Miracle-dz/UniFAR-FTUs huggingface dataset:
A systems biology approach to the Arabidopsis circadian clock

Circadian clocks involve feedback loops that generate rhythmic expression of key genes. Molecular genetic studies in the higher plant Arabidopsis theliene have revealed a complex clock network. We begin by modelling the first part of the Arabidopsis clock network to be identified, a transcriptional feedback loop comprising TIMING OF CAB EXPRESSION 1 (TOCl), LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). As for many biological systems, there are no experimental values for the parameters in our model, and the data available for parameter fitting is noisy and varied. To tackle this we construct a cost function, which quantifies the agreement between our model and various key experimental features. We then undertake a global search of parameter space, to test whether the proposed circuit can fit the experimental data. Our optimized solution for the Arabidopsis clock model is unable to account for significant experimental data. Thanks to our search of parameter space, we are able to interpret this as a failure of the network architecture. We develop an extended clock model that is based upon a wider range of data and accurately predicts additional experimental results. The model comprises two interlocking feedback loops comparable to those identified experimentally in other circadian systems. We propose that each loop receives input signals from light, and that each loop includes a hypothetical component that had not been explicitly identified. Analysis of the model predicts the properties of these components, including an acute light induction at dawn that is rapidly repressed by LHY and CCAL We find this unexpected regulation in RNA levels of the evening-expressed gene GIGANTEA (GI), supporting our proposed network and making GI a strong candidate for this component. We go on to develop reduced models of the Arabidopsis clock to aid conceptual understanding, and add a further proposed feedback loop to develop a 3-loop model of the circadian clock. This 3-loop model is able to reproduce further key experimental data.
Origin and Function

What is an Antibiotic? The word “antibiotic” comes from the terms “anti,” meaning “against” or “opposing,” and “bios,” meaning “life,” and refers to a substance that works against bacterial life. Originally the term was used to describe substances, such as penicillin or streptomycin, produced by.
Proposal for a new therapeutic high dosage of Pidotimod in children with Periodic fever, aphthous stomatitis, pharyngitis, adenitis (PFAPA) syndrome: an interventional study.

Background. Despite to PFAPA syndrome is considered a benign and self-limited condition in childhood its impact on patients and families can be remarkable in many cases. Currently, the therapeutic options for managing are non-specific and no consensus exists about the best treatment to use. Pidotimod has been suggested as a new potential treatment in PFAPA syndrome for its immunodulatory effects. We conducted a preliminary, prospective, controlled, open, cross-over trial to assess the efficacy and the safety of Pidotimod in the treatment of children with PFAPA syndrome. Methods. 22 children with PFAPA syndrome were randomly allocated to treatment with pidotimod (with 2 vials of 400mg daily) in combination with betamethasone 0.5-1 mg on need, based on parents/caregivers' decision (group A) or betamethasone 0.5-1mg on need, based on parents/caregivers' decision (group B). Each treatment period was for 3 months (Phase 1), after that patients were switched to the other arm for other 3 months (Phase 2). Efficacy was expressed in terms of number of episodes of fever, pharyngitis, or aphthous stomatitis, as well as the additional use of betamethasone on need. Safety and tolerability of the Pidotimod were evaluated on the basis of the number and type of adverse events (AEs) recorded during the treatment.Results. Patients receiving Pidotimod and use betametasone showed a significant decrease in frequency of fevers (p=0.002); number of episodes of pharyngitis (p=0.049); aphthous stomatitis (p=0.036) as well as the betamethasone use on need (p=0.007). Overall, 19/22 (86.4%) showed benefits from Pidotimod administration. The safety profile of Pidotimod was excellent as no serious adverse events have been reported in the treated groups.Conclusions. We firstly showed that high dosage of Pidotimod could be an effective and safe to reduce the PFAPA attacks in children.
Comparison of optical passive integrated devices based on three materials for optical clock distribution

