Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular dynamics simulation in nanoscale heat transfer: A review

The exponential growth of research activities in nanotechnologies, as well the rapidly increasing utilization of microscale technologies in societal applications, is affecting directly the development and implementation of corresponding numerical methodologies in many scientific and technological areas, including heat transfer. Of particular interest are length scales at which the continuum approach ceases to be valid. Molecular Dynamics (MD) simulation is a very promising, general method to study such scales, allowing for the direct simulation of the motion and interaction of particles (atoms or molecules). This paper reviews recent works on molecular dynamics in heat transfer, focusing on, but not limited to, challenging interfacial and phase change phenomena to demonstrate the advantages, potential, and the current limitations of this methodology.
Flexible approximation of structured interactions in decentralized Markov decision processes

Our work is motivated by cooperative planning problems where agents can affect each others’ transitions and rewards, and so benefit from coordinating their actions, but in doing so must account for durational uncertainty in these actions. To reason about this uncertainty efficiently, agents can employ temporal decoupling (a paradigm that has been explored in a variety of restricted contexts [2, 3]) to constrain interactions to occur by selected time points, representing the uncertain occurrence for each time point with a probabilistic promise [5]. Here we summarize a reformulation of Becker’s Event-driven DEC-MDP problems [1] that uses commitment models to exploit temporal structure. We argue that, in addition to representing optimal solutions, our approach enables more efficient, scalable computation of approximate solutions and a natural flexibility by which interactions can be modeled with more or less detail.
Developing a test collection for biomedical word sense disambiguation

Ambiguity, the phenomenon that a word has more than one sense, poses difficulties for many current Natural Language Processing (NLP) systems. Algorithms that assist in the resolution of these ambiguities, i.e. which make unambiguous a word, or more generally, a text string, will boost performance of these systems. To test such techniques in the biomedical language domain, we have developed a Word Sense Disambiguation (WSD) test collection that comprises 5,000 unambiguous instances for 50 ambiguous UMLS Metathesaurus strings.
Nitric Oxide Limits the Expansion of Antigen-Specific T Cells in Mice Infected with the Microfilariae of Brugia pahangi

ABSTRACT Infection of BALB/c mice with the microfilariae (Mf) of the filarial nematode Brugia pahangi results in an antigen-specific proliferative defect that is induced by high levels of NO. Using carboxyfluorescein diacetate succinimydl ester and cell surface labeling, it was possible to identify a population of antigen-specific T cells from Mf-infected BALB/c mice that expressed particularly high levels of CD4 (CD4hi). These cells proliferated in culture only when inducible NO synthase was inhibited and accounted for almost all of the antigen-specific proliferative response under those conditions. CD4hi cells also expressed high levels of CD44, consistent with their status as activated T cells. A similar population of CD4hi cells was observed in cultures from Mf-infected gamma interferon receptor knockout (IFN-γR−/−) mice. Terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling staining revealed that the CD4+ T cells from Mf-infected wild-type mice were preferentially susceptible to apoptosis compared to CD4+ T cells from IFN-γR−/− mice. These studies suggest that the expansion of antigen-specific T cells in Mf-infected mice is limited by NO.
Identification of Integrin α 3 as a New Substrate of the Adenovirus E 4 orf 6 / E 1 B 55 K E 3 Ubiquitin Ligase Complex

5 Departments of Biochemistry 1 and Oncology 2 and the Goodman Cancer Center 3 , McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada, H3G 1Y6. 4 Heinrich-Pette-Institute for Experimental Virology and Immunology, Martinistr. 52, 20251 Hamburg, Germany 10 *Corresponding author: Phone: (514) 398-7268 Fax: (514) 398-7384 E-mail: philip.branton@mcgill.ca
Analysis of SEND Protocol through Implementation and Simulation

