Miracle-dz/UniFAR-FTUs huggingface dataset:
Bifurcation of solutions to Hamiltonian boundary value problems

A bifurcation is a qualitative change in a family of solutions to an equation produced by varying parameters. In contrast to the local bifurcations of dynamical systems that are often related to a change in the number or stability of equilibria, bifurcations of boundary value problems are global in nature and may not be related to any obvious change in dynamical behaviour. Catastrophe theory is a well-developed framework which studies the bifurcations of critical points of functions. In this paper we study the bifurcations of solutions of boundary-value problems for symplectic maps, using the language of (finite-dimensional) singularity theory. We associate certain such problems with a geometric picture involving the intersection of Lagrangian submanifolds, and hence with the critical points of a suitable generating function. Within this framework, we then study the effect of three special cases: (i) some common boundary conditions, such as Dirichlet boundary conditions for second-order systems, restrict the possible types of bifurcations (for example, in generic planar systems only the A-series beginning with folds and cusps can occur); (ii) integrable systems, such as planar Hamiltonian systems, can exhibit a novel periodic pitchfork bifurcation; and (iii) systems with Hamiltonian symmetries or reversing symmetries can exhibit restricted bifurcations associated with the symmetry. This approach offers an alternative to the analysis of critical points in function spaces, typically used in the study of bifurcation of variational problems, and opens the way to the detection of more exotic bifurcations than the simple folds and cusps that are often found in examples.
String Dualities and Gaugings of Supergravity

This thesis is devoted to various questions connected with duality. It is composed of two parts. The first part discusses some aspects of timelike T-duality. We explore the possibility of compactification of supergravity theories with various signatures (low energy limit of $M$-theories which are dual under timelike T-dualities) on parallelizable internal seven dimensional (pseudo-)spheres. We show that, beside the standard theory, only one of the dual theories known as $M'$-theory can admit such a solution. The effective four dimensional theory is non-supersymmetric and due to the presence of torsion the symmetry of seven dimensional (pseudo-)sphere breaks down to $Spin(3,4)$. In the second part, in an attempt to have a systematic discussion of gaugings in supergravity, we show the isomorphism between the space of local deformations of the appropriate zero coupling limit of the embedding tensor Lagrangian and that of the second-order scalar-vector Lagrangian, describing the bosonic sector of supergravity ignoring gravity, in a chosen duality frame determined by embedding tensors. We analyze the BV-BRST deformation of a class of scalar-vector coupled Lagrangians, which contains supergravity Lagrangians as examples, and find a set of constraints that guarantee the consistency of the deformations of the Lagrangians. We show in principle that for a large class of theories considered in this thesis, the only deformations are those of the Yang-Mills type associated with a subgroup of the rigid symmetries.
On some parabolic systems arising from a nuclear reactor model with nonlinear boundary conditions

In this paper, we are concerned with a reaction diffusion system arising from a nuclear reactor model in bounded domains with nonlinear boundary conditions. We show the existence of a stationary solution and its ordered uniqueness. It is also shown that every positive stationary solution possesses threshold property to determine blow-up or globally existence for solutions of nonstationary problem.
Lyophilization process engineering and thermostability of ID93 + GLA-SE, a single-vial adjuvanted subunit tuberculosis vaccine candidate for use in clinical studies

Promising clinical efficacy results have generated considerable enthusiasm for the potential impact of adjuvant-containing subunit tuberculosis vaccines. The development of a thermostable tuberculosis vaccine formulation could have significant benefits on both the cost and feasibility of global vaccine distribution. The tuberculosis vaccine candidate ID93 + GLA-SE has reached Phase 2 clinical testing, demonstrating safety and immunogenicity as a two-vial point-of-care mixture. Earlier publications have detailed efforts to develop a lead candidate single-vial lyophilized thermostable ID93 + GLA-SE vaccine formulation. The present report describes the lyophilization process development and scale-up of the lead candidate thermostable ID93 + GLA-SE composition. The manufacture of three full-scale engineering batches was followed by one batch made and released under current Good Manufacturing Practices (cGMP). Up to 4.5 years of stability data were collected. The cGMP lyophilized ID93 + GLA-SE passed all manufacturing release test criteria and maintained stability for at least 3 months when stored at 37°C and up to 24 months when stored at 5°C. This work represents the first advancement of a thermostable adjuvant-containing subunit tuberculosis vaccine to clinical testing readiness.
Mathematical appraisal of SARS-CoV-2 Omicron epidemic outbreak in unprecedented Shanghai lockdown

