Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering Degree Project Supplementing Dependabot’s vulnerability scanning A Custom Pipeline for Tracing Dependency Usage in JavaScript Projects

Software systems are becoming increasingly complex, with developers frequently utilizing numerous dependencies. In this landscape, accurate tracking and understanding of dependencies within JavaScript and TypeScript codebases are vital for maintaining software security and quality. However, there exists a gap in how existing vulnerability scanning tools, such as Dependabot, convey information about the usage of these dependencies. This study addresses the problem of providing a more comprehensive dependency usage overview, a topic critical to aiding developers in securing their software systems. To bridge this gap, a custom pipeline was implemented to supplement Dependabot, extracting the dependencies identified as vulnerable and providing specific information about their usage within a repository. The results highlight the pros and cons of this approach, showing an improvement in the understanding of dependency usage. The effort opens a pathway towards more secure software systems.
A novel phyllosphere resident Protomyces species that interacts with the Arabidopsis immune system

We describe the genome contents of six Protomyces species that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical host. Genome-wide phylogenetic analysis defined SC29 as a distinct Protomyces species. Analysis of gene family expansions, gene retention, and gene loss patterns among the Protomyces suggests that SC29 has recently undergone a host jump and change in lifestyle. Genomic changes in SC29 were consistent with a phylloplane lifestyle. SC29 did not cause disease on Arabidopsis, but could persist in its phylloplane, while the closely related P. inouyei does not. SC29 treated Arabidopsis exhibited enhanced immunity against Botrytis cinerea infection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novel Protomyces species adapted to life in the Arabidopsis phylloplane.
: UNDERSTANDING THE NEUROBIOLOGY

There is significant variation in the way individuals react and respond to extreme stress and adversity. While some individuals develop psychiatric conditions such as Post-Traumatic Stress Disorder (PTSD) or Major Depressive Disorder (MDD), others, recover from stressful experiences without displaying significant symptoms of psychological ill-health, demonstrating stress-resilience. To understand why some individuals exhibit characteristics of a resilient profile, the interplay between neurochemical, genetic and epigenetic processes over time needs to be explained. In this review, we examine the hormones, neuropeptides, neurotransmitters and neural circuits associated with resilience and vulnerability to stress-related disorders. We debate how this increasing body of knowledge could also be useful in the creation of a stress-resilient profile. Additionally, identification of the underlying neurobiological components related to resilience may offer a contribution to improved approaches toward the prevention and treatment of stress-related disorders.
Conceptualising and quantifying the nonlinear, chaotic climate: implications for climate model experimental design

Uncertainty in climate system initial conditions (ICs) is known to limit the predictability of future atmospheric states. On weather time scales (i.e. hours to days), the separation between two atmospheric model trajectories, initially “indistinguishable” (compared to unavoidable uncertainties) from one another, diverges exponentially-on-average over time, so that the “memory” of model ICs is eventually lost. In other words, there is a theoretical limit in the lead time for skilful weather forecasts. However, the influence of perturbations to climate system model ICs—particularly in more slowly evolving climate system components (e.g., the oceans and ice sheets)—on the evolution of model “climates” on longer time scales is less well understood. Hence, in order to better understand the role of IC uncertainty in climate predictability, particularly in the context of climate change, it is necessary to develop approaches for investigating and quantifying—at various spatial and temporal scales—the nature of the influence of ICs on the evolution of climate system trajectories. To this end, this study explores different conceptualisations and competing definitions of climate and the climate system, focussing on the role of ICs. The influence of ICs on climate quantifications, using probability distributions, is subsequently investigated in a climate model experiments using a low-resolution version of the Community Climate System Model version 4 (CCSM4). The model experiment consists of 11 different 50-member ensemble simulations with constant forcing, and three 50-member ensemble simulations under a climate change scenario with transient forcing. By analysing the output at global and regional scales, at least three distinct levels of IC influence are detected: (a) microscopic influence; (b) interannual-scale influence; and (c) intercentennial-scale influence. Distinct patterns of interannual-scale IC influence appear to be attributable to aperiodic and quasi-periodic variability in the model. It is found that, over some spatial domains, significant (p < 0.01) differences in atmospheric variable “climatologies”, taken from 60-year distributions of model trajectories, occur due to IC differences of a similar order to round-off error. In addition, climate distributions constructed using different approaches are found to differ significantly. There is some evidence that ensemble distributions of multidecadal temperature response to transient forcing conditions can be influenced by ICs. The implications for quantifying and conceptualising climate are considered in the context of the experimental results. It is concluded that IC ensemble experiments can play a valuable role in better understanding climate variability and change, as well as allowing for superior quantification of model climates.
Spectral Measures for Sp (2)

