Miracle-dz/UniFAR-FTUs huggingface dataset:
Community structure detection in complex biological networks

With the advent of high-throughput technology there has been a large increase in the availability of biological data, such as interaction data of genes, proteins and metabolites. It is therefore necessary to develop ways in which these data can be efficiently modelled and analysed. Networks offer a natural modelling framework for complex biological systems and as such, network theory and related computational approaches have proven important in bioinformatics. A particular facet of network theory that has been employed to analyse biological networks is community structure detection. Community structure is a modular network topology where communities are defined as groups of nodes with dense intra-community connections and less dense inter-community connections. Methods to uncover such communities in complex biological networks have the potential to contribute towards a better understanding of the underlying organisation of a system. Consequently, this thesis focuses on the development of a series of mathematical programming models to address various manifestations of the community structure detection problem. The aim is to produce more information-rich models that can accurately represent the features of biological systems; with weighted and unweighted interactions, disjoint and overlapping communities and network dynamics all being considered. First, the detection of disjoint communities in unweighted networks is approached through a two-stage procedure, known as iMod. A mixed integer nonlinear programming (MINLP) model optimises modularity to find an initial partition which is then improved by iteratively solving a mixed integer quadratic programming (MIQP) model. A comparative analysis shows that iMod finds globally optimal solutions for networks of up to 512 nodes and outperforms all other methods tested when applied to larger networks. Subsequently, the MINLP model is generalised to weighted networks, known accordingly as WeiMod. Competitive results are found when WeiMod is compared with several other well known methods from the literature. Next, the work on disjoint community structure is extended to find overlapping modules. An MINLP model, known as OverMod, transforms disjoint to overlapping communities through the optimisation of the community strength metric. OverMod is compared with similar methods from the literature and is further assessed on protein-protein interaction (PPI) networks to test the method’s ability to extract meaningful biological results. It is shown that proteins assigned to more than one module exhibit topological and functional properties indicative of their strategically important role in the organisation of the PPI networks. The work on disjoint and
Orchestrated feedback regulation between melatonin and sex hormones involving GPER1‐PKA‐CREB signaling in the placenta

Maintaining placental endocrine homeostasis is crucial for a successful pregnancy. Pre‐eclampsia (PE), a gestational complication, is a leading cause of maternal and perinatal morbidity and mortality. Aberrant elevation of testosterone (T0) synthesis, reduced estradiol (E2), and melatonin productions have been identified in preeclamptic placentas. However, the precise contribution of disrupted homeostasis among these hormones to the occurrence of PE remains unknown. In this study, we established a strong correlation between suppressed melatonin production and decreased E2 as well as elevated T0 synthesis in PE placentas. Administration of the T0 analog testosterone propionate (TP; 2 mg/kg/day) to pregnant mice from E7.5 onwards resulted in PE‐like symptoms, along with elevated T0 production and reduced E2 and melatonin production. Notably, supplementation with melatonin (10 mg/kg/day) in TP‐treated mice had detrimental effects on fetal and placental development and compromised hormone synthesis. Importantly, E2, but not T0, actively enhanced melatonin synthetase AANAT expression and melatonin production in primary human trophoblast (PHT) cells through GPER1‐PKA‐CREB signaling pathway. On the other hand, melatonin suppressed the level of estrogen synthetase aromatase while promoting the expressions of androgen synthetic enzymes including 17β‐HSD3 and 3β‐HSD1 in PHT cells. These findings reveal an orchestrated feedback mechanism that maintains homeostasis of placental sex hormones and melatonin. It is implied that abnormal elevation of T0 synthesis likely serves as the primary cause of placental endocrine disturbances associated with PE. The suppression of melatonin may represent an adaptive strategy to correct the imbalance in sex hormone levels within preeclamptic placentas. The findings of this study offer novel evidence that identifies potential targets for the development of innovative therapeutic strategies for PE.
Using simple chaotic models to interpret climate under climate change: Implications for probabilistic climate prediction