Neighbor Discovery (ND) protocol has been proposed to discover neighboring hosts and routers in IPv6 wired or wireless local networks. Even though ND protocol is very useful, it has a weakness to security because it allows a malicious user to impersonate a legitimate host or a router by forging ND protocol messages. To address the security problem, IETF (Internet Engineering Task Force) has proposed SEcure Neighbor Discovery (SEND) protocol. The key functions of SEND protocol include address ownership proof mechanism, ND protocol message protection mechanism, reply attack prevention mechanism, and router authentication mechanism. In this paper, we analyze SEND protocol in the view point of security through several experiments. For this, we implement SEND protocol in IPv6 real system and develop a simulation environment. Based on the experimental results, we also propose a monitoring-based ND message differentiation scheme which is able to make up for security vulnerability of SEND protocol effectively.
COSMOGENIC 10BE SURFACE EXPOSURE DATING AND NUMERICAL MODELING OF LATE PLEISTOCENE GLACIERS AND LAKES IN NORTHWESTERN NEVADA

iii ACKNOWLEDGEMENTS . iv DEDICATION . v LIST OF FIGURES . viii LIST OF APPENDIX TABLES . xi LIST OF APPENDIX FIGURES. xii CHAPTER 1: INTRODUCTION . 1 CHAPTER 2: REGIONAL SETTING . 12 Great Basin . 12 Santa Rosa Range . 13 Pine Forest Range . 15 Lake Franklin . 16 Glacial Features . 17 Moraines. 17 Glacial Erratics . 19 CHAPTER 3: METHODS . 21 Theory of Cosmogenic Be Surface Exposure Dating . 21 Cosmogenic Be Exposure Dating of Moraines in the Santa Rosa and Pine Forest Ranges . 22 Glacier Modeling Procedure . 23 Lake Modeling Procedure . 26 Evaporation Calibration . 28 CHAPTER 4: RESULTS AND DISCUSSION . 36 Cosmogenic Be Surface Exposure Dating Results . 36 Cosmogenic Be Surface Exposure Dating Discussion . 38 vii Glacier and Lake Modeling Results for the Northwest and Northcentral Great Basin . 41 Glacier and Lake Modeling Discussion . 52 CHAPTER 5: CONCLUSION . 56 REFERENCES . 59 APPENDIX A: METHODS . 67 Field Methods . 67 Lab Methods . 68 APPENDIX B: TABLES FOR CHRONOLOGY . 72 APPENDIX C: MODELED ICE EXTENT OUTPUTS . 75 APPENDIX D: INPUT DATA FOR GLACIER AND LAKE MODELING . 80
Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
Contrasting Roles of Programmed Death-Ligand 1 Expression in Tumor and Stroma in Prognosis of Esophageal Squamous Cell Carcinoma

Simple Summary Esophageal squamous cell carcinoma (ESCC) often recurs in advanced stages. With immune checkpoint inhibitors becoming a treatment option for recurrent ESCCs, assessing programmed death-ligand 1 (PD-L1) expression in tumor tissue has gained importance. However, challenges remain due to subjective interpretation methods, the unclear significance of staining intensity, and the contrasting roles of stromal and tumoral PD-L1 expression. Our study addresses these issues through a robust, machine learning-aided calculation of H-scores for PD-L1 expression, conducting separate analyses of tumoral and stromal areas in 194 cases of surgically resected ESCCs. Survival analysis revealed that high tumoral PD-L1 expression is an independent factor associated with prolonged survival. In contrast, high stromal PD-L1 expression correlated with less advanced pathological stages and a prolonged response to cytotoxic chemotherapy. This study highlights distinct PD-L1 roles in ESCC’s tumoral and stromal areas, underlining the importance of understanding these mechanisms in the tumor immune microenvironment to develop better treatments and improve patient outcomes. Abstract The assessment of programmed death-ligand 1 (PD-L1) expression in esophageal squamous cell carcinoma (ESCC) has become increasingly important with the rise of immune checkpoint inhibitors (ICIs). However, challenges persist, including subjective interpretation and the unclear significance of staining intensity, as well as contrasting roles in tumoral and stromal regions. Our study enhances the understanding of PD-L1 in ESCCs by analyzing its expression in tumors and stroma with H-scores, highlighting its distinct clinicopathological impacts. In a retrospective cohort of 194 ESCC specimens from surgical resection, we quantified PD-L1 expression in tumoral and stromal compartments using H-scores, analyzing whole slide images with digital pathology analysis software. Kaplan–Meier analysis demonstrated that higher PD-L1 expression is significantly associated with improved postoperative overall survival (OS) and recurrence-free survival (RFS) in both tumoral and stromal areas. Multivariable analysis identified high tumoral PD-L1 expression as an independent prognostic factor for prolonged OS and RFS (HR = 0.47, p = 0.007; HR = 0.54, p = 0.022, respectively). In a separate analysis, high stromal PD-L1 expression was found to correlate with less advanced pathological stages and a prolonged response to cytotoxic chemotherapy, with no similar correlation found for ICI treatment response. This study reveals PD-L1’s contrasting role in the ESCC tumor immune microenvironment, impacting prognosis, tumor stage, and treatment response.
Occurrence of Dichloroacetamide Herbicide Safeners and Co-Applied Herbicides in Midwestern U.S. Streams