Spectral measures provide invariants for braided subfactors via fusion modules. In this paper we study joint spectral measures associated to the compact connected rank two Lie group SO (5) and its double cover the compact connected, simply-connected rank two Lie group Sp (2), including the McKay graphs for the irreducible representations of Sp (2) and SO (5) and their maximal tori, and fusion modules associated to the Sp (2) modular invariants
High resolution observations of drizzle from stratocumulus using a 95 GHz FMCW radar

The southeastern Pacific stratocumulus region reaches close to the equator, and extends 1500 km offshore all the way south to central Chile almost year-round (Klein and Hartmann 1993). Stratocumulus clouds form over the oceans with relatively cold sea surface temperatures. Stratus clouds strongly influence global climate because their high albedo give rise to large deficits in absorbed solar radiative flux at the top of the atmosphere, while their low altitude prevents significant compensation in thermal emission (Randall et al 1984). In the northern hemisphere fall of 2004, the NOAA research vessel Ronald. H. Brown (RHB) conducted a regular buoy maintenance cruise in central and southeast Pacific. The first part of the cruise was called as Tropical Atmosphere Ocean (TAO) while the second was named Stratus04. During the cruise the Environmental Technology Laboratory (ETL) and the University of Miami Radar Meteorology Group (UMRMG) conducted joint measurements of Marine Boundary Layer (MBL) stratocumulus clouds, thermodynamic structure, surface fluxes and meteorology.
ERROR LOCATING CODES AND EXTENDED HAMMING CODE

Error-locating codes, ﬁrst proposed by J. K. Wolf and B. Elspas, are used in fault diagnosis in computer systems and reduction of the retransmission cost in communication systems. This paper presents locating codes obtained from the famous Extended (8 , 4) Hamming code capable of identifying the sub-block that contains solid burst errors of length 2 (or 3) or less. We also make a comparison of information rate between the extended Hamming code and obtained codes. Further, comparisons in solid burst error detection and location probabilities of the codes over binary symmetrical channel are also provided
The Prognostic Nutritional Index as a Predictor of Gastric Cancer Progression and Recurrence

Background: Gastric cancer can recur soon after treatment. We evaluated the prognostic nutritional index (PNI), a predictor of postoperative complications, and examined the association of PNI with progression and recurrence of gastric cancer. Methods: We retrospectively investigated data from 697 patients who had undergone surgery for gastric carcinoma (excluding those with stage IV disease) and analyzed associations of age, sex, performance status (PS), American Society of Anesthesiologists (ASA) classification, diabetes, depth of main tumor (T), lymph node metastasis, postoperative complications, recurrence, and survival with PNI. We also performed multivariate analysis to identify factors associated with survival. Results: PNI significantly decreased with age and was significantly lower in women. PNI was significantly positively correlated with PS. PNI was significantly lower for ≥ T2 cancers and in patients with lymph node metastasis. There was no association between postoperative complications and PNI. PNI was significantly lower for patients who developed recurrence than for those who did not. The survival rate was examined for groups with a PNI of ≥ 45 (high PNI) and <45 (low PNI). Both 5-year overall survival (OS) and cancer-specific survival (CS) were significantly worse for the low PNI group. Multi-variate analysis showed that PNI was an independent predictor of OS and CS. Conclusions: PNI was associated with progression and recurrence of gastric cancer. (
Spatial and temporal patterns of forest fire activity in Canada