We report different passive integrated devices characterization based on three materials (SOI, a-Si:H and SiNx) for the realization of an optical compact link compatible with CMOS technology. The low level of losses obtained on the passive elementary components for the optical link (strip guides, micro bend and MMI beam splitter) shows the feasibility of photonic integration on silicon using amorphous silicon.
FAKTOR RISIKO INFEKSI SALURAN KEMIH OLEH MULTI DRUG RESISTANT ORGANISMS PADA PASIEN YANG DIRAWAT DI RSUP DR KARIADI

Latar Belakang: Infeksi saluran kemih (ISK) oleh multidrug-resistant organisms atau MDRO adalah ISK yang disebabkan oleh bakteri yang resisten terhadap 3 atau lebih kelas antibiotik. Terjadi peningkatan kejadian ISK oleh MDRO dalam 2 dekade terakhir. Tujuan: Untuk menganalisis faktor yang bermakna dalam menimbulkan ISK oleh MDRO di Rumah Sakit Dr. Kariadi Semarang. Metode: Jenis penelitian ini adalah case control dengan mengambil data secara restrospektif dari rekam medis pasien RSUP Dr. Kariadi tahun 2011-2012. Faktorfaktor yang diteliti terdiri dari usia, kateter urin, antibiotik, hemodialisa, keganasan hematologi, DM, ulkus DM, ICU, dan perawatan jangka panjang. Variabel tergantung adalah kejadian ISK oleh MDRO. Analisis statistik bivariat menggunakan uji chi-square dan analisis multivariat menggunakan regresi logistik dengan SPSS 15.00 Hasil: Penggunaan kateter urin merupakan faktor yang bermakna menimbulkan ISK oleh MDRO (p=0,011). Faktor yang lain seperti usia (p=0,616), penggunaan antibiotik (p=0,084), hemodialisa (p=0,153), keganasan hematologi (p=0,5), DM (p=0,25), Ulkus DM (p=0,5), perawatan ICU (p=0,433), dan perawatan jangka panjang (p=0,834) memiliki nilai p≥0,05 sehingga tidak bermakna menimbulkan ISK oleh MDRO. Kesimpulan: Penggunaan kateter urin merupakan faktor risiko kejadian ISK oleh MDRO. Usia, antibiotik, hemodialisa, keganasan hematologi, DM, ulkus DM, ICU, dan perawatan jangka panjang bukan merupakan faktor risiko ISK oleh MDRO. Kata Kunci: Infeksi saluran kemih, faktor risiko, multidrug-resistant organisms (MDRO)
Development

Clefts of the palate and/or lip are the most common among human craniofacial malformations and involve multiple genetic and environmental factors. Defects can only be corrected surgically and require complex life-long treatments. Our studies utilized the well-characterized Pax9 mouse model with a consistent cleft palate phenotype to test small-molecule Wnt agonist therapies. We first show that the absence of Pax9 alters the expression of Wnt pathway genes including Dkk1 and Dkk2, proven antagonists of Wnt signaling. The functional interactions between Pax9 and Dkk1 is shown by the genetic rescue of secondary palate clefts in Pax9Dkk1;Wnt1Cre embryos. The controlled intravenous delivery of small-molecule Wnt agonists (Dkk inhibitors) into pregnant Pax9 mice restored Wnt signaling and led to the growth and fusion of palatal shelves as marked by an increase in cell proliferation and osteogenesis in-utero while other organ defects were not corrected. This work underscores the importance of Pax9dependent Wnt signaling in palatogenesis and suggests that such a functional upstream molecular relationship can be exploited for the development of therapies for human cleft palates that arise from single gene disorders. D ev el o pm en t • A cc ep te d m an us cr ip t
Desiccation of the Transboundary Hamun Lakes: Natural or Anthropogenic?