Dichloroacetamide safeners (e.g., AD-67, benoxacor, dichlormid, and furilazole) are co-applied with chloroacetanilide herbicides to protect crops from herbicide toxicity. While such safeners have been used since the early 1970s, there are minimal data about safener usage, occurrence in streams, or potential ecological effects. This study focused on one of these research gaps, occurrence in streams. Seven Midwestern U.S. streams (five in Iowa and two in Illinois), with extensive row-crop agriculture, were sampled at varying frequencies from spring 2016 through summer 2017. All four safeners were detected at least once; furilazole was the most frequently detected (31%), followed by benoxacor (29%), dichlormid (15%), and AD-67 (2%). The maximum concentrations ranged from 42 to 190 ng/L. Stream detections and concentrations of safeners appear to be driven by a combination of timing of application (spring following herbicide application) and precipitation events. Detected concentrations were below known toxici.
Occupational Health and Safety Knowledge correlated with The Use of PPE among Home Industry Furniture Workers in the Production Process

Work accident is an unexpected event that can cause loss and damage to both physical, and property and cause death. One way to prevent work accidents is to increase understanding related to occupational health and safety so that workers have the behavior of using Personal Protective Equipment (PPE) in accordance with the need to protect themselves in order to avoid work accidents. The aim of this study was to determine the correlation between knowledge about occupational health and safety and the use of Personal Protective Equipment (PPE) for furniture home industry workers in the production process in Balongrejo Village, Berbek District, Nganjuk Regency. The design of the study used correlational with a cross-sectional approach with a total of 42 respondents which selected by the Proportional Random Sampling technique. The independent variable in this study was knowledge of occupational health and safety and the dependent variable was the use of personal protective equipment (PPE). The results of the Spearman rank test showed that there was a correlation between Occupational Health and Safety Knowledge and the use of PPE for Home Furniture Industry workers in the production process in Balongrejo Village, Berbek District, Nganjuk Regency with strong correlation strength. The knowledge of workers with the behavior of using PPE is directly proportional so that the better the knowledge possessed, the better the behavior reflected, therefore it is important for nurses as educators to provide education to workers regarding the use of personal protective equipment
Rational homotopy type of subspace arrangements