Exploring the reliability of model based projections is an important pre-cursor to evaluating their societal relevance. In order to better inform decisions concerning adaptation (and mitigation) to climate change, we must investigate whether or not our models are capable of replicating the dynamic nature of the climate system. Whilst uncertainty is inherent within climate prediction, establishing and communicating what is plausible as opposed to what is likely is the first step to ensuring that climate sensitive systems are robust to climate change. Climate prediction centers are moving towards probabilistic projections of climate change at regional and local scales (Murphy et al., 2009). It is therefore important to understand what a probabilistic forecast means for a chaotic nonlinear dynamic system that is subject to changing forcings. It is in this context that we present the results of experiments using simple models that can be considered analogous to the more complex climate system, namely the Lorenz 1963 and Lorenz 1984 models (Lorenz, 1963; Lorenz, 1984). Whilst the search for a low-dimensional climate attractor remains illusive (Fraedrich, 1986; Sahay and Sreenivasan, 1996) the characterization of the climate system in such terms can be useful for conceptual and computational simplicity. Recognising that a change in climate is manifest in a change in the distribution of a particular climate variable (Stainforth et al., 2007), we first establish the equilibrium distributions of the Lorenz systems for certain parameter settings. Allowing the parameters to vary in time, we investigate the dependency of such distributions to initial conditions and discuss the implications for climate prediction. We argue that the role of chaos and nonlinear dynamic behaviour ought to have more prominence in the discussion of the forecasting capabilities in climate prediction.
Evolution géodynamique du craton Ouest Africain au nord du Ghana

Cette these porte sur l'histoire geologique paleoproterozoique du Craton Ouest Africain au nord du Ghana, pendant l’orogenese Eburneenne (2.15-2.07 Ga). La geologie regionale est presentee a l'aide de nouvelles cartes lithologique, metamorphique et structurale, issues de l'interpretation de donnees geophysiques et de terrain. Le nord du Ghana est constitue de ceintures de roches vertes, de gneisses et de granitoides. Ceux-ci ont une affinite calco-alkaline ou sont analogues aux TTG archeens, et se sont formes entre 2.21 et 2.11 Ga. L'isotopie Lu-Hf indique que l'ensemble des magmas est juvenile, avec des temps de residence crustaux de 2.45-2.30 Ga. Le metamorphisme au nord du Ghana revele une diversite de regimes thermiques. Des reliques metamorphiques temoignent d'un geotherme apparent froid (BT-HP, 15°C/km). Elles sont sur-imprimees par un episode metamorphique MP – MT (20°C/km) dans les facies amphibolite a granulite, a partir de 2145 Ma, puis par une autre phase metamorphique en facies amphibolite (25-30°C/km) entre 2125 et 2105 Ma. L’evolution metamorphique est interpretee comme la consequence d’une interaction entre epaississement crustal et fluage gravitaire de la pile orogenique. Il est propose qu'un evenement magmatique produise des fragments d'une croute juvenile precoce, precurseur du Craton Ouest Africain a partir de 2.45 Ga. Le nord du Ghana pourrait representer une suture entre deux compartiments cratoniques distincts entres en collision. La geodynamique paleoproterozoique semble unique dans l'histoire de la Terre et represente un etat transitoire de son evolution seculaire, entre un regime « archaique »' et la tectonique des plaques moderne.
SeLINA: A Self-Learning Insightful Network Analyzer

