Miracle-dz/UniFAR-FTUs huggingface dataset:
Finite element study of vortex‐induced cross‐flow and in‐line oscillations of a circular cylinder at low Reynolds numbers

Vortex-induced vibrations of a circular cylinder placed in a uniform flow at Reynolds number 325 are investigated using a stabilized space–time finite element formulation. The Navier–Stokes equations for incompressible fluid flow are solved for a two-dimensional case along with the equations of motion of the cylinder that is mounted on lightly damped spring supports. The cylinder is allowed to vibrate, both in the in-line and in the cross-flow directions. Results of the computations are presented for various values of the structural frequency of the oscillator, including those that are sub and superharmonics of the vortex-shedding frequency for a stationary cylinder. In most of the cases, the trajectory of the cylinder corresponds to a Lissajou figure of 8. Lock-in is observed for a range of values of the structural frequency. Over a certain range of structural frequency (Fs), the vortex-shedding frequency of the oscillating cylinder does not match Fs exactly; there is a slight detuning. This phenomenon is referred to as soft-lock-in. Computations show that this detuning disappears when the mass of the cylinder is significantly larger than the mass of the surrounding fluid it displaces. A self-limiting nature of the oscillator with respect to cross-flow vibration amplitude is observed. It is believed that the detuning of the vortex-shedding frequency from the structural frequency is a mechanism of the oscillator to self-limit its vibration amplitude. The dependence of the unsteady solution on the spatial resolution of the finite element mesh is also investigated. Copyright © 1999 John Wiley & Sons, Ltd.
Identifying influential nodes in complex contagion mechanism

Identifying influential nodes in complex networks is one of the most important and challenging problems to help optimize the network structure, control the spread of the epidemic and accelerate the spread of information. In a complex network, the node with the strongest propagation capacity is known as the most influential node from the perspective of propagation. In recent years, identifying the key nodes in complex networks has received increasing attention. However, it is still a challenge to design a metric that has low computational complexity but can accurately identify important network nodes. Currently, many centrality metrics used to evaluate the influence capability of nodes cannot balance between high accuracy and low time complexity. Local centrality suffers from accuracy problems, while global metrics require higher time complexity, which is inefficient for large scale networks. In contrast, semi-local metrics are with higher accuracy and lower time cost. In this paper, we propose a new semi-local centrality measure for identifying influential nodes under complex contagion mechanisms. It uses the higher-order structure within the first and second-order neighborhoods of nodes to define the importance of nodes with near linear time complexity, which can be applied to large-scale networks. To verify the accuracy of the proposed metric, we simulated the disease propagation process in four real and two artificial networks using the SI model under complex propagation. The simulation results show that the proposed method can identify the nodes with the strongest propagation ability more effectively and accurately than other current node importance metrics.
Vascular endothelial growth factor isoforms differentially protect neurons against neurotoxic events associated with Alzheimer’s disease

Alzheimer’s disease (AD) is the most common cause of dementia, the chronic and progressive deterioration of memory and cognitive abilities. AD can be pathologically characterised by neuritic plaques and neurofibrillary tangles, formed by the aberrant aggregation of β-amyloid and tau proteins, respectively. We tested the hypothesis that VEGF isoforms VEGF-A165a and VEGF-A165b, produced by differential splice site selection in exon 8, could differentially protect neurons from neurotoxicities induced by β-amyloid and tau proteins, and that controlling expression of splicing factor kinase activity could have protective effects on AD-related neurotoxicity in vitro. Using oxidative stress, β-amyloid, and tau hyperphosphorylation models, we investigated the effect of VEGF-A splicing isoforms, previously established to be neurotrophic agents, as well as small molecule kinase inhibitors, which selectively inhibit SRPK1, the major regulator of VEGF splicing. While both VEGF-A165a and VEGF-A165b isoforms were protective against AD-related neurotoxicity, measured by increased metabolic activity and neurite outgrowth, VEGF-A165a was able to enhance neurite outgrowth but VEGF-A165b did not. In contrast, VEGF-A165b was more effective than VEGF-A165a in preventing neurite “dieback” in a tau hyperphosphorylation model. SRPK1 inhibition was found to significantly protect against neurite “dieback” through shifting AS of VEGFA towards the VEGF-A165b isoform. These results indicate that controlling the activities of the two different isoforms could have therapeutic potential in Alzheimer’s disease, but their effect may depend on the predominant mechanism of the neurotoxicity—tau or β-amyloid.
Case report: Immediate revascularization for symptomatic hepatic artery pseudoaneurysm after orthotopic liver transplantation? A case series and literature review