Un arrangement central A est un ensemble fini de sous-espaces vectoriels dans un espace vectoriel complexe V de dimension finie. L'espace topologique complementaire M(A) est l'ensemble des points de V qui n'appartiennent a aucun des sous-espaces de A. Dans ce travail, nous etudions la topologie de l'espace M(A) du point de vue de l'homotopie rationnelle. L'outil cle qui a servi de depart a cette these est un modele rationnel de M(A) qui s'avere relativement simple a manipuler. A l'aide de ce modele, nous obtenons plusieurs resultats sur la topologie de M(A). Citons par exemple des formules de recursion qui permettent de calculer certains invariants topologiques, dont les nombres de Betti, une preuve du fait que la caracteristique d'Euler de l'espace M(A) est nulle ou encore une description des arrangements (verifiant une condition technique) dont le complementaire est un wedge rationnel de spheres. Enfin, les resultats principaux de cet ouvrage sont une caracterisation des arrangements dont le complementaire a le type d'homotopie d'un produit de spheres, et la preuve du fait que si le complementaire n'est pas un produit de spheres, alors son algebre de Lie d'homotopie contient la sous-algebre de Lie libre a deux generateurs.
Fatigue Improvement after Eculizumab in Paroxysmal Nocturnal Hemoglobinuria: Apropos of a Case

A 54-year-old male presented with shortness of breath and was diagnosed with pulmonary emboli. Laboratory studies revealed hemolytic anemia. Flow cytometry showed a prominent white blood cell clone without CD59 in 85% (NV 0-3.0) and red blood cells with 8.5% CD59 absence (NV 0-3.0) confirming a diagnosis of paroxysmal nocturnal hemoglobinuria. Eculizumab was started to decrease the possibility of a thrombotic recurrence, with incidentally, a marked subjective improvement of symptomatology, as fatigue, was seen. We reviewed current literature regarding the improvement in fatigue seen in patients with paroxysmal nocturnal hemoglobinuria treated with eculizumab.
Evaluation of anxiolytic and sedative effect of essential oil and hydroalcoholic extract of Ocimum basilicum L. and chemical composition of its essential oil

Ocimum basilicum belongs to Lamiaceae family and has been used for the treatment of wide range of diseases in traditional medicine in Iranian folk medicine. Due to the progressive need to anti-anxiety medications and because of the similarity between O. basilicum and Salvia officinalis, which has anti-anxiety effects, we decided to investigate the anxiolytic and sedative activity of hydroalcoholic extract and essential oil of O. basilicum in mice by utilizing an elevated plus maze and locomotor activity meter. The chemical composition of the plant essential oil was also determined. The essential oil and hydroalcoholic extract of this plant were administered intraperitoneally to male Syrian mice at various doses (100, 150 and 200 mg/kg of hydroalcoholic extract and 200 mg/kg of essential oil) 30 min before starting the experiment. The amount of hydroalcoholic extract was 18.6% w/w and the essential oil was 0.34% v/w. The major components of the essential oil were methyl chavicol (42.8%), geranial (13.0%), neral (12.2%) and β-caryophyllene (7.2%). HE at 150 and 200 mg/kg and EO at 200 mg/kg significantly increased the time passed in open arms in comparison to control group. This finding was not significant for the dose of 100 mg/kg of the extract. None of the dosages had significant effect on the number of entrance to the open arms. Moreover, both the hydroalcoholic extract and the essential oil decreased the locomotion of mice in comparison to the control group. This study shows the anxiolytic and sedative effect of hydroalcoholic extract and essential oil of O. basilicum. The anti-anxiety and sedative effect of essential oil was higher than the hydroalcoholic extract with the same doses. These effects could be due to the phenol components of O. basilicum.
Cost-efficient virtual machine management : provisioning, admission control, and consolidation

