Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Understanding of Gastric Cancer Based upon Physiological Role of Gastrin and ECL Cells

Simple Summary Generally, we know that cancers represent genetic changes in tumour cells, but we most often do not know the causes of cancers or how they develop. Our knowledge of the regulation of gastric acid secretion is well known, with the gastric hormone gastrin maintaining gastric acidity by stimulation of the enterochromaffin-like (ECL) cell to release histamine, which subsequently augments acid secretion. Furthermore, it seems to be a general principle that stimulation of function (which, for the ECL cell, is release of histamine) in a parallel way stimulates the proliferation of the same cell. Long-term hyperstimulation of cell division predisposes to genetic changes and, thus, development of tumours. All conditions with reduced gastric acidity result in an increased risk of gastric tumours due to elevated gastrin in order to restore gastric acidity. It is probable that Helicobacter pylori infection (the most important cause of gastric cancer), as well as drugs inhibiting gastric acid secretion induce gastric cancer in the long-term, due to an elevation of gastrin caused by reduced gastric acidity. Gastric carcinomas have been shown to express ECL cell markers, further strengthening this relationship. Abstract The stomach is an ideal organ to study because the gastric juice kills most of the swallowed microbes and, thus, creates rather similar milieu among individuals. Combined with a rather easy access to gastric juice, gastric physiology was among the first areas to be studied. During the last century, a rather complete understanding of the regulation of gastric acidity was obtained, establishing the central role of gastrin and the histamine producing enterochromaffin-like (ECL) cell. Similarly, the close connection between regulation of function and proliferation became evident, and, furthermore, that chronic overstimulation of a cell with the ability to proliferate, results in tumour formation. The ECL cell has long been acknowledged to give rise to neuroendocrine tumours (NETs), but not to play any role in carcinogenesis of gastric adenocarcinomas. However, when examining human gastric adenocarcinomas with the best methods presently available (immunohistochemistry with increased sensitivity and in-situ hybridization), it became clear that many of these cancers expressed neuroendocrine markers, suggesting that some of these tumours were of neuroendocrine, and more specifically, ECL cell origin. Thus, the ECL cell and its main regulator, gastrin, are central in human gastric carcinogenesis, which make new possibilities in prevention, prophylaxis, and treatment of this cancer.
Inhibition of AKT-Signaling Sensitizes Soft Tissue Sarcomas (STS) and Gastrointestinal Stromal Tumors (GIST) to Doxorubicin via Targeting of Homology-Mediated DNA Repair

Activation of the phosphoinositide 3-kinase (PI3K)/Akt/mTOR pathway is well documented for a broad spectrum of human malignancies supporting their growth and progression. Accumulating evidence has also implicated AKT as a potent modulator of anti-cancer therapies via regulation of DNA damage response and repair (DDR) induced by certain chemotherapeutic agents and ionizing radiation (IR). In the present study, we examined the role of AKT signaling in regulating of Rad51 turnover and cytotoxic effects of topoisomerase II inhibitor, doxorubicin (Dox) in soft tissue sarcomas (STS) and gastrointestinal stromal tumors (GIST) in vitro. Blocking of AKT signaling (MK-2206) enhanced cytotoxic and pro-apoptotic effects of Dox in vast majority of STS and GIST cell lines. The phosphorylated form of Akt co-immunoprecipitates with Rad51 after Dox-induced DNA damage, whereas Akt inhibition interrupts this interaction and decreases Rad51 protein level by enhancing protein instability via proteasome-dependent degradation. Inhibition of Akt signaling in Dox-treated cells was associated with the increased number of γ-H2AX-positive cells, decrease of Rad51 foci formation and its colocalization with γ-H2AX foci, thereby revealing unsuccessful DDR events. This was also in consistency with an increase of tail moment (TM) and olive tail moment (OTM) in Dox-treated GIST and STS cells cultured in presence of Akt inhibitor after Dox washout. Altogether, our data illustrates that inhibition of AKT signaling is STS and GIST might potentiate the cytotoxic effect of topoisomerase II inhibitors via attenuating the homology-mediated DNA repair.
Viral Infections of the Central Nervous System in Children: A Systematic Review