Introduction Hepatic artery pseudoaneurysm (HAPA), a rare vascular complication that can develop after liver transplantation, is associated with a high mortality rate and graft loss. To salvage the liver graft, immediate revascularization, either through surgical or endovascular intervention, is required. However, currently there is no consensus on the optimal strategy. Here, we report three cases of liver transplant recipients diagnosed with HAPA and treated with immediate revascularization. In addition, we present an overview of HAPA cases described in the literature and make recommendations on how to treat this rare complication. Methods All adults transplanted in our center between 2005 and 2021 were retrospectively reviewed. Literature search was done in PubMed for original studies between 1980 and 2021 reporting early hepatic artery (pseudo) aneurysm after liver transplantation requiring either surgical or endovascular intervention. Results From a total of 1,172, 3 liver transplant patients were identified with a symptomatic HAPA and treated with immediate revascularization. HAPA occurred 73, 27, and 8 days after liver transplantation and was treated with immediate revascularization (two surgical and one endovascular intervention). Literature review identified 127 cases of HAPA. HAPA was managed with endovascular therapy in 20 cases and by surgical intervention in 89 cases. Overall reported mortality rate was 39.6%, whereas overall graft survival was 45.2%. Conclusion Immediate surgical or radiological interventional excision and prompt revascularization to salvage liver grafts is feasible but still associated with a high mortality.
Genomic and phenotypic insight into Xanthomonas vesicatoria strains with different aggressiveness on tomato

Xanthomonas vesicatoria is one of the causal agents of bacterial spot, a disease that seriously affects the production of tomato (Solanum lycopersicum) and pepper (Capsicum annum) worldwide. In Argentina, bacterial spot is found in all tomato producing areas, with X. vesicatoria being one of the main species detected in the fields. Previously, we isolated three X. vesicatoria strains BNM 208, BNM 214, and BNM 216 from tomato plants with bacterial spot, and found they differed in their ability to form biofilm and in their degree of aggressiveness. Here, the likely causes of those differences were explored through genotypic and phenotypic studies. The genomes of the three strains were sequenced and assembled, and then compared with each other and also with 12 other publicly available X. vesicatoria genomes. Phenotypic characteristics (mainly linked to biofilm formation and virulence) were studied in vitro. Our results show that the differences observed earlier between BNM 208, BNM 214, and BNM 216 may be related to the structural characteristics of the xanthan gum produced by each strain, their repertoire of type III effectors (T3Es), the presence of certain genes associated with c-di-GMP metabolism and type IV pili (T4P). These findings on the pathogenicity mechanisms of X. vesicatoria could be useful for developing bacterial spot control strategies aimed at interfering with the infection processes.
Role of endogenous and exogenous antioxidants in risk of six cancers: evidence from the Mendelian randomization study

Background: Although oxidative stress is known to contribute to cancer, and endogenous and exogenous antioxidants are thought to prevent tumorigenesis by suppressing oxidative stress-induced DNA damage, antioxidants have also been reported to show negative effects on tumor formation, necessitating characterization of the causal associations between antioxidants and cancer risk. Methods: In this study, Mendelian randomization (MR) analysis, primarily inverse-variance weighted MR, was used to assess the causal effect of six endogenous and five exogenous diet-derived antioxidants on the risk of six cancers. MR-Egger intercept test and Cochran’s Q statistic were utilized to assess pleiotropy and heterogeneity, respectively. Results: For endogenous antioxidants, a bidirectional two-sample MR analysis was conducted. Our findings suggested that serum albumin has a negative causal association with the risk of prostate cancer [odds ratio (OR) = 0.78, 95% confidence interval (CI): 0.68–0.91, p = 0.001]. The risks of the six cancers showed no significant associations with endogenous antioxidants in the converse MR analysis. For exogenous antioxidants, the unidirectional two-sample MR analysis exhibited a nominal relationship between the serum retinol level and non-small-cell lung cancer risk (OR = 0.29, 95% CI: 0.11–0.76, p = 0.011). Conclusions: Thus, our study revealed the protective effects of genetic susceptibility to high circulating albumin levels on prostate cancer, providing potential targeted interventions for prostate cancer prevention.
The changing landscape of nuclear medicine and a new era: the “NEW (Nu) CLEAR Medicine”: a framework for the future

Nuclear Medicine is witnessing a revolution across a large spectrum of patient care applications, hardware, software and novel radiopharmaceuticals. We propose to offer a framework of the nuclear medicine practice of the future that incorporates multiple novelties and coined as the NEW (nu) Clear medicine. All these new developments offer a significant clarity and real clinical impact, and we need a concerted effort from all stakeholders in the field for bedside implementation and success.
Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies

The functionality and longevity of hematopoietic tissue is ensured by a tightly controlled balance between self-renewal, quiescence, and differentiation of hematopoietic stem cells (HSCs) into the many different blood lineages. Cell fate determination in HSCs is influenced by signals from extrinsic factors (e.g., cytokines, irradiation, reactive oxygen species, O2 concentration) that are translated and integrated by intrinsic factors such as Transcription Factors (TFs) to establish specific gene regulatory programs. TFs also play a central role in the establishment and/or maintenance of hematological malignancies, highlighting the need to understand their functions in multiple contexts. TFs bind to specific DNA sequences and interact with each other to form transcriptional complexes that directly or indirectly control the expression of multiple genes. Over the past decades, significant research efforts have unraveled molecular programs that control HSC function. This, in turn, led to the identification of more than 50 TF proteins that influence HSC fate. However, much remains to be learned about how these proteins interact to form molecular networks in combination with cofactors (e.g. epigenetics factors) and how they control differentiation, expansion, and maintenance of cellular identity. Understanding these processes is critical for future applications particularly in the field of cell therapy, as this would allow for manipulation of cell fate and induction of expansion, differentiation, or reprogramming of HSCs using specific cocktails of TFs. Here, we review recent findings that have unraveled the complexity of molecular networks controlled by TFs in HSCs and point towards possible applications to obtain functional HSCs ex vivo for therapeutic purposes including hematological malignancies. Furthermore, we discuss the challenges and prospects for the derivation and expansion of functional adult HSCs in the near future.
The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system

Post-transcriptional gene regulation is a fundamental mechanism that helps regulate the development and healthy aging of the nervous system. Mutations that disrupt the function of RNA-binding proteins (RBPs), which regulate post-transcriptional gene regulation, have increasingly been implicated in neurological disorders including amyotrophic lateral sclerosis, Fragile X Syndrome, and spinal muscular atrophy. Interestingly, although the majority of RBPs are expressed widely within diverse tissue types, the nervous system is often particularly sensitive to their dysfunction. It is therefore critical to elucidate how aberrant RNA regulation that results from the dysfunction of ubiquitously expressed RBPs leads to tissue specific pathologies that underlie neurological diseases. The highly conserved RBP and alternative splicing factor Caper is widely expressed throughout development and is required for the development of Drosophila sensory and motor neurons. Furthermore, caper dysfunction results in larval and adult locomotor deficits. Nonetheless, little is known about which proteins interact with Caper, and which RNAs are regulated by Caper. Here we identify proteins that interact with Caper in both neural and muscle tissue, along with neural specific Caper target RNAs. Furthermore, we show that a subset of these Caper-interacting proteins and RNAs genetically interact with caper to regulate Drosophila gravitaxis behavior.
On the interaction of tropical‐cyclone‐scale vortices. I: Observations

A detailed analysis is made of the observed behaviour in interaction, tropical-cyclone-scale vortices in the western North Pacific region. It is found that all multiple-vortex interactions can be broken down into a common model of binary interaction. The classical Fujiwhara model of converging cyclonic rotation about a centroid followed by merger is rarely followed. Capture tends to occur rapidly, within several hours, and is followed by a period of relatively stable cyclonic orbit. Cyclone merger occurs by one vortex experiencing a loss of convective organization, followed by horizontal shearing and incorporation into the outer circulation of the other vortex. However, a substantial proportion of interacting cyclones escape from the interaction, and the changeover from a stable orbiting configuration occurs rapidly. A model of binary interaction is presented. Cases where swarms of mesoscale vortices are formed in convectively active regions without tropical cyclones are also documented. These vortices have a much narrower range of influence (a few hundred kilometres) then that observed for tropical cyclones. When groups of vortices come within this range they are observed to conform to the same interaction model as observed for tropical cyclones.
Metaphor: A Computational Perspective by Tony Veale, Ekaterina Shutova and Beata Beigman Klebanov

The literary imagination may take flight on the wings of metaphor, but hard-headed scientists are just as likely as doe-eyed poets to reach for a metaphor when the descriptive need arises. Metaphor is a pervasive aspect of every genre of text and every register of speech, and is as useful for describing the inner workings of a "black hole" (itself a metaphor) as it is the affairs of the human heart. The ubiquity of metaphor in natural language thus poses a significant challenge for Natural Language Processing (NLP) systems and their builders, who cannot afford to wait until the problems of literal language have been solved before turning their attention to figurative phenomena. This book offers a comprehensive approach to the computational treatment of metaphor and its figurative brethren-including simile, analogy, and conceptual blending-that does not shy away from their important cognitive and philosophical dimensions. Veale, Shutova, and Beigman Klebanov approach metaphor from multiple computational perspectives, providing coverage of both symbolic and statistical approaches to interpretation and paraphrase generation, while also considering key contributions from philosophy on what constitutes the "meaning" of a metaphor. This book also surveys available metaphor corpora and discusses protocols for metaphor annotation. Any reader with an interest in metaphor, from beginning researchers to seasoned scholars, will find this book to be an invaluable guide to what is a fascinating linguistic phenomenon.
Structure and Binding Kinetics of Monoclonal Antibody 1G1 Support the Inclusion of the Respiratory Syncytial Virus G Protein in Vaccine Development