The SARS-CoV-2 Omicron outbreak is ongoing in Shanghai, home to 25 million population. Here, we presented a novel mathematical model to evaluate the Omicron spread and Zero-COVID strategy. Our model provided important parameters, the average quarantine ratio, the detection interval from being infected to being tested positive, and the spreading coefficient to understand the epidemic progression better. Moreover, we found that the key to a relatively accurate long-term forecast was to take the variation/relaxation of the parameters into consideration based on the flexible execution of the quarantine policy. This allowed us to propose the criteria for estimating the parameters and outcome for the ending stage that is likely to take place in late May. Altogether, this model helped to give a correct mathematical appraisal of the SARS-CoV-2 Omicron outbreak under the strict Zero-COVID policy in China.
Safety and efficacy of extracorporeal shock wave lithotripsy vs. flexible ureteroscopy in the treatment of urinary calculi: A systematic review and meta-analysis

Objective This study aims to compare the safety and efficacy of extracorporeal shock wave lithotripsy (SWL) and flexible ureteroscopy lithotripsy (f-URS) in treating urinary tract stones. Methods We systematically searched PubMed, Embase, and Cochrane for literature comparing SWL with f-URS. The primary outcomes we focused on were stone-free rate (SFR) and complications; the secondary outcomes were operation time, hospital stay, retreatment rate, number of sessions, and auxiliary procedures rate. We used ReviewManager version 5.4. 1 and STATA version 14.2 for meta-analysis. Results Seventeen studies with a total of 2,265 patients were included in the meta-analysis, including 1,038 patients in the SWL group and 1,227 patients in the f-URS group. The meta-analysis indicated that patients in the f-URS group had higher SFR than those in the SWL group [odds ratio (OR): 2.00, 95% confidence interval (CI): 1.29–3.12, p = 0.002]. In addition, we found no significant difference in complications (OR: 1.08, 95% CI: 0.85–1.37) between the two treatments. Also, we found that the retreatment rate and the auxiliary procedure rate in the f-URS group were significantly lower than those in the SWL group (OR: 0.08, 95% CI: 0.02–0.24, p < 0.00001; OR: 0.30, 95% CI: 0.11–0.83, p = 0.02). Moreover, the number of sessions in the f-URS group was significantly lower than that in the SWL group [mean difference (MD): −1.96, 95% CI: −1.55 to −0.33, p = 0.003]. However, the operation time and hospital stay in the f-URS group were significantly longer than those in the SWL group (MD: 11.24, 95% CI: 3.51–18.56, p = 0.004; MD: 1.14, 95% CI: 0.85–1.42, p < 0.00001). Conclusion For 1–2-cm urinary stones, f-URS can achieve a higher SFR than SWL while having a lower retreatment rate, number of sessions, and auxiliary procedure rate. For urinary stones <1 cm, there was no significant difference in SFR between SWL and f-URS groups. The SWL group has a shorter operative time and hospital stay than the f-URS group.
A $L^{2}$ to $L^{\infty}$ approach for the Landau Equation

Consider the Landau equation with Coulomb potential in a periodic box. We develop a new $L^{2}\rightarrow L^{\infty }$ framework to construct global unique solutions near Maxwellian with small $L^{\infty }\ $norm. The first step is to establish global $L^{2}$ estimates with strong velocity weight and time decay, under the assumption of $L^{\infty }$ bound, which is further controlled by such $L^{2}$ estimates via De Giorgi's method \cite{golse2016harnack} and \cite{mouhot2015holder}. The second step is to employ estimates in $S_{p}$ spaces to control velocity derivatives to ensure uniqueness, which is based on Holder estimates via De Giorgi's method \cite{golse2016harnack}, \cite{golse2015holder}, and \cite{mouhot2015holder}.
Probiotics modulate gastrointestinal microbiota after Helicobacter pylori eradication: A multicenter randomized double-blind placebo-controlled trial