Understanding the behavior of a network from a large scale traffic dataset is a challenging problem. Big data frameworks offer scalable algorithms to extract information from raw data, but often require a sophisticated fine-tuning and a detailed knowledge of machine learning algorithms. To streamline this process, we propose self-learning insightful network analyzer (SeLINA), a generic, self-tuning, simple tool to extract knowledge from network traffic measurements. SeLINA includes different data analytics techniques providing self-learning capabilities to state-of-the-art scalable approaches, jointly with parameter auto-selection to off-load the network expert from parameter tuning. We combine both unsupervised and supervised approaches to mine data with a scalable approach. SeLINA embeds mechanisms to check if the new data fits the model, to detect possible changes in the traffic, and to, possibly automatically, trigger model rebuilding. The result is a system that offers human-readable models of the data with minimal user intervention, supporting domain experts in extracting actionable knowledge and highlighting possibly meaningful interpretations. SeLINA's current implementation runs on Apache Spark. We tested it on large collections of real-world passive network measurements from a nationwide ISP, investigating YouTube, and P2P traffic. The experimental results confirmed the ability of SeLINA to provide insights and detect changes in the data that suggest further analyses.
Epstein-Barr virus BALF3 mediates genomic instability and progressive malignancy in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a head and neck cancer prevalent throughout Southern China and Southeast Asia. Patient death following relapse after primary treatment remains all too common but the cause of NPC relapse is unclear. Clinical and epidemiological studies have revealed the high correlation among NPC development, Epstein-Barr virus (EBV) reactivation and host genomic instability. Previously, recurrent EBV reactivation was shown to cause massive genetic alterations and enhancement of tumor progression in NPC cells and these may be required for NPC relapse. Here, EBV BALF3 has the ability to induce micronuclei and DNA strand breaks. After recurrent expression of BALF3 in NPC cells, genomic copy number aberrations, determined by array-based comparative genomic hybridization, had accumulated to a significant extent and tumorigenic features, such as cell migration, cell invasion and spheroid formation, increased with the rounds of induction. In parallel experiments, cells after highly recurrent induction developed into larger tumor nodules than control cells when inoculated into NOD/SCID mice. Furthermore, RNA microarrays showed that differential expression of multiple cancer capability-related genes and oncogenes increased with recurrent BALF3 expression and these changes correlated with genetic aberrations. Therefore, EBV BALF3 is a potential factor that mediates the impact of EBV on NPC relapse.
Dose–response effect of incremental lateral-wedge hardness on the lower limb Biomechanics during typical badminton footwork

ABSTRACT Badminton footwork has been characterised with jump-landing, cross step, side side and lunges, which requires movement agility to facilitate on-court performance. A novel badminton shoe design with systematic increase of lateral wedge hardness (Asker C value of 55, 60, 65, and 70) was developed and investigated in this study, aiming to analyse the dose–response effect of incremental wedge hardness on typical badminton footwork. Stance time and joint stiffness were employed to investigate the footwork performance, and the factorial Statistical non-Parametric Mapping and Principal Component Analysis (PCA) were used to quantify the biomechanical responses over the stance. As reported, shorter contact times (decreased by 8.9%–13.5%) and increased joint stiffness (in side step) of foot-ankle complex were found, suggesting improved footwork stability and agility from increased hardness. Time-varying differences were noted during the initial landing and driving-off phase of cross and side steps and drive-off returning of lunges, suggesting facilitated footwork performance. The reconstructed modes of variations from PCA further deciphered the biomechanical response to the wedge dosage, especially during drive-off, to understand the improved footwork agility and stability.
A Cognitive Control Perspective of Self-Control Strength and Its Depletion

Self-control strength is a central construct to theories of willpower, optimal functioning, freedom from addiction, and abilities to override problematic social motives and behaviors (e.g., aggression). Understanding the processing basis of self-control strength, and more particularly its depletion, is thus of paramount importance to both basic and applied literatures. Self-control strength, the present review suggests, can be profitably viewed in cognitive control terms, particularly so in relation to operations of a brain-based cognitive control circuit involving the anterior cingulate cortex (linked to monitoring potential or actual unwanted outcomes) and the dorsolateral prefrontal cortex (linked to controlling potential or actual unwanted outcomes). Also, sufficient task motivation is important to operations of this circuit and depletion effects might be understood in terms of such depletion effects on task motivation. Multiple sources of evidence are marshaled in support of this cognitive control perspective of self-control strength. It is concluded that viewing self-control strength in cognitive control terms has considerable merit. Social, cognitive, personality, and clinical sources of data are integrated in the analysis.
Glaciers, Polar Caps and Ice Mantling: The Effect of Obliquity on Martian Climate

