Miracle-dz/UniFAR-FTUs huggingface dataset:
From Road to Lab to Math

Today, in the midst of economic crisis, senior executives at US automakers and influential industry analysts frequently reflect on the progression that safety testing has taken from the crude trials done on the road, to controlled laboratory experiments, and to today’s complex math-based simulation models. They use stories of this seemingly linear and natural sequence to justify further investment in simulation technologies. The analysis presented in this paper shows that change in the structures of automakers’ organizations co-evolved with regulations specifying who was at fault in vehicle impacts, how vehicles should be built to withstand the force of an impact, and how testing should be done to assure that vehicles met those requirements. Changes in the regulatory environment were bolstered by new theories about crash test dynamics and changing technologies with which to test those theories. Thus, as new technological and regulatory innovations co-evolved with innovations in organizational structuring, ideas about how to best conduct crash tests shifted and catalyzed new cycles of technological, regulatory, and organizational innovation. However, this co-evolutionary story tells us that the move from road to lab to math was not natural or linear as today’s managerial rhetoric would have us believe. Rather, the logic of math-based simulation was the result of technological, regulatory and organizational changes that created an industry-wide ideology that supported the move toward math while making it appear natural within the shifting structure of the industry.
Antibacterial properties of in situ and surface functionalized impregnation of silver sulfadiazine in polyacrylonitrile nanofiber mats

Background Silver, incorporation with natural or synthetic polymers, has been used as an effective antibacterial agent since decades. Silver has potential applications in healthcare especially in nanoparticles form but silver sulfadiazine (AgSD) is the most efficient antibacterial agent especially for burn wound dressings. Method In this report, mechanical, structural, and antibacterial properties of PAN nanofibers incorporation with silver sulfadiazine are mainly focused. AgSD was loaded for the first time on electrospinning as well as self-synthesized AgSD on PAN nanofibers by solution immersion method and then compared the results of both. Results Occurrence of chemical reaction among the functional groups of AgSD and PAN were analyzed using FTIR, for both types of specimen. Morphological and surface properties of prepared nanofiber mats were characterized by scanning electron microscope, and it resulted in uniform nanofibers without bead formation. Diameter of nanofibers was slightly increased with addition of AgSD by in situ and immersion methods respectively. Nanoparticles distribution was analyzed by transmission electron microscopy. Thermal properties were analyzed by thermo-gravimetric analyzer and it was observed that AgSD decreased thermal stability of PAN which is better from biomedical perspective. X-ray diffraction declared crystalline structure of nanofiber mats. Presence of Ag and S contents in nanofiber mats was analyzed by X-ray photo spectroscopy. Antibacterial properties of nanofiber mats were investigated by disc diffusion method was carried out. E. coli and Bacillus bacteria strain were used as gram-negative and gram-positive respectively. Zone inhibition of the bacteria was used as a tool to determine effectiveness of AgSD released from PAN nanofiber mats. The antibacterial properties of PAN nanofibers impregnated with AgSD were determined with both types of bacteria strains to compare with control one. Conclusion On the basis of characterization results it is concluded that PAN/AgSD (immersion) nanofiber mats have better structural and antibacterial properties than that of PAN/AgSD (in situ) nanofiber mats. So, from our point of view, self-synthesized AgSD is recommended for further production of nanofiber mats for antibacterial applications.
Rett syndrome: analysis of MECP2 and clinical characterization of 31 patients.

UNLABELLED Only recently have mutations in MECP2 been found to be a cause of Rett Syndrome (RTT), a neuro-developmental disorder characterized by mental retardation, loss of expressive speech, deceleration of head growth and loss of acquired skills that almost exclusively affects females. We analysed the MECP2 gene in 31 patients diagnosed with RTT. Sequencing of the coding region and the splice sites revealed mutations in 24 females (77.40%). However, no abnormalities were detected in any of the parents that were available for investigation. Eleven mutations have not been described previously. Confirming two earlier studies, we found that most mutations are truncating and only a few of them are missense mutations. Several females carrying the same mutation display different phenotypes indicating that factors other than the type or position of mutations influence the severity of RTT. Four females with RTT variants were included in the study. Three of these presented with preserved speech while the fourth patient with congenital RTT lacked the initial period of normal development. Detection of mutations in these cases reveals that they are indeed variants of RTT. They represent the mild and the severe extremes of RTT. CONCLUSIONS mutations in MECP2 seem to be the main cause for RTT and can be expected to be found in approximately 77% of patients that fulfil the criteria for RTT. Therefore analysis of MECP2 should be performed if RTT is suspected. Three mutation hotspots (T158M, R168X and R255X) were confirmed and a further one (R270X) newly identified. We recommend screening for these mutations before analysing the coding region.
Topical Cyclosporine A in the Treatment of Dry Eye: A Systematic Review and Meta-analysis