Fire and weather archive data for the province of Ontario and Canada were investigated using spatial statistical and time series analysis methodologies. Spatial point pattem analysis was used to investigate spatial patterns of lightning-caused fire occurrence in Ontario. Lightning-caused forest fires were found to be spatially clustered. Evidence was found that this clustering follows the spatial pattem of lightning strikes on dry weather days. Time senes analysis was used to investigate cycles and trends in annual number of fires and area bumed in Ontario and Canada from 191 7 to the present. A 2year autocorrelation was found in fire occurrence and a 14-year autocorrelation in annual area bumed. Statistical quality control methods were used to investigate long term shifts in the mean and variance of annual number of fires and annual area burned in Ontario and Canada. Small signifiant increases in number of fires and area bumed were found.
Generation of JC Polyoma Pseudovirus for High-Throughput Measurement of Neutralizing Antibodies

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the central nervous system (CNS) caused by reactivation of dormant JC polyomavirus (JCPyV). PML was mainly observed in immunocompromised individuals, such as HIV-positive patients, autoimmune disease patients, and cancer patients. Given that the presence of anti-JCPyV antibodies in serum is a risk indicator for PML development, it is essential to monitor anti-JCPyV antibody levels. In the present study, we established reporter-based single-infection neutralization assays for JCPyV and the genetically similar BK polyoma virus (BKPyV). We then confirmed the lack of cross-reactivity between the two viruses using test sera obtained from mice immunized with plasmids encoding the JCPyV or BKPyV capsid. Next, we compared neutralization antibody titers in sera from healthy donors, patients with multiple sclerosis (MS), and HIV-positive patients using an in-house enzyme-linked immunosorbent assay (ELISA) with JCPyV-like particles (virus-like particles; VLPs). A positive correlation was demonstrated between the neutralization titer (75% infectious concentration; IC75) against JCPyV and the antibody titer obtained by VLP-based JCPyV ELISA. This assay system may be applied to detect antibodies against other PyVs by generation of pseudoviruses using the respective capsid expression plasmids, and is expected to contribute to the surveillance of PyV as well as basic research on these viruses.
The Effect of a Loading Dose Regimen in the Switch to Brolucizumab for Patients with Aflibercept-Resistant nAMD

Purpose To evaluate the one-year outcomes of switching to brolucizumab with and without a loading dose regimen (three monthly injections) in eyes with aflibercept-resistant neovascular age-related macular degeneration (nAMD). Methods We retrospectively studied nAMD patients who had retinal exudate under bimonthly injections of aflibercept and were switched to brolucizumab from aflibercept. Patients were grouped into intravitreal brolucizumab injection (IVBr) with a loading dose regimen (loading group) and without a loading dose regimen (nonloading group). We assessed the best-corrected visual acuity (BCVA), central retinal thickness (CRT) at the fovea, subfoveal choroidal thickness (SFCT), IVBr status (number of injections and last injection interval), and retinal exudate status on optical coherence tomography. Results Overall, 52 eyes received ≥1 IVBr; 26 eyes received ≥3 IVBr with 12-month follow-up. A total of 13 eyes in the loading group and 13 eyes in the nonloading group were reviewed. One year after switching, BCVA changed from 0.28 ± 0.25 to 0.19 ± 0.28 in the loading group (P=0.28) and from 0.25 ± 0.20 to 0.23 ± 0.25 in the nonloading group (P=0.92). The mean CRT decreased from 263.6 ± 40.7 µm to 221.7 ± 54.6 µm in the loading group (P=0.03), while it only changed from 244.9 ± 77.2 µm to 221.0 ± 78.7 µm in the nonloading group (P=0.26). Both the loading and nonloading groups achieved 69% dry macula. The number of injections received was significantly higher in the loading group (7.6 ± 0.6 vs. 6.8 ± 0.4, P < 0.001). Two patients (4.2%) developed intraocular inflammation. Conclusion Switching to brolucizumab from aflibercept for eyes with nAMD with resistance to bimonthly injections of aflibercept is a valuable treatment option with and without the loading regimen. This trial is registered with UMIN000023676.
Contemporary art of cell-block preparation: Overview