This paper investigates the hydrologic and water management reasons behind the desiccation of the Hamun Lakes in the Iran-Afghanistan border region. We analysed changes in Hirmand (or Helmand) River flow, the main tributary providing 70% of the lakes’ total inflow, and precipitation during 1960-2016 by calculating standardized indices for precipitation (SPI) and discharge (SDI). Also, we applied Normalized Difference Spectral Indices (NDSIs) using satellite images from 1987 to present to observe monthly areal change of the lakes. The transboundary water body is responding to changes in regional water management, which has severely reduced the lakes’ inflow. Upstream water regulation in Afghanistan coupled with reservoir construction on the Iranian side has caused nearly full desiccation of major parts of the lake system. There is a discernible shift in the relation between the Hirmand River flow at the international border and upstream precipitation over the lakes’ basin before and after 2004. From 1960 to 2003, high river flows were expected to feed the lakes due to high precipitation over the basin. However, the Hirmand River flow at the border declined after 2004 despite large amounts of upstream precipitation, including the largest recorded amounts, especially in the Hindu Kush mountains. Further, environmental water stress caused by anthropocentric water management in Iran by reservoir construction has impacted the area of the lakes. Although a long period of drought from 1998-2004, i.e. climatic driver, decreased the lakes’ area, the lake system is primarily falling victim to anthropogenic flow alterations in the transboundary river basin. The lakes’ shrinkage places socio-economic stress on an already-vulnerable region with important public health implications as the exposed lake beds turn into major sources of sand and dust storms.
WiMAX timing and frequency synchronization based on training sequence

In all wireless communication systems and especially in OFDM and MIMO-OFDM system synchronization is crucial. The receivers do not know the beginning and the end of the OFDM symbols, so the placement of the FFT window. Moreover, they have their own sampling frequency asynchronous with that of the transmitter. These two points show two synchronization concepts: time and frequency. An error of time synchronization in the reception may cause loss of the orthogonality of subcarriers. This is why it is important to have a robust synchronization algorithm and know its effect on system performance. Several estimation techniques for time and frequency offset have been proposed in the literature, but varied test conditions make comparison difficult. In this paper, we use Schmidl and Cox algorithm as a symbol timing synchronization algorithm for OFDM system. We also see the preamble structure using the equations provided in the IEEE 802.16d. Simulation results show the effect caused by carrier frequency offset (CFO) and timing frequency offset (STO) on the performance of an OFDM system in a WiMAX context.
Optimizing Live Digital Evidence Mining Using Structural Subroutines of Apriori Algorithm

The Scope and Complexity of the Internet has grown exponentially. This growth has made digital forensic investigation a very challenging task. Even the modest intra-organizational networks have sufficient network traffic to pose a problem for digital crime investigators to police and collect evidences. Another problem in Network based Crime Investigation is that Offline Mining Techniques do not yield pervasive evidence. At the same time due to voluminous traffic, live evidence mining becomes a challenge. This paper presents a technique to optimize the live evidence mining by using the principles of apriori algorithm to trigger the evidence collection mechanism at right and opportune moment. The crux of this technique is answering "When & What Information" to Collect about a subject of investigation or Data.
MULTI-MIRROR SYSTEM FOR HIGH-SPEED CAMERA MONITORING APPLICATIONS

Non-contact measurement methods that uses high-speed cameras are now becoming fundamental tools in research laboratories and are playing a key role in analysing and troubleshooting manufacturing processes. A common requirement in monitoring applications is the capability to observe objects and scenes simultaneously from different points of view. Multi-camera array systems is one of the solutions, but due to synchronization aspect and high cost of implementation, other possibilities are being sought. In many cases, a suitable method can be a catadioptric system connected with a single high-speed camera. In this solution, a combination of refractive (lenses) and reflective (mirrors) components are used. This enables one to observe a number of surfaces of the analysed object from different points of view, including orthogonal or even opposite directions. This paper presents the capability of a high-speed camera vision system with a multi-mirror lens set-up that enables simultaneous observation of an object from eight different points of view. The proposed technique has advantages and drawbacks, and they are described in detail.
First data on long-legged flies (Diptera, Dolichopodidae) of the Onezhskoye Pomorye National Park (Arkhangelsk Region, Russia)