Introduction Surface conditions on Mars are currently cold and dry, with water ice unstable on the surface except near the poles and surface liquid water thought to be never present. However, geologically recent glacier-like landforms have been identified in the tropics and mid-latitudes of Mars, an ice-rich mantling seems to cover both hemisphere above 60°latitude The corresponding climate changes seem to have been recorded in the multi-layered polar deposits.
Etude de la circulation oceanique en mediterranee occidentale

Les principaux processus gouvernant la circulation en mediterranee occidentale sont etudies a l'aide d'un modele numerique tridimensionnel. Pour ce faire, on realise plusieurs experiences permettant de tester les influences des differents forcages (transports aux detroits de gibraltar et de sicile, flux thermohalins, action mecanique du vent). On montre que les transports aux detroits engendrent une circulation de surface cyclonique sur l'ensemble du bassin induite par la propagation de fronts de kelvin baroclines. La superposition des flux thermohalins reduit l'intensite de la circulation en mer tyrrhenienne tandis qu'apparait un transport de surface du bassin algerien dans le bassin liguro-provencal. La formation d'eau profonde entraine une diminution hivernale du transport de surface vers le sud dans le canal d'ibiza. D'apres une etude de sensibilite, le vent est susceptible d'engendrer une circulation cyclonique dans le bassin liguro-provencal et de renforcer le courant liguro-provencal, dont la dynamique est similaire a celle des courants de bord ouest. La circulation obtenue apres 20 ans d'integration represente bien les principaux traits de la circulation de surface deduite des observations, mais elle pose probleme pour la repartition des masses d'eau a profondeur intermediaire: l'eau intermediaire froide formee dans le nord du bassin reste piegee dans cette region et maintient l'eau levantine intermediaire dans le bassin algerien
If They Won’t Know, I Won’t Wait: Anticipated Social Consequences Drive Children’s Performance on Self-Control Tasks

This research evaluated the hypothesis that the act of offering an incentive produces anticipated social benefits that are distinct from the benefits associated with the incentive itself. Across three preregistered studies, 3- to 5-year-old children in China (total N = 210) were given an opportunity to wait for an additional sticker (Studies 1 and 3) or an edible treat (Study 2). Rewards were dispensed via a timer-controlled box that allowed the experimenter’s apparent ability to learn how long children waited to be manipulated experimentally. Children waited only about half as long when they believed the experimenter would not find out how long they waited. When children were offered three prizes for waiting, anticipated social benefits still drove behavior at least as much as the reward. The findings demonstrate that children as young as 3 years are sensitive to anticipated social rewards when responding to offers of incentives.
Evidence for Past Flow in the Martian North Polar Layered Deposits from Ice Flow Inverse Modeling

FLOW INVERSE MODELING. D.P. Winebrenner 1 , M. Koutnik 2 , E.D. Waddington 2 , A.V. Pathare 3,4 , B.C. Murray 4 , S. Byrne 5 , and J.L. Bamber 6 , 1 Applied Physics Laboratory and Dept. of Earth and Space Sciences, Box 355640, University of Washington, Seattle, WA 98195, dpw@apl.washington. edu, 2 Dept. of Earth and Space Sciences, Box 351310, University of Washington, Seattle, WA 98195, 3 Planetary Science Institute, 1700 E. Ft. Lowell, Suite 106, Tucson, AZ, 85719, 4 Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, 5 Lunar and Planetary Laboratory, University of Arizona, Tucson AZ 85721, 6 Bristol Glaciology Centre, University of Bristol, Bristol BS8 1SS,United Kingdom.
Remote ischaemic preconditioning increase tolerance to experimentally induced cold pain