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection with significant mortality in infant, immunocompromised, and elderly populations. No approved vaccines or antiviral therapies exist to combat RSV and traditional vaccine development strategies have failed. The G protein on the surface of RSV contributes to the pathogenicity of the virus and is a target of the human adaptive immune response. Previous studies reveal that neutralizing monoclonal antibodies bind to distinct three dimensional epitopes on the G protein. The conformational epitope of another anti-G antibody, 1G1, is explored in this work by x-ray crystallography and binding kinetics assays. The epitope of 1G1 has been determined to lie between residues 157 and 197 of the G protein by binding assays and early x-ray crystallography studies demonstrate the feasibility of determining a precise conformational epitope. Continued efforts in crystallization and kinetic analysis will allow for the construction of a precise atomic resolution structure of 1G1 bound to the RSV G protein and accurate quantification of the affinity of the interaction. Knowledge of how the human immune system neutralizes RSV through the G protein will support innovative efforts to create new vaccines and antiviral therapies.
Structural Analysis of Poetic Language: Examples of Kazakh poetry

The language of poetry is different from the language of other literary genres. The language of the poem consists of many layers of meaning. It has ambiguity, homonymy, and connotative words. In this study, I analyze poem ‘Muse’ by contemporary Kazakh poet M. Makataev using the structural approach in order to find the elements (diction, imagery, rhyme, rhythm, pattern, sound and sense, and tone) and to figure out the exquisite features of his poetic art through a deconstructive study of the poem. Furthermore, I define the status of the poetic language and also analyze the poem on the grounds of different linguistic devices like its lexical features and to see how the structure of a poem can effect on the whole meaning of the poem. The poem expresses the idea in line by using diction, imagery, rhyme, rhythm, pattern, sound and sense, and tone as the elements of the poem. The elements in the poem have a role in the process of arrangement. It means that the elements take a part in consideration of the poet in his writing process.
Electroless Ni alloy plating as a diffusion barrier for through silicon vias in three-dimensional packaging

Ni- and Co-based amorphous films are alternative diffusion barrier materials for Cu interconnection in three-dimensional (3D) packaging applications. In this paper, electroless Ni–P and Ni–W–P films deposited in through-silicon vias (TSVs) were prepared as a diffusion barrier and seed layer of Cu filling by using Sn–Pd activation pretreatment. The thermal stability of the electroless Ni alloy films subjected to rapid thermal annealing (RTA) in H2 atmosphere was investigated. The barrier properties of the electroless Ni alloy films were evaluated over a range of temperatures using auger electron spectroscopy (AES) and energy dispersive X-ray spectroscopy (EDS) line-scan. The microstructures, crystal structures and electrical resistivity were also examined. It was found that Ni alloy films are amorphous as deposited, that the films retain amorphous or amorphous-like structures after undergoing annealing at 400 °C for 1 h, and that they are feasible for the diffusion barrier layer for 3D Cu interconnect technology.
Toward Highly Reliable Programmable Data Planes: Verification of P4 Code Generation

Data plane programming gained much attention in the past years, having a fast-growing community both in academia and industry. Many tools have emerged to simplify and/or help the development of reliable data plane programs, including fuzzing, formal verification, and different code generators. However, even the tools themselves must be verified to meet the most stringent dependability requirements. In this paper, we investigate various tools and methods to verify code generators leveraging P4 through the example of P4RROT (an open source code generator focusing on the application layer). We show that our approach is efficient and can indeed successfully find bugs. We identify two bugs and propose reusable ideas, such as the use of ghost code.
Demographic Analysis of Smartphone Application Usage Related to eHealth

: Smartphone application usage according to battery percentage was examined with 68 participants. A one way chi square test found that there was a pattern with participant’s application usage that couldn’t have been due to chance alone, meaning that users consumed more battery for certain applications in a twenty four hour time span, over other applications. A one way chi square analysis also indicated a preference of iOS devices over android ones within the female gender. A frequency analysis also indicated that only one user had a health application as his number one used app according to battery consumption, while only two users out of 68 had any sort of health application usage at all. Results from analyzing user’s battery consumption suggest a lack of health application usage on mobile devices