The fauna of Dolichopodidae in the Arkhangelsk Region was studied sporadically and currently in-cludes 50 species. Onezhskoye Pomorye National Park (Arkhangelsk Region, Russia) was established in 2013 to protect the pristine forests and coastal ecosystems of the hardly accessible territories along the White Sea coast of the Onega Peninsula. The insect fauna of the National Park was almost un-known until recently, with only 17 Diptera species from the Culicidae and Chironomidae families listed in the online cadaster. During the short expedition to Onezhskoye Pomorye National Park in July–August 2020, more than 350 Dolichopodidae specimens were collected with yellow pan traps and sweep netting on routes that mainly passed through coastal habitats. Nineteen species of Dolichopodi-dae have been reported for the first time from this territory. Thirteen species are reported for the first time from the Arkhangelsk region, bringing the total number of known species to 63. The species list is given and supplied with brief comments on habitat and distribution. Photos of some typical habitats are provided. Most of the discovered species are widespread throughout the Palaearctic Region. Rarer species include Dolichopus diadema, which probably represents a southern Palaearctic element, and Hydrophorus norvegicus, which was previously known only from Fennoscandia.
Preliminary Stated-Preference Research on the Impact of LUST Sites on Property Values: Focus Group Results

The purpose of this research effort is to examine the feasibility of designing a stated preference instrument to elicit the public’s willingness-to-pay (WTP) for remediation of leaking underground storage tank (LUST) sites (or perhaps prevention of releases). Nearly 500,000 releases have been documented from the over 600,000 USTs nationwide. Approximately 80 percent of these sites have been cleaned up. In the three Maryland counties that are the focus of this and the companion hedonic property value study there have been nearly 400 documented releases in the last 10 years. We report the results from four focus groups and four three-on-one interviews conducted in Maryland. The results of this focus group research provide a foundation for development of a stated preference study of the benefits of EPA’s UST program.
Cross-layer modeling and optimization of next-generation internet networks

Scaling traditional telecommunication networks so that they are able to cope with the volume of future traffic demands and the stringent European Commission (EC) regulations on emissions would entail unaffordable investments. For this very reason, the design of an innovative ultra-high bandwidth power-efficient network architecture is nowadays a bold topic within the research community. So far, the independent evolution of network layers has resulted in isolated, and hence, far-from-optimal contributions, which have eventually led to the issues today's networks are facing such as inefficient energy strategy, limited network scalability and flexibility, reduced network manageability and increased overall network and customer services costs. Consequently, there is currently large consensus among network operators and the research community that cross-layer interaction and coordination is fundamental for the proper architectural design of next-generation Internet networks. This thesis actively contributes to the this goal by addressing the modeling, optimization and performance analysis of a set of potential technologies to be deployed in future cross-layer network architectures. By applying a transversal design approach (i.e., joint consideration of several network layers), we aim for achieving the maximization of the integration of the different network layers involved in each specific problem. To this end, Part I provides a comprehensive evaluation of optical transport networks (OTNs) based on layer 2 (L2) sub-wavelength switching (SWS) technologies, also taking into consideration the impact of physical layer impairments (PLIs) (L0 phenomena). Indeed, the recent and relevant advances in optical technologies have dramatically increased the impact that PLIs have on the optical signal quality, particularly in the context of SWS networks. Then, in Part II of the thesis, we present a set of case studies where it is shown that the application of operations research (OR) methodologies in the desing/planning stage of future cross-layer Internet network architectures leads to the successful joint optimization of key network performance indicators (KPIs) such as cost (i.e., CAPEX/OPEX), resources usage and energy consumption. OR can definitely play an important role by allowing network designers/architects to obtain good near-optimal solutions to real-sized problems within practical running times.
Practical reinforcement learning using representation learning and safe exploration for large scale Markov decision processes