ABSTRACT Ischaemic preconditioning (IPC) applied locally and remotely has been shown to reduce pain which may underpin its ergogenic effect on exercise performance, however, it is unclear how many IPC cycles are needed to induce hypoalgesia. Therefore the purpose of this study was to examine the number of cycles of IPC on experimental pain perception. Sixteen healthy participants underwent four, randomised, experimental sessions where they either underwent a sham protocol (1 × 5 min at 20 mmHg), and 1, 2 or 3 cycles × 5 min of remote IPC at 105% of limb occlusion pressure. Ten minutes post-intervention, participants underwent a cold-pressor test where pain threshold, pain tolerance and pain intensity were examined and compared between conditions with a one-way repeated measure analysis of variance. Pain threshold was not different between conditions (P = 0.065); but pain tolerance was increased by ∼30% in the 1 × 5 condition, 2 × 5 condition, and 3 × 5 condition compared to the sham condition. No differences in pain tolerance were seen between the different numbers of cycles (all P > 0.05). There was also no difference in the perception of pain 30 s into the cold pressor test (P = 0.279). Remote IPC appears to significantly improve tolerance to pain which may have significant implications for endurance performance and exercise rehabilitation, but this warrants further investigation. Highlights We found that one, two or three cycles of ischaemic preconditioning improved cold pain tolerance by 30% compared to a sham protocol, but there was no clear effect of IPC on pain threshold or pain intensity. The pain reported during IPC decreased from cycle one to cycle three in the three cycle condition, suggesting a potential conditioned pain modulation effect. An increase in pain tolerance may explain why IPC can improve exercise performance and IPC itself could be used as a tool to improve tolerance to pain.
Disturbance ecology of high-elevation five-needle pine ecosystems in western North America

This paper synthesizes existing information about the disturbance ecology of high-elevation five-needle pine ecosystems, describing disturbances regimes, how they are changing or are expected to change, and the implications for ecosystem persistence. As it provides the context for ecosystem conservation/restoration programs, we devote particular attention to wildfire and its interactions with mountain pine beetle (Dendroctonus ponderosae Hopkins) outbreaks and white pine blister rust (Cronartium ribicola J.C. Fisch.).
Parent and healthcare provider views of live varicella vaccination of pediatric solid organ transplant recipients

Live attenuated varicella vaccine (LAVV) has historically been contraindicated in children who are immunocompromised due to solid organ transplant (SOT) because of safety concerns. Recently, clinical guidelines were developed that support post‐transplant varicella vaccination in selected SOT recipients based on emerging evidence of LAVV safety. This qualitative study sought to explore barriers and facilitators to implementing the new guidelines, as well as acceptability of LAVV among healthcare providers (HCPs) and parents.
Physical cleansing reduces the mindset effect in problem-solving

ABSTRACT The present study investigated whether physical cleansing can reduce the mindset effect in problem-solving in two experiments. Both experiments followed the same procedure. In the first stage, participants formed a mindset through the Luchins’ water-jar task (Experiment 1) or the idiom maze task (Experiment 2). The second stage is cleansing manipulation. In Experiment 1, participants were asked to clean their hands with wipes (cleansing condition) or examine the packaging of the wipes (no-cleansing condition). In Experiment 2, participants were asked to watch a washing-hands video (cleansing condition) or watch an examining-pen video (no-cleansing condition). At last, all participants completed the mindset effect test problems. The results showed that the participants in the cleansing condition were less affected by the mindset than those in the no-cleansing condition, indicating that physical cleansing reduced the mindset effect. Our results provide new evidence for the clean-slate effects and support the hypothesis that physical cleansing is an embodied process of psychological separation.
Human Embryology

The study of human embryology has a very long history. Modern embryology owes its initial development to the key embryo collections that began in the 19th century. The first large collection was that of Carnegie, and this was followed later by the major 7 collections. The second role of the Carnegie collection was for researchers to establish a defined set of Carnegie stages based on embryo morphological features. Today, embryos are imaged three-dimensionally (3D) by a range of imaging modalities including, magnetic resonance microscopy (MRM), episcopic fluorescence image capture (EFIC), phase-contrast X-ray computed tomography (pCT), and optical projection tomography (OPT). Historically, embryo serial images were reconstructed using wax-plate and model techniques. The above new 3D imaging techniques now allow 3D computer reconstructions, analysis, and even 3D printing. This chapter will describe how the classical embryology collections and techniques have developed into today’s imaging and analysis techniques, giving new insights to human embryonic development. human embryos at increasingly earlier stages. To obtain data on early human development,