Background Helicobacter pylori (H. pylori) eradication has been reported to cause short-term disruption of gut microbiota. It is acknowledged that probiotics supplementation mitigates side effects induced by H. pylori eradication, yet its role on alleviating dysbiosis of microbiota is obscure. Objectives To evaluate the impact of probiotics on gastrointestinal microbiota after eradication therapy. Methods This was a multicenter, double-blinded, randomized trial done at seven centers in China. A total of 276 treatment-naïve H. pylori-positive patients were randomly assigned to receive 14-day bismuth-containing quadruple therapy (esomeprazole, bismuth, amoxicillin, furazolidone) combined with probiotics (Bifidobacterium Tetragenous viable Bacteria Tablets) (n=140) or placebo (n=136) for 28 days. Saliva, gastric mucosa and fecal samples were collected before and after therapy for 16S rRNA gene sequencing. Results The incidence of gastrointestinal adverse events was lower in probiotics group compared to placebo group (23.6% vs 37.7%, p=0.016), while there was no significant difference in eradication rate. We found dramatic perturbations of gut microbiota immediately following eradication, with the predominance of Proteobacteria in replacement of commensal Firmicutes and Bacteroidetes, and gradually restored after two weeks. The reduction of gut Bacteroidetes caused by eradication drugs was neutralized with probiotics supplementation. The gastric microbiota was completely reconstituted with H. pylori depleted and other taxa flourished. Of note, patients treated with probiotics showed smaller fluctuations of gastric microbiota compared to those with placebo. We also observed changes of saliva microbiota after H. pylori eradication, illustrated by the overgrowth of Neisseria and depletion of Streptococcus. The expansion of some pathogenic genera, including Porphyromonas, Leptotrichia, in the mouth was suppressed by probiotics. Conclusion This study not only demonstrated the beneficial effect of probiotics implementation on side events during H. pylori eradication but also provided a comprehensive profile of microbiome alterations along gastrointestinal tract that modulated by probiotics.
Amorphic complexity

We introduce amorphic complexity as a new topological invariant that measures the complexity of dynamical systems in the regime of zero entropy. Its main purpose is to detect the very onset of disorder in the asymptotic behaviour. For instance, it gives positive value to Denjoy examples on the circle and Sturmian subshifts, while being zero for all isometries and Morse–Smale systems. After discussing basic properties and examples, we show that amorphic complexity and the underlying asymptotic separation numbers can be used to distinguish almost automorphic minimal systems from equicontinuous ones. For symbolic systems, amorphic complexity equals the box dimension of the associated Besicovitch space. In this context, we concentrate on regular Toeplitz flows and give a detailed description of the relation to the scaling behaviour of the densities of the p-skeletons. Finally, we take a look at strange non-chaotic attractors appearing in so-called pinched skew product systems. Continuous-time systems, more general group actions and the application to cut and project quasicrystals will be treated in subsequent work.
Survival analyses of the ZeOxaNMulti trial: Follow-up randomized, double-blinded, placebo-controlled trial of oral PMA-zeolite to prevent chemotherapy-induced side effects, especially peripheral neuropathy

Following the previously published results of the clinical randomized ZeOxaNMulti trial, we evaluated the potential of the tested product PMA-ZEO (Multizeo Med) in the prevention of chemotherapy-induced side effects (especially peripheral neuropathy) within a 30-month follow-up analysis. The aim was to determine the disease-free survival (DFS), progression-free survival (PFS), and overall survival (OS) in a study-population suffering from colorectal cancer that was previously enrolled in the ZeOxaNMulti trial from April 2015 to October 2018. The participants of the study were randomized to receive either PMA-ZEO or placebo while undergoing oxaliplatin-based chemotherapy. A total of 104 patients (pts) (51% of participants randomized to the PMA-ZEO group and 49% to the placebo group), out of a total of 120 pts included in the ZeOxaNMulti trial in 2015, were followed up until March 2021 and were included in the follow-up analysis. According to the chemotherapy line, 44.2% of patients received chemotherapy in an adjuvant setting, and 55.8% of patients received chemotherapy as first-line treatment. The statistical analysis for DFS, PFS, and OS was performed by comparison of the end results with data from the PMA-ZEO/placebo-intervention start point. The analysis of OS did not show statistically significant differences in the first-line chemotherapy patients randomized to PMA-ZEO than among the placebo group (p = 0.1) over the whole period of follow-up (30 months). However, focusing on the PMA-ZEO supplementation time point (7 months), a positive and statistically significant trend (p = 0.004) was documented in the OS analysis for the first-line chemotherapy patients with increasing months of PMA-ZEO treatment compared to the placebo group. Furthermore, borderline statistical significance was reached for PFS at the PMA-ZEO supplementation time point (7 months) in the first-line chemotherapy patients (p = 0.05) for cancer progression events. After stratification of the first-line chemotherapy patients, statistically relevant trends for OS for age, comorbidities, and oxaliplatin dosage (cycles) were also determined. The overall results for DFS (adjuvant patients), PFS (first-line chemotherapy patients), and OS (adjuvant and first-line chemotherapy patients) were generally slightly better in the PMA-ZEO group than in the placebo group, even though no statistically significant results were obtained between the groups within the follow-up period until 2021 (30 months). Based on this follow-up analysis, protective effects of PMA-zeolite supplementation can be deduced. A positive trend and more importantly, significant results in PFS and OS for specific patient groups during and/or after PMA-ZEO treatment were determined, which supports the use of PMA-ZEO as an oncological supportive therapy.
Comparative genomics study of Staphylococcus aureus isolated from cattle and humans reveals virulence patterns exclusively associated with bovine clinical mastitis strains