Viral infections of the central nervous system such as meningitis, encephalitis or meningoencephalitis, are important causes of significant morbidities and mortality worldwide. Early diagnosis and prompt treatment will lead to better outcomes, but any delay may results in high fatality with serious neurologic sequelae among survivors. We conducted a systematic review of published literature on the clinical presentation, diagnosis, treatment and complications of viral infections of the central nervous system from 1980 to 2019 on four databases comprising of PubMed, PubMed Central, Google Scholar and Medline to give the current understanding for better patient management. This systematic review demonstrates the management approach of viral infections of the central nervous system in children from the point of clinical presentation, diagnosis, treatment and complications. Definitive treatment remained unknown; however, certain antiviral drugs were proved to be effective. Therefore, prevention through childhood vaccination is the best management option.
Gyrocardiography: A Review of the Definition, History, Waveform Description, and Applications

Gyrocardiography (GCG) is a non-invasive technique of analyzing cardiac vibrations by a MEMS (microelectromechanical system) gyroscope placed on a chest wall. Although its history is short in comparison with seismocardiography (SCG) and electrocardiography (ECG), GCG becomes a technique which may provide additional insight into the mechanical aspects of the cardiac cycle. In this review, we describe the summary of the history, definition, measurements, waveform description and applications of gyrocardiography. The review was conducted on about 55 works analyzed between November 2016 and September 2020. The aim of this literature review was to summarize the current state of knowledge in gyrocardiography, especially the definition, waveform description, the physiological and physical sources of the signal and its applications. Based on the analyzed works, we present the definition of GCG as a technique for registration and analysis of rotational component of local cardiac vibrations, waveform annotation, several applications of the gyrocardiography, including, heart rate estimation, heart rate variability analysis, hemodynamics analysis, and classification of various cardiac diseases.
Peri-Implant Diseases: Diagnosis, Clinical, Histological, Microbiological Characteristics and Treatment Strategies. A Narrative Review

Since the use of dental implants is continuously increasing, it is imperative for dental practitioners to understand the nature and treatment of peri-implant diseases. The purpose of this manuscript is to comprehensively review peri-implant diseases, their characteristics, as well as their non-surgical and surgical treatment. To that end, the current literature was searched and a narrative review was conducted. It is essential that the case definitions described in the 2017 World Workshop on the Classification of Periodontal and Peri-implant Diseases and Conditions are used to diagnose and classify peri-implant health, peri-implant mucositis and peri-implantitis. While recent epidemiologic studies on peri-implant diseases exist, there is great heterogeneity in the definition of these conditions. Several risk factors and indicators are reported in the literature, with smoking and diabetes being the most universally accepted. In peri-implant mucositis, non-surgical treatment seems to be sufficient. However, for the treatment of peri-implantitis, a surgical approach, which includes open-flap debridement, apically positioned flap and guided bone regeneration, is considered more appropriate. A great variety of adjuncts to mechanical treatment have been reported with controversial results. Finally, studies comparing results from different peri-implantitis treatments are warranted in randomized controlled clinical trials in order to provide stronger evidence-based approaches.
There and Back Again: Learning to Simulate Radar Data for Real-World Applications

Simulating realistic radar data has the potential to significantly accelerate the development of data-driven approaches to radar processing. However, it is fraught with difficulty due to the notoriously complex image formation process. Here we propose to learn a radar sensor model capable of synthesising faithful radar observations based on simulated elevation maps. In particular, we adopt an adversarial approach to learning a forward sensor model from unaligned radar examples. In addition, modelling the backward model encourages the output to remain aligned to the world state through a cyclical consistency criterion. The backward model is further constrained to predict elevation maps from real radar data that are grounded by partial measurements obtained from corresponding lidar scans. Both models are trained in a joint optimisation. We demonstrate the efficacy of our approach by evaluating a down-stream segmentation model trained purely on simulated data in a real-world deployment. This achieves performance within four percentage points of the same model trained entirely on real data.
Recursive Association Rule Mining

