may represent a useful tool for future hard X-ray observations of newly discovered AGN. We are unable to associate the reflection components (continuum and Fe line) with the absorbing gas as a torus, a more complex scenario being necessary. In the Compton thin sources, a fraction (but not all) of the Fe line needs to be produced in a gas located closer to the BH than the thick torus, and this is possibly associated with the optical BLR, responsible also for the absorption. We still need a Compton thick medium (not intercepting the line of sight) likely associated to a torus, which contributes to the Fe line and produces the observed reflection continuum above 10 keV. The Iwasawa-Taniguchi effect can not be confirmed with our data. Finally, the comparison with a sample of unobscured AGN shows that, type 1 and type 2 (once corrected for absorption) Seyfert are characterized by the same nuclear/accretion properties (luminosity, bolometric luminosity, Eddington ratio), supporting the unified view.