Staphylococcus aureus causes nosocomial and intramammary infections in humans and cattle, respectively. A large number of virulence factors are thought to play important roles in the pathogenesis of this bacterium. Currently, genome-wide and data-analysis studies are being used to better understand its epidemiology. In this study, we conducted a genome wide comparison and phylogenomic analyses of S. aureus to find specific virulence patterns associated with clinical and subclinical mastitis strains in cattle and compare them with those of human origin. The presence/absence of key virulence factors such as adhesin, biofilm, antimicrobial resistance, and toxin genes, as well as the phylogeny and sequence type of the isolates were evaluated. A total of 248 genomes (27 clinical mastitis, 43 subclinical mastitis, 21 milk, 53 skin-related abscesses, 49 skin infections, and 55 pus from cellulitis) isolated from 32 countries were evaluated. We found that the cflA, fnbA, ebpS, spa, sdrC, coa, emp, vWF, atl, sasH, sasA, and sasF adhesion genes, as well as the aur, hglA, hglB, and hglC toxin genes were highly associated in clinical mastitis strains. The strains had diverse genetic origins (72 protein A and 48 sequence types with ST97, ST8 and ST152 being frequent in isolates from clinical mastitis, abscess, and skin infection, respectively). Further, our phylogenomic analyses suggested that zoonotic and/or zooanthroponotic transmission may have occurred. These findings contribute to a better understanding of S. aureus epidemiology and the relationships between adhesion mechanisms, biofilm formation, antimicrobial resistance, and toxins and could aid in the development of improved vaccines and strain genotyping methods.
String C-group representations of alternating groups

We prove that for any integer $n\geq 12$, and for every $r$ in the interval $[3, \ldots, \lfloor (n-1)/2\rfloor]$, the group $A_n$ has a string C-group representation of rank $r$ therefore showing that the only alternating group whose set of ranks is not an interval is $A_{11}$.
Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments

Spread of antibiotic resistance is a significant challenge for our modern health care system, and even more so in developing countries with higher prevalence of both infections and resistant bacteria. Faulty usage of antibiotics has been pinpointed as a driving factor in spread of resistant bacteria through selective pressure. However, horizontal gene transfer mediated through bacteriophages may also play an important role in this spread. In a cohort of Tanzanian patients suffering from bacterial infections, we demonstrate significant differences in the oral microbial diversity between infected and non-infected individuals, as well as before and after oral antibiotics treatment. Further, the resistome carried both by bacteria and bacteriophages vary significantly, with blaCTX-M1 resistance genes being mobilized and enriched within phage populations. This may impact how we consider spread of resistance in a biological context, as well in terms of treatment regimes.
Salvianolic acid A regulates pyroptosis of endothelial cells via directly targeting PKM2 and ameliorates diabetic atherosclerosis