Mining frequent itemsets and association rules is an essential task within data mining and data analysis. In this paper, we introduce PrefRec, a recursive algorithm for finding frequent itemsets and association rules. Its main advantage is its recursiveness with respect to the items. It is particularly efficient for updating the mining process when new items are added to the database or when some are excluded. We present in a complete way the logic of the algorithm as well as its various applications. Finally we present experiments carried out in the R language comparing PrefRec with Apriori and Eclat the two most powerful algorithms in this language. To achieve this we built an R package to run our algorithm.
Surface Complexation Modeling: Hydrous Ferric Oxide

The Generalized Two--Layer Model. Experimental Data. Data Compilation and Treatment Methods. Properties of Hydrous Ferric Oxide, Cation Sorption on Hydrous Ferric Oxide. Anion Sorption on Hydrous Ferric Oxide. Use of the Model and Data Base. The Coulombic Effect. Coherence and Extrapolation of Results. References. Appendices. Author Index. Subject Index.
How to Measure Your App: A Couple of Pitfalls and Remedies in Measuring App Performance in Online Controlled Experiments

Effectively measuring, understanding, and improving mobile app performance is of paramount importance for mobile app developers. Across the mobile Internet landscape, companies run online controlled experiments (A/B tests) with thousands of performance metrics in order to understand how app performance causally impacts user retention and to guard against service or app regressions that degrade user experiences. To capture certain characteristics particular to performance metrics, such as enormous observation volume and high skewness in distribution, an industry-standard practice is to construct a performance metric as a quantile over all performance events in control or treatment buckets in A/B tests. In our experience with thousands of A/B tests provided by Snap, we have discovered some pitfalls in this industry-standard way of calculating performance metrics that can lead to unexplained movements in performance metrics and unexpected misalignment with user engagement metrics. In this paper, we discuss two major pitfalls in this industry-standard practice of measuring performance for mobile apps. One arises from strong heterogeneity in both mobile devices and user engagement, and the other arises from self-selection bias caused by post-treatment user engagement changes. To remedy these two pitfalls, we introduce several scalable methods including user-level performance metric calculation and imputation and matching for missing metric values. We have extensively evaluated these methods on both simulation data and real A/B tests, and have deployed them into Snap's in-house experimentation platform.
QUESTDB: A database of highly accurate excitation energies for the electronic structure community

We describe our efforts of the past few years to create a large set of more than 500 highly accurate vertical excitation energies of various natures (π → π*, n → π*, double excitation, Rydberg, singlet, doublet, triplet, etc.) in small‐ and medium‐sized molecules. These values have been obtained using an incremental strategy which consists in combining high‐order coupled cluster and selected configuration interaction calculations using increasingly large diffuse basis sets in order to reach high accuracy. One of the key aspects of the so‐called QUEST database of vertical excitations is that it does not rely on any experimental values, avoiding potential biases inherently linked to experiments and facilitating theoretical cross comparisons. Following this composite protocol, we have been able to produce theoretical best estimates (TBEs) with the aug‐cc‐pVTZ basis set for each of these transitions, as well as basis set corrected TBEs (i.e., near the complete basis set limit) for some of them. The TBEs/aug‐cc‐pVTZ have been employed to benchmark a large number of (lower‐order) wave function methods such as CIS(D), ADC(2), CC2, STEOM‐CCSD, CCSD, CCSDR(3), CCSDT‐3, ADC(3), CC3, NEVPT2, and so on (including spin‐scaled variants). In order to gather the huge amount of data produced during the QUEST project, we have created a website (https://lcpq.github.io/QUESTDB_website) where one can easily test and compare the accuracy of a given method with respect to various variables such as the molecule size or its family, the nature of the excited states, the type of basis set, and so on. We hope that the present review will provide a useful summary of our effort so far and foster new developments around excited‐state methods.
Spectrum of the incompressible viscous Rayleigh-Taylor system.