While creating intelligent agents who can solve stochastic sequential decision making problems through interacting with the environment is the promise of Reinforcement Learning (RL), scaling existing RL methods to realistic domains such as planning for multiple unmanned aerial vehicles (UAVs) has remained a challenge due to three main factors: 1) RL methods often require a plethora of data to find reasonable policies, 2) the agent has limited computation time between interactions, and 3) while exploration is necessary to avoid convergence to the local optima, in sensitive domains visiting all parts of the planning space may lead to catastrophic outcomes. To address the first two challenges, this thesis introduces incremental Feature Dependency Discovery (iFDD) as a representation expansion method with cheap per-timestep computational complexity that can be combined with any online, value-based reinforcement learning using binary features. In addition to convergence and computational complexity guarantees, when coupled with SARSA, iFDD achieves much faster learning (i.e., requires much less data samples) in planning domains including two multi-UAV mission planning scenarios with hundreds of millions of state-action pairs. In particular, in a UAV mission planning domain, iFDD performed more than 12 times better than the best competitor given the same number of samples. The third challenge is addressed through a constructive relationship between a planner and a learner in order to mitigate the learning risk while boosting the asymptotic performance and safety of an agent's behavior. The framework is an instance of the intelligent cooperative control architecture where a learner initially follows a safe policy generated by a planner. The learner incrementally improves this baseline policy through interaction, while avoiding behaviors believed to be risky. The new approach is demonstrated to be superior in two multi-UAV task assignment scenarios. For example in one case, the proposed method reduced the risk by 8%, while improving the performance of the planner up to 30%. Thesis Supervisor: Jonathan P. How Title: Richard C. Maclaurin Professor of Aeronautics and Astronautics Thesis Supervisor: Nicholas Roy Title: Associate Professor of Aeronautics and Astronautics
Boost chopper-fed ZVS-PWM DC-DC converter with parasitic oscillation surge suppression-based auxiliary edge resonant snubber

This paper presents a high-frequency boost type ZVS-PWM chopper-fed DC-DC power converter with a single active auxiliary edge-resonant snubber in load stage, which can be designed for power conditioners such as solar photovoltaic generation, fuel cell generation, battery and super capacitor energy storages. Its principle operation in steady state is described in addition to a prototype setup. The experimental results of boost type ZVS-PWM chopper proposed here, are evaluated and verified with a practical design model in terms of its switching voltage and current waveforms, the switching v-i trajectory and the temperature performance of IGBT module, the actual power conversion efficiency, and the EMI of radiated and conducted emissions. And then discussed and compared with the hard switching scheme from an experimental point of view. Finally, this paper proposes a practical method to suppress parasitic oscillation due to the active auxiliary resonant switch at ZCS turn-off mode transition with the aid of an additional lossless clamping diode loop, and reduced the EMI conducted emission in this paper.
PERFORMANCE EVALUATION OF DATA LINK LAYER (MAC/LLC) PROTOCOLS PROPOSED FOR STANDARDIZATION

In this paper, the results of performance evaluations by computer simulations of beacon-vehicle communication protocols and their options for Dedicated Short Range Communications (DSRC), currently being proposed as candidates for standardization of the data link layer in Europe are presented. A comparison is made between these and the protocols being proposed in North America. Special emphasis is given to the performance analysis of systems for automatic fee collection and dynamic route guidance. With this respect the current state of the European standardization process concerning the specification of the physical layer and the data link layer, applications and traffic scenarios have been considered. The presented investigations show clearly that the application requirements will be met by the proposed DSRC standard proposals and the transaction success rate will be sufficiently high. Due to their higher flexibility the asynchronous link layer protocols proposed by the European standardization body CEN/TC278 (WG9) have some advantages related to the synchronous protocols. The simulation tools used for the presented investigations are able to assist for system design and evaluation of the system performance. (A) For the covering abstract see IRRD 868006.