Rescuing endothelial cells from pyroptotic cell death emerges as a potential therapeutic strategy to combat diabetic atherosclerosis. Salvianolic acid A (SAA) is a major water-soluble phenolic acid in the Salvia miltiorrhiza Bunge, which has been used in traditional Chinese medicine (TCM) and health food products for a long time. This study investigated whether SAA-regulated pyruvate kinase M2 (PKM2) functions to protect endothelial cells. In streptozotocin (STZ)-induced diabetic ApoE−/− mice subjected to a Western diet, SAA attenuated atherosclerotic plaque formation and inhibited pathological changes in the aorta. In addition, SAA significantly prevented NLRP3 inflammasome activation and pyroptosis of endothelial cells in the diabetic atherosclerotic aortic sinus or those exposed to high glucose. Mechanistically, PKM2 was verified to be the main target of SAA. We further revealed that SAA directly interacts with PKM2 at its activator pocket, inhibits phosphorylation of Y105, and hinders the nuclear translocation of PKM2. Also, SAA consistently decreased high glucose-induced overproduction of lactate and partially lactate-dependent phosphorylation of PKR (a regulator of the NLRP3 inflammasome). Further assay on Phenylalanine (PKM2 activity inhibitor) proved that SAA exhibits the function in high glucose-induced pyroptosis of endothelial cells dependently on PKM2 regulation. Furthermore, an assay on c16 (inhibitor of PKR activity) with co-phenylalanine demonstrated that the regulation of the phosphorylated PKR partially drives PKM2-dependent SAA modulation of cell pyroptosis. Therefore, this article reports on the novel function of SAA in the pyroptosis of endothelial cells and diabetic atherosclerosis, which provides important insights into immunometabolism reprogramming that is important for diabetic cardiovascular disease complications therapy.
HIGH-ENERGY PROPERTIES OF THE ENIGMATIC Be STAR γ CASSIOPEIAE

We present the results of a broadband X-ray study of the enigmatic Be star Gamma Cassiopeiae (herein γ Cas) based on observations made with both the Suzaku and INTEGRAL observatories. γ Cas has long been recognized as the prototypical example of a small subclass of Be stars with moderately strong X-ray emission dominated by a hot thermal component in the 0.5–12 keV energy range (Lx ≈ 1032–1033 erg s−1). This places them at the high end of the known luminosity distribution for stellar emission, but several orders of magnitude below typical accretion-powered Be X-ray binaries. The INTEGRAL observations spanned an eight-year baseline and represent the deepest measurement to date at energies above ∼50 keV. We find that the INTEGRAL data are consistent within statistics to a constant intensity source above 20 keV, with emission extending up to ∼100 keV, and that searches for all of the previously reported periodicities of the system at lower energies led to null results. We further find that our combined Suzaku and INTEGRAL spectrum, which we suggest is the most accurate broadband X-ray measurement of γ Cas to date, is fitted extremely well with a thermal plasma emission model with a single absorption component. We found no compelling need for an additional non-thermal high-energy component. We discuss these results in the context of a currently favored models for γ Cas and its analogs.
DISTRIBUTIONS OF GAMMA-RAY BURSTS AND BLAZARS IN THE Lp–Ep-PLANE AND POSSIBLE IMPLICATIONS FOR THEIR RADIATION PHYSICS

We present a spectral analysis for a sample of redshift-known gamma-ray bursts (GRBs) observed with Fermi/GBM. Together with the results derived from our systematical spectral energy distribution modeling with the leptonic models for a Fermi/LAT blazar sample, we compare the distributions of the GRBs and the blazars by plotting the synchrotron peak luminosity (Ls) and the corresponding peak photon energy Es of blazars in the Lp–Ep-plane of GRBs, where Lp and Ep are the peak luminosity and peak photon energy of the GRB time-integrated νfν spectrum, respectively. The GRBs are in the high-Lp, high-Ep corner of the plane and a tight Lp–Ep relation is found, i.e., . Both flat spectrum radio quasars (FSRQs) and low-synchrotron peaking BL Lac objects (LBLs) are clustered in the low-Ep, low-Lp corner. Intermediate- and high-synchrotron peaking BL Lac objects (IBLs and HBLs) have Es ∼ 2 × 10−3–102 keV and Ls ∼ 1044–1047 erg s−1, but no dependence of Ls on Es is found. We show that the tight Lp–Ep relation of GRBs is potentially explained with the synchrotron radiation of fast-cooling electrons in a highly magnetized ejecta, and the weak anti-correlation of Ls–Es for FSRQs and LBLs may be attributed to synchrotron radiation of slow-cooling electrons in a moderately magnetized ejecta. The distributions of IBLs and HBLs in the Lp–Ep-plane may be interpreted with synchrotron radiation of fast-cooling electrons in a matter-dominated ejecta. These results may present a unified picture for the radiation physics of relativistic jets in GRBs and blazars within the framework of the leptonic synchrotron radiation models.