The linear instability study of the viscous Rayleigh-Taylor model in the neighborhood of a laminar smooth density profile $\rho_0(x_3)$ amounts to the study of the following ordinary differential equation of order 4: \begin{equation}\label{MainEq} -\lambda^2 [ \rho_0 k^2 \phi - (\rho_0 \phi')'] = \lambda \mu (\phi^{(4)} - 2k^2 \phi'' + k^4 \phi) - gk^2 \rho_0'\phi, \end{equation} where $\lambda$ is the growth rate in time, $k$ is the wave number transverse to the density profile. We first derive the growth rate obtained for the toy model where $\rho_0(x_3) = \rho_+ 1_{\{x_3>0\}} + \rho_- 1_{\{x_3<0\}}$, hence generalizing the well known inviscid Rayleigh-Taylor study between two immiscible fluids. In the general case of a smooth increasing profile, we prove that, contrary to the toy model, and in accordance with the results of \cite{HL03}, there is an infinite sequence of non trivial solutions $(\lambda_n, \phi_n)$, with $\lambda_n\rightarrow 0$ when $n\rightarrow +\infty$ and $\phi_n\in H^4(\mathbf{R})$, first in the case of $\rho'_0$ compactly supported, dealing with a problem on a compact interval, then when $\rho_0$ converges at $\pm\infty$ to finite limits $\rho_{\pm}$. We thus provide a spectral analysis of the linearized viscous Rayleigh-Taylor problem showing that there are infinitely many unstable eigenmodes.
Transits close to the Lagrangian solutions L 1, L 2 in the elliptic restricted three-body problem

In the last decades a peculiar family of solutions of the circular restricted three body problem has been used to explain the temporary captures of small bodies and spacecrafts by a planet of the Solar System. These solutions, which transit close to the Lagrangian points L 1, L 2 of the CRTBP, have been classified using the values of approximate local integrals and of the Jacobi constant. The use for small bodies of the Solar System requires to consider a hierarchical extension of the model, from the CRTBP to the full N planetary problem. The elliptic restricted three body, which is the first natural extension of the CRTBP, represents already a challenge, since global first integrals such as the Jacobi constant are not known for this problem. In this paper we extend the classification of the transits occurring close to the Lagrangian points L 1, L 2 of the ERTBP using a combination of the Floquet theory and Birkhoff normalizations. Provided that certain non-resonance conditions are satisfied, we conjugate the Hamiltonian of the problem to an integrable normal form Hamiltonian with remainder, which is used to define approximate local first integrals and to classify the transits of orbits through a neighbourhood of the Lagrange equilibria according to the values of these integrals. We provide numerical demonstrations for the Earth–Moon ERTBP.
Who’s debugging the debuggers? exposing debug information bugs in optimized binaries

Despite the advancements in software testing, bugs still plague deployed software and result in crashes in production. When debugging issues —sometimes caused by “heisenbugs”— there is the need to interpret core dumps and reproduce the issue offline on the same binary deployed. This requires the entire toolchain (compiler, linker, debugger) to correctly generate and use debug information. Little attention has been devoted to checking that such information is correctly preserved by modern toolchains’ optimization stages. This is particularly important as managing debug information in optimized production binaries is non-trivial, often leading to toolchain bugs that may hinder post-deployment debugging efforts. In this paper, we present Debug2, a framework to find debug information bugs in modern toolchains. Our framework feeds random source programs to the target toolchain and surgically compares the debugging behavior of their optimized/unoptimized binary variants. Such differential analysis allows Debug2 to check invariants at each debugging step and detect bugs from invariant violations. Our invariants are based on the (in)consistency of common debug entities, such as source lines, stack frames, and function arguments. We show that, while simple, this strategy yields powerful cross-toolchain and cross-language invariants, which can pinpoint several bugs in modern toolchains. We have used Debug2 to find 23 bugs in the LLVM toolchain (clang/lldb), 8 bugs in the GNU toolchain (GCC/gdb), and 3 in the Rust toolchain (rustc/lldb)—with 14 bugs already fixed by the developers.
The Application of Weak-Anion Exchange Chromatography for the Analysis of Organic Zwitterions Using LC/MS/MS