Purpose: Cyclosporine A (CsA) is considered a potentially effective treatment for dry eye syndrome (DES), which is now one of the most common ocular problems whose exact mechanism is unknown. Because randomized controlled trials (RCTs) reported to date have shown varying results in the efficacy and safety of CsA in different types of DES, we conducted a systematic review and meta-analysis of RCTs on CsA versus placebo in treating DES to evaluate the treatment efficacy and safety of CsA. Methods: We searched for RCTs published after 1990, in MEDLINE, EMBASE, the Cochrane library, and ClinicalTrials.gov. The RCTs that were included compared topical CsA and placebo for DES treatment by evaluating scores of ocular surface disease index, tear break-up time, or Schirmer test. Cochrane risk of bias tool was used for assessing the risk of bias. Results: We included 12 RCTs involving 3034 eyes of 1660 participants. We observed statistically significant improvements on scores of break-up time (standardized mean difference [SMD], 0.80; 95% confidence interval [CI], 0.13–1.46; I2 = 95%) and scores of Schirmer test with anesthesia (SMD, 0.78; 95% CI, 0.09–1.46; I2 = 97%) after treatment with topical CsA. Scores of ocular surface disease index (SMD, 0.77; 95% CI, −1.05 to 2.58; I2 = 98%) and scores of Schirmer test without anesthesia (SMD, 0.08; 95% CI, −0.11 to 0.27; I2 = 0%) were not improved. Adverse events (odds ratio [OR], 1.61; 95% CI, 1.28–2.02; I2 = 21%) were observed. Conclusions: Topical CsA could be an effective treatment for DES, especially for DES associated with conjunctival injury. Further RCTs with larger sample sizes for different clinical types of DES are warranted to determine the efficacy and limitation for different clinical types of DES.
A cis-acting element in the major immediate-early (IE) promoter of human cytomegalovirus is required for negative regulation by IE2

The major immediate-early promoter (MIEP) of human cytomegalovirus (CMV) contains a number of different enhancer elements in both repetitive and nonrepetitive sequences that influence the level of downstream transcription. This report describes a cis-acting element in the MIEP that responds to negative regulation by the IE2 gene product. Deletion analysis demonstrated that the cis-acting repressor element is located between the TATA box and the transcription initiation site from -13 to -1. The DNA sequence of the repressor element is 5'-CGTTTAGTGAACC-3'. The sequence is found in both the human and simian CMV MIEPs but not the murine CMV MIEP or in several other enhancer-containing promoters. The repressor element was isolated in a DNA fragment from -13 to +3 and was found to be functional in either orientation. It could be transferred to a heterologous enhancer-containing promoter and was functional when placed between the TATA box and the transcription initiation site. The element did not function when placed downstream of the transcription initiation site. Therefore, the cis-acting repressor element is position dependent. The role of the repressor element and the IE2 gene product in human CMV productive or latent infection is discussed.
Identiﬁcation and characterization of photomedins: novel olfactomedin-domain-containing proteins with chondroitin sulphate-E-binding activity

We screened more than 60000 RIKEN mouse cDNAs for novel ECM (extracellular matrix) proteins by extensive computational screening followed by recombinant expression and immunohistochemical characterization. We identiﬁed two novel olfactomedin-family proteins characterized by the presence of tandem CXCXCX 9 C motifs in the N-terminal region, a coiled-coil domain and an olfactomedin domain in the C-terminal region. These proteins, named photomedin-1 and photomedin-2, were secreted as di-sulphide-bonded dimers (photomedin-1) or oligomers/multimers (photomedin-2) with O-linked carbohydrate chains, although photomedin-1 was proteolytically processed in the middle of the molecule after secretion. In the retina, photomedin-1 was selectively expressed in the outer segment of photoreceptor cells and photomedin-2 was expressed in all retinal neurons. Among a panel of ECM components, including glycosaminoglycans, photomedins preferentially bound to chondroitin sulphate-E and heparin. These results, together, indicate that photomedins are novelolfactomedin-domain-containingextracellularproteinscap-ableofbindingtoproteoglycanscontainingtheseglycosamino-glycanchains.
Maximum likelihood estimation for the bombing model

Perhaps the best known example of a random set is the Boolean model. It is the union of `grains'' such as discs, squares or triangles which are placed at the points of a Poisson point process. The Poisson points are called the `germs''. We are interested in estimating the intensity, say lambda, of the Poisson process from a sample of a Boolean model of discs (the bombing model). A natural estimate is the number of germs in the observation region divided by the area of that region. Unfortunately, we do not observe the presence of a given germ when its associated disc is completely covered by other discs. On the other hand, we observe the exact location of a germ when we observe any part of its associated disc''s boundary. We demonstrate how to apply Coupling From The Past to sample from the conditional distribution, given the data, of the unobserved germs. Such samples allow us to approximate the maximum likelihood estimator of the intensity. We discuss and compare two methods to do so. The first method is based on a Monte Carlo approximation of the likelihood function. The second is a stochastic version of the EM algorithm.
Pengembangan Durian Batu Busuak, Kelurahan Lambung Bukit, Kota Padang

ABSTRAK: Kampung Batu Busuk Kelurahan Lambung Bukit Kecamatan Pauh merupakan salah satu sentra produksi buah durian di Sumatera Barat.Walaupun nama durian Batu Busuk sudah terkenal dan banyak dicari oleh pencinta durian pada saat musim durian, namun belum ada upaya untuk mengangkat durian Batu Busuk untuk bisa dikenal lebih luas. Langkah awal untuk mengangkat nama durian Batu Busuk adalah membenahi identitas varietas durian Batu Busuk, karena sampai sekarang karakteristik dari durian Batu Busuk yang sesungguhnya tidak jelas.Tanaman yang sudah dikarakterisasi juga perlu diperbanyak agar kedepan, buah yang dihasilkan oleh kelurahan Batu Busuk adalah buah dengan karakter unggul tertentu. Masyarakat atau petani yang menanam durian juga perlu memiliki keahlian memperbanyak durian unggulnya. Penerapan ipteks yang dilakukan pada kegiatan pengabdian pada masyarakat ini menggunakan beberapa metode antara lain penyuluhan, demonstrasi aplikasi dan demplot pembibitan durian. Hasil kegiatan menunjukkan bahwa kegