Network Formation Games under adversary attack with immunization: an introduction to the scientific research

En aquesta tesi de grau estudiem el model de Jocs de Formació de Xarxa amb atac i immunització introduït per Goyal et al. El model consta d'agents que volen maximitzar el benefici per connectar-se amb altres agents, fet que implica el cost de crear connexions. A més, un adversari atacarà la xarxa generada pels agents i els agents poden decidir immunitzar-se contra l'atac pagant un cost addicional. Goyal et al. van proposar diferents tipus d'adversaris. L'objectiu és comprendre el model enfocant-se a l'adversari d'atac aleatori i obtenir resultats de connectivitat, benestar social, diversitat de xarxes d'equilibri i dinàmiques de millor resposta basats en treballs previs. Pel que fa a l'adversari d'atac aleatori, demostrem que quan el cost de crear una aresta CE > 1 la xarxa d'equilibri no trivial (amb almenys una aresta i almenys un vèrtex immunitzat) resultant G és un graf connex, i quan CE i el cost de la immunització CI són constants i CE > 1, llavors el benestar de G és n^2-O(n^(5/3)). També estudiem la diversitat de xarxes d'equilibri i demostrem que entre els tipus de xarxes d'equilibri per l'adversari de màxima matança presentat per Goyal et al., graf nul, arbres, cicles, flors i graf bipartit complet també són equilibris per l'adversari d'atac aleatori amb lleugera diferència als paràmetres, les xarxes bosc tenen un cas particular d'equilibri per l'adversari d'atac aleatori però en general són només equilibri respecte a l'adversari de màxima matança. Finalment, estudiem la convergència de la dinàmica de millor resposta pel que fa a l'adversari d'atac aleatori i demostrem que pot ciclar. Concloem la nostra recerca amb una simulació de la dinàmica de millor resposta, observem que convergeix ràpidament a un equilibri eficient per l'adversari d'atac aleatori.In this bachelor thesis we study the Network Formation Games model with attack and immunization introduced by Goyal et al. The model consists of agents who want to maximize their benefit by connecting with other agents, which involves the cost of creating connections. Furthermore, an adversary will attack the network generated by agents and the agents can decide to immunize against the attack paying an additional cost. Different types of adversaries were proposed by Goyal et al. The objective is to gain an understanding of the model focusing on the random attack adversary and obtain results of connectivity, social welfare, diversity of equilibrium networks and best response dynamics based on previous works. With respect to the random attack adversary we prove that when cost of creating an edge CE > 1 the resulting non-trivial equilibrium network (with at least one edge and at least one immunized vertex) G is a connected graph, and when CE and cost of immunization CI are constants and CE > 1 then the welfare of G is n^2-O(n^(5/3)). We also study the diversity of equilibrium networks and we show that among the types of equilibrium networks for the maximum carnage adversary presented by Goyal et al., empty graph, trees, cycles, flowers and complete bipartite graph are also equilibria for the random attack adversary with slight difference in parameters, the forest networks have a particular case of equilibrium for the random attack adversary but in general they are only equilibrium with respect to the maximum carnage adversary. Finally, we study the convergence of the best response dynamics with respect to the random attack adversary and we prove that it can cycle. We conclude our research with a simulation of the best response dynamics, we observe that it converges rapidly to an efficient equilibrium for the random attack adversary

MIMO Antenna Polynomial Weighted Average Design Method of Downward-Looking Array SAR

MIMO antenna polynomial weighted average design method of downward-looking array SAR was proposed from the angle of surveying and mapping in this paper, in order to solve the ill-posed problem that an equivalent virtual array can be implemented by a variety of physical transmitter-receiver arrays for bistatic MIMO linear array. For wave band, resolution, elevation precision, and working height concerned by the applications of surveying and mapping, the length of equivalent virtual array and actual physical array meeting the needs of large scale topographical mapping was solved. Then array numbers and position vectors of MIMO downward-looking array SAR of real aerial mapping platform were optimized. According to this design, some simulation experiments and comparisons were processed. The results proved the rationality and effectiveness of this array configuration by comparing the differences of 3D imaging results and the original simulation scene, counting mean and standard deviation of elevation reconstruction error eliminating the influence of shadow areas, and counting the probability of elevation reconstruction error within half a resolution of the whole scene and individual building area

A Conserved Hydrophobic Patch on Vβ Domains Revealed by TCRβ Chain Crystal Structures: Implications for Pre-TCR Dimerization

The αβ T cell receptor (TCR) is a multimeric complex whose β chain plays a crucial role in thymocyte development as well as antigen recognition by mature T lymphocytes. We report here crystal structures of individual β subunits, termed N15β (Vβ5.2Dβ2Jβ2.6Cβ2) and N30β (Vβ13Dβ1Jβ1.1Cβ2), derived from two αβ TCRs specific for the immunodominant vesicular stomatitis virus octapeptide (VSV-8) bound to the murine H-2Kb MHC class I molecule. The crystal packing of the N15β structure reveals a homodimer formed through two Vβ domains. The Vβ/Vβ module is topologically very similar to the Vα/Vβ module in the N15αβ heterodimer. By contrast, in the N30β structure, the Vβ domain’s external hydrophobic CFG face is covered by the neighboring molecule’s Cβ domain. In conjunction with systematic investigation of previously published TCR single-subunit structures, we identified several conserved residues forming a concave hydrophobic patch at the center of the CFG outer face of the Vβ and other V-type Ig-like domains. This hydrophobic patch is shielded from solvent exposure in the crystal packing, implying that it is unlikely to be thermodynamically stable if exposed on the thymocyte surface. Accordingly, we propose a dimeric pre-TCR model distinct from those suggested previously by others and discuss its functional and structural implications

Microbial profiling identifies potential key drivers in gastric cancer patients

Gastric cancer (GC) is the fifth most commonly diagnosed cancer and the third leading cause of cancer-related death in the world. Microbiota is believed to be associated with GC. Growing evidences showed Helicobacter pylori played a key role in GC development. However, little was known about the microbiota in gastric juices and tissues in GC patients, and thus it was difficult to understand other potential microbial causation for GC. Here, we collected the gastric juice and surgically removed gastric tissues from GC patients to give insight into GC microbiota. Most microbes identified in the gastric samples were opportunistic pathogens or resident flora of the human microbiota. Further network analyses identified five opportunistic pathogens as keystone species. H. pylori is the direct cause of GC, but other opportunistic microbes might also function in GC development. The microbiota in the gastric juice and gastric tissue of the GC patients were complex, and some dominant opportunistic pathogens contributed to the GC development. This study introduces microbiota in gastric juice, gastric normal tissue and gastric cancer tissue of GC patients, and highlights the potential keystone microbes functioned during GC development

X-Ray Induced Photodynamic Therapy: A Combination of Radiotherapy and Photodynamic Therapy

Conventional photodynamic therapy (PDT)'s clinical application is limited by depth of penetration by light. To address the issue, we have recently developed X-ray induced photodynamic therapy (X-PDT) which utilizes X-ray as an energy source to activate a PDT process. In addition to breaking the shallow tissue penetration dogma, our studies found more efficient tumor cell killing with X-PDT than with radiotherapy (RT) alone. The mechanisms behind the cytotoxicity, however, have not been elucidated. In the present study, we investigate the mechanisms of action of X-PDT on cancer cells. Our results demonstrate that X-PDT is more than just a PDT derivative but is essentially a PDT and RT combination. The two modalities target different cellular components (cell membrane and DNA, respectively), leading to enhanced therapy effects. As a result, X-PDT not only reduces short-term viability of cancer cells but also their clonogenecity in the long-run. From this perspective, X-PDT can also be viewed as a unique radiosensitizing method, and as such it affords clear advantages over RT in tumor therapy, especially for radioresistant cells. This is demonstrated not only in vitro but also in vivo with H1299 tumors that were either subcutaneously inoculated or implanted into the lung of mice. These findings and advances are of great importance to the developments of X-PDT as a novel treatment modality against cancer

Abnormal Voxel-Wise Degree Centrality in Patients With Late-Life Depression: A Resting-State Functional Magnetic Resonance Imaging Study.

Objectives:Late-life depression (LLD) has negative impacts on somatic, emotional and cognitive domains of the lives of patients. Elucidating the abnormality in the brain networks of LLD patients could help to strengthen the understanding of LLD pathophysiology, however, the studies exploring the spontaneous brain activity in LLD during the resting state remain limited. This study aimed at identifying the voxel-level whole-brain functional connectivity changes in LLD patients. Methods:Fifty patients with late-life depression (LLD) and 33 healthy controls were recruited. All participants underwent a resting-state functional magnetic resonance imaging scan to assess the voxel-wise degree centrality (DC) changes in the patients. Furthermore, DC was compared between two patient subgroups, the late-onset depression (LOD) and the early-onset depression (EOD). Results:Compared with the healthy controls, LLD patients showed increased DC in the inferior parietal lobule, parahippocampal gyrus, brainstem and cerebellum (p < 0.05, AlphaSim-corrected). LLD patients also showed decreased DC in the somatosensory and motor cortices and cerebellum (p < 0.05, AlphaSim-corrected). Compared with EOD patients, LOD patients showed increased centrality in the superior and middle temporal gyrus and decreased centrality in the occipital region (p < 0.05, AlphaSim-corrected). No significant correlation was found between the DC value and the symptom severity or disease duration in the patients after the correction for multiple comparisons. Conclusions:These findings indicate that the intrinsic abnormality of network centrality exists in a wide range of brain areas in LLD patients. LOD patients differ with EOD patients in cortical network centrality. Our study might help to strengthen the understanding of the pathophysiology of LLD and the potential neural substrates underlie related emotional and cognitive impairments observed in the patients

Intraflagellar Transport (IFT) Protein IFT25 Is a Phosphoprotein Component of IFT Complex B and Physically Interacts with IFT27 in Chlamydomonas

BACKGROUND: Intraflagellar transport (IFT) is the bidirectional movement of IFT particles between the cell body and the distal tip of a flagellum. Organized into complexes A and B, IFT particles are composed of at least 18 proteins. The function of IFT proteins in flagellar assembly has been extensively investigated. However, much less is known about the molecular mechanism of how IFT is regulated. METHODOLOGY/PRINCIPAL FINDINGS: We herein report the identification of a novel IFT particle protein, IFT25, in Chlamydomonas. Dephosphorylation assay revealed that IFT25 is a phosphoprotein. Biochemical analysis of temperature sensitive IFT mutants indicated that IFT25 is an IFT complex B subunit. In vitro binding assay confirmed that IFT25 binds to IFT27, a Rab-like small GTPase component of the IFT complex B. Immunofluorescence staining showed that IFT25 has a punctuate flagellar distribution as expected for an IFT protein, but displays a unique distribution pattern at the flagellar base. IFT25 co-localizes with IFT27 at the distal-most portion of basal bodies, probably the transition zones, and concentrates in the basal body region by partially overlapping with other IFT complex B subunits, such as IFT46. Sucrose density gradient centrifugation analysis demonstrated that, in flagella, the majority of IFT27 and IFT25 including both phosphorylated and non-phosphorylated forms are cosedimented with other complex B subunits in the 16S fractions. In contrast, in cell body, only a fraction of IFT25 and IFT27 is integrated into the preassembled complex B, and IFT25 detected in complex B is preferentially phosphorylated. CONCLUSION/SIGNIFICANCE: IFT25 is a phosphoprotein component of IFT particle complex B. IFT25 directly interacts with IFT27, and these two proteins likely form a subcomplex in vivo. We postulate that the association and disassociation between the subcomplex of IFT25 and IFT27 and complex B might be involved in the regulation of IFT

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

DataSheet1_Can participation in cooperatives promote the adoption of green production techniques by Chinese apple growers: Counterfactual estimation based on propensity score matching.docx

As one of the key links of agricultural green sustainable development, it is an effective path to popularize green production technology and promote farmers’ adoption of green production technology by using cooperatives as an organizational vehicle. Based on the survey of 314 apple farmers in Shaanxi and Gansu provinces, the degree of adoption of green production technology was measured by the coefficient of variation method. At the same time, in view of the selection bias of farmers’ participation in cooperatives, the propensity score matching method was used to evaluate the influence of farmers’ participation in cooperatives on the adoption of green production techniques. The results showed that participation in cooperatives increases the probability of farmers adopting green production techniques from 25.29% to 30.29%, indicating that cooperatives increase the degree to which farmers adopt green production techniques. In addition, increased cognition of green production, which increases the price and net profit of products sold and reduces expectations of green production risks, is the primary channel through which cooperatives lead farmers to adopt green production technologies. Participation in cooperatives, though, increased input costs for apple production. In order to strengthen the active role of cooperatives in the popularization of green production technologies, more support should be given to cooperatives, and emphasis should be placed on strengthening their institutional development so that they can be standardized and developed at a high quality.</p