A rapid and accurate quantitative method was developed and validated for the analysis of four urinary organic acids with nitrogen containing functional groups, formiminoglutamic acid (FIGLU), pyroglutamic acid (PYRGLU), 5-hydroxyindoleacetic acid (5-HIAA), and 2-methylhippuric acid (2-METHIP) by liquid chromatography tandem mass spectrometry (LC/MS/MS). The chromatography was developed using a weak anion-exchange amino column that provided mixed-mode retention of the analytes. The elution gradient relied on changes in mobile phase pH over a concave gradient, without the use of counter-ions or concentrated salt buffers. A simple sample preparation was used, only requiring the dilution of urine prior to instrumental analysis. The method was validated based on linearity (r 2 ≥ 0.995), accuracy (85– 115%), precision (C.V. < 12%), sample preparation stability (≤ 5%, 72h), and established patient ranges. The method was found to be both efficient and accurate for the analysis of urinary zwitterionic organic acids.
Phosphorene Nanoribbons, Phosphorus Nanotubes, and van der Waals Multilayers

We perform a comprehensive first-principles study of the electronic properties of phosphorene nanoribbons, phosphorus nanotubes, multilayer phosphorene sheets, and heterobilayers of phosphorene and two-dimensional (2D) transition-metal dichalcogenide (TMDC) monolayer. The tensile strain and electric-field effects on electronic properties of low-dimensional phosphorene nanostructures are also investigated. Our calculations show that the bare zigzag phosphorene nanoribbons (z-PNRs) are metals regardless of the ribbon width, whereas the bare armchair phosphorene nanoribbons (a-PNRs) are semiconductors with indirect bandgaps and the bandgaps decrease with increasing ribbon width. We find that compressive (or tensile) strains can reduce (or enlarge) the bandgap of the bare a-PNRs while an in-plane electric field can significantly reduce the bandgap of the bare a-PNRs, leading to the semiconductor-to-metal transition beyond certain electric field. For edge-passivated PNR by hydrogen, z-PNRs become semiconductor.
Transient High-Pressure Hydrogen Jet Measurements

Jets produced by prototype multi-hole gaseous injectors were visualized using schlieren methods. Hydrogen and helium were injected at pressures ranging from 1.3 bar to 104 bar into chamber densities ranging from 1.15 to 12.8 kg/m, resulting in jets spanning from subsonic to highly underexpanded conditions. The jet tip penetration rate was found to increase with injection pressure, and decrease with increasing chamber density, as expected. The jet angle was also measured, but variability in the results restricted the quantitative assessment of trends. The complex expansion and shock structures within the underexpanded jets were clearly visible, and the distance between the expansion wave fronts was found to scale directly with the ratio of the exit to chamber pressure. Two injector characteristics, the discharge coefficient and rate shape, were measured to describe injector performance. The discharge coefficient was found to range from 0.19 to 0.33, while the rate shape displayed “top hat” behavior for all conditions tested. Five normalization models that included the effects of expansion outside the nozzle, jet angle variation, and discharge coefficient variation were investigated to analyze their importance in the collapse of the penetration rate data from the threeand seven-hole injectors. The nondimensional penetration was found to be linearly dependent on the square root of the nondimensional time, indicating self-similar behavior for each investigated normalization scheme. The uncertainty of the slopes of individual runs was quantified and was found to vary for each method, with no clearly superior method.
Ion-molecule reactions of hydrocarbon ions in C2H2 and HCN

Rate coefficients and product distributions have been determined for reaction of the ions C/sub x/H/sub y//sup +/ (1 less than or equal to x less than or equal to 4, 0 less than or equal to y less than or equal to 4) with C/sub 2/H/sub 2/ and HCN. The measurements were obtained using the ion cyclotron resonance (ICR) technique at 298 K. In several reactions an association product was observed at pressures as low as 1 x 10/sup -6/ torr, and in these cases stabilization of the intermediate was assumed to be by photon emission. Most of the reactions studied yield ions having a larger carbon skeleton than the reactant ion. These reactions provide routes for building large organic and organonitrogen molecules in combustion zones of unsaturated hydrocarbon flames and in astrochemical environments.