One of the main challenges in Software Engineering is to cope with the transition from an industry based on software as a product to software as a service. The field of Software Engineering should provide the necessary methods and tools to develop and deploy new cost-efficient and scalable digital services. In this thesis, we focus on deployment platforms to ensure cost-efficient scalability of multi-tier web applications and on-demand video transcoding service for different types of load conditions. Infrastructure as a Service (IaaS) clouds provide Virtual Machines (VMs) under the pay-per-use business model. Dynamically provisioning VMs on demand allows service providers to cope with fluctuations on the number of service users. However, VM provisioning must be done carefully, because over-provisioning results in an increased operational cost, while underprovisioning leads to a subpar service. Therefore, our main focus in this thesis is on cost-efficient VM provisioning for multi-tier web applications and on-demand video transcoding. Moreover, to prevent provisioned VMs from becoming overloaded, we augment VM provisioning with an admission control mechanism. Similarly, to ensure efficient use of provisioned VMs, web applications on the under-utilized VMs are consolidated periodically. Thus, the main problem that we address is cost-efficient VM provisioning augmented with server consolidation and admission control on the provisioned VMs. We seek solutions for two types of applications: multi-tier web applications that follow the request-response paradigm and on-demand video transcoding that is based on video streams with soft realtime constraints. Our first contribution is a cost-efficient VM provisioning approach for multi-tier web applications. The proposed approach comprises two subapproaches: a reactive VM provisioning approach called ARVUE and a hybrid reactive-proactive VM provisioning approach called Cost-efficient Resource Allocation for Multiple web applications with Proactive scaling. Our second contribution is a prediction-based VM provisioning approach for ondemand video transcoding in the cloud. Moreover, to prevent virtualized servers from becoming overloaded, the proposed VM provisioning approaches are augmented with admission control approaches. Therefore, our third contribution is a session-based admission control approach for multi-tier web
Elevated Stream Pathogenic Indicator Bacteria Concentrations in Livestock Grazing Areas across a Single National Forest

Livestock presence in proximity to forest streams has been shown to contribute pathogenic bacteria in excess of water quality standards established to protect human health. However, the degree to which livestock fecal contamination in streams on national forest lands is either a limited or a potentially widespread occurrence is still debated. This study provides additional insight into the matter. We analyzed water in small streams near known cattle grazing areas within the Stanislaus National Forest in the Sierra Nevada, California from 2012 to 2016. Fourteen stream sites were sampled before and after cattle were released onto the forest (four of these sites were sampled across multiple years) to compare indicator bacteria concentrations (fecal coliform—FC, Escherichia coli—EC) to standards established for recreational contact for surface waters. One control site was also sampled. There were 194 water quality violations of either state or federal regulatory standards for recreational contact, all of which occurred once cattle were on the forest. Mean (max) FC and EC concentrations were on orders of magnitude higher after cattle were released onto the forest [FC 1307 (30,000) and EC 1033 (17,000) MPN/100 mL] than during the time period before cattle were on the forest [FC 19 (220) and EC 17 (220) MPN/100 mL; FC, F1,210 = 105, p < 0.001; EC, F1,210 = 85.5, p < 0.001]. In addition, the presence of cattle, visual evidence of recent cattle-related disturbances, and sampling week were important predictor variables of FC and EC. These findings support the link between cattle presence and increased levels of stream pathogenic bacteria, and also demonstrate that stream pathogenic bacteria pollution occurs widely across the forest. This research indicates the need to consider alternative range management practices to better protect water quality and human health.
Stability and the negative mode for a Schwarzschild black hole in a finite cavity

It has been proposed that translationally invariant black branes are classically stable if and only if they are locally thermodynamically stable. Reall has outlined a general argument to demonstrate this, and studied in detail the case of charged black p-branes in type II supergravity. We consider the application of his argument in the simplest nontrivial case, an uncharged asymptotically flat brane enclosed in a finite cylindrical cavity. In this simple context, it is possible to give a more complete argument than in the cases considered earlier, and it is therefore a particularly attractive example of the general approach.
Listeria monocytogenes Scott A transports glucose by high-affinity and low-affinity glucose transport systems

Listeria monocytogenes transported glucose by a high-affinity phosphoenolpyruvate-dependent phosphotransferase system and a low-affinity proton motive force-mediated system. The low-affinity system (Km = 2.9 mM) was inhibited by 2-deoxyglucose and 6-deoxyglucose, whereas the high-affinity system (Km = 0.11 mM) was inhibited by 2-deoxyglucose and mannose but not 6-deoxyglucose. Cells and vesicles artificially energized with valinomycin transported glucose or 2-deoxyglucose at rates greater than those of de-energized cells, indicating that a membrane potential could drive uptake by the low-affinity system.