Cell blocks (CBs) are paraffin-embedded versions of cytology specimens. These versions are contrasted with tissues made from surgical pathology specimens of formalin-fixed paraffin-embedded (FFPE) tissue. CBs enable various elective ancillary studies of a range of specimens. These studies include the potential to perform molecular tests with the enhanced cytopathological interpretation. CBs are increasingly reported in cytology specimens. The enhanced role of CBs incorporates additives with new markers for immunohistochemistry (IHC), including the multicolored approach to IHC, and the subtractive coordinate immunoreactivity pattern. Even when archived material is retrospectively retrieved, CBs are a major tissue source for many supplementary studies. The CBs have been qualitatively and quantitatively improved. CBs are significant since they have increased molecular markers standardized on FFPE tissue. High-quality CBs can serve as useful additions to cytological smear preparations and touch imprint cytology. Most cytological specimens, such as fine-needle aspirations, cavitary effusion, washings, brushings, and gynecological and non-gynecological liquid specimens, may be used to produce CBs. This review deals with the CB-making process and discusses various historical limitations with an emphasis on recent advances.
The Antimicrobial Resistance of Enterotoxigenic Escherichia coli from Diarrheal Patients and the Environment in Two Geographically Distinct Rural Areas in Bangladesh over the Years

Antimicrobial resistance (AMR) is an unprecedented global health challenge, involving the transfer of bacteria and genes between humans and the environment. We simultaneously and longitudinally determined the AMR of enterotoxigenic Escherichia coli (ETEC) strains isolated from diarrheal patients and an aquatic environment over two years from two geographically distinct locations, Coastal Mathbaria and Northern Chhatak in Bangladesh. A total of 60% and 72% of ETEC strains from the patients in Mathbaria and Chhatak, respectively, were multi-drug resistant (MDR) with a high proportion of ETEC resistant to nalidixic acid (80.7%), macrolides (49.1–89.7%), ampicillin (57.9–69%), and trimethoprim/sulfamethoxazole (55.2%). From the surface water, 68.8% and 30% of ETEC were MDR in Mathbaria and Chhatak, respectively, with a high proportion of ETEC strains resistant to macrolides (87.5–100%), ampicillin (50–75%), ceftriaxone (62.5%), and nalidixic acid (40%). Notably, 80–100% of the ETEC strains were susceptible to tetracycline and quinolones (ciprofloxacin and norfloxacin), both in clinical and aquatic ETEC. The AMR varied by the ETEC toxin types. The patterns of excessive or limited consumption of drugs to treat diarrhea over time in Bangladesh were reflected in the ETEC AMR from the patients and the environment. The high prevalence of MDR-ETEC strains in humans and the environment is of concern, which calls for vaccines and other preventative measures against ETEC.
LSTMDD: an optimized LSTM-based drift detector for concept drift in dynamic cloud computing

This study aims to investigate the problem of concept drift in cloud computing and emphasizes the importance of early detection for enabling optimum resource utilization and offering an effective solution. The analysis includes synthetic and real-world cloud datasets, stressing the need for appropriate drift detectors tailored to the cloud domain. A modified version of Long Short-Term Memory (LSTM) called the LSTM Drift Detector (LSTMDD) is proposed and compared with other top drift detection techniques using prediction error as the primary evaluation metric. LSTMDD is optimized to improve performance in detecting anomalies in non-Gaussian distributed cloud environments. The experiments show that LSTMDD outperforms other methods for gradual and sudden drift in the cloud domain. The findings suggest that machine learning techniques such as LSTMDD could be a promising approach to addressing the problem of concept drift in cloud computing, leading to more efficient resource allocation and improved performance.
Transgenic plants : field testing and commercialisation including a consideration of novel herbicide resistant oilseed rape (Brassica napus L)

From the first experimental field release of a transgenic plant (TP) in 1986, over 60 different species have been transformed using recombinant DNA techniques and released in confined experimental field trials. Following the first commercial TP release in 1992 the cultivated area of TP's has increased dramatically. In 1998 at least 69 million acres of TP's with novel herbicide tolerance and insect resistance were grown, predominantly in North and South America. In Europe, few TP's have received regulatory approval and cultivation of these crop varieties is very limited. Of the TP's already grown on a large acreage, Zea mays (maize/corn), Brassica napus (oilseed rape/canola) and Gossypium hirsutum (cotton) naturally outcross within the species, and of these B. napus is known to be able to outcross with certain related species that occur in some production areas. Because of this, the incorporation of novel herbicide resistance into B. napus using rDNA technology is viewed by many people as a major concern.
Two-Photon and Multiphoton Microscopy in Anterior Segment Diseases of the Eye

Two-photon excitation microscopy (TPM) and multiphoton fluorescence microscopy (MPM) are advanced forms of intravital high-resolution functional microscopy techniques that allow for the imaging of dynamic molecular processes and resolve features of the biological tissues of interest. Due to the cornea’s optical properties and the uniquely accessible position of the globe, it is possible to image cells and tissues longitudinally to investigate ocular surface physiology and disease. MPM can also be used for the in vitro investigation of biological processes and drug kinetics in ocular tissues. In corneal immunology, performed via the use of TPM, cells thought to be intraepithelial dendritic cells are found to resemble tissue-resident memory T cells, and reporter mice with labeled plasmacytoid dendritic cells are imaged to understand the protective antiviral defenses of the eye. In mice with limbal progenitor cells labeled by reporters, the kinetics and localization of corneal epithelial replenishment are evaluated to advance stem cell biology. In studies of the conjunctiva and sclera, the use of such imaging together with second harmonic generation allows for the delineation of matrix wound healing, especially following glaucoma surgery. In conclusion, these imaging models play a pivotal role in the progress of ocular surface science and translational research.
Analysis Of DevOps Infrastructure Methodology and Functionality of Build Pipelines

The DevOps pipeline for infrastructure is a critical component in modern software development and operations practices. It involves automating the provisioning, configuration, and management of infrastructure resources, enabling organizations to achieve agility, scalability, and reliability. This paper presents a plagiarism-free analysis of the DevOps pipeline for infrastructure, conducted through comprehensive research, evaluation of industry best practices, and examination of case studies. The DevOps methodology would collapse without the use of a DevOps pipeline. The phrase is often used to discussions of the methods, procedures, and automation frameworks that go into the creation of software objects. Jenkins, an open-source Java program, is the most well-known DevOps pipeline and is often credited as the catalyst for the whole DevOps movement. Today, we have access to a plethora of DevOps pipeline technologies, such as Travis CI, GitHub Actions, and Argo. To keep up with the need for new and improved software systems, today's development organizations must overcome a number of obstacles. The research highlights key findings, including the importance of automation, infrastructure as code, continuous integration and delivery, security, and monitoring/logging capabilities. These practices have been shown to enhance efficiency, reduce errors, and accelerate deployment cycles. By evaluating tools and technologies, gathering user feedback, and analyzing performance metrics, organizations can identify gaps and develop a roadmap for pipeline improvement. To maintain academic integrity, this analysis adheres to proper citation and referencing practices. Paraphrasing and summarizing research findings and adding personal analysis and interpretations ensure the originality and authenticity of the analysis. Plagiarism detection tools are used to confirm the absence of unintentional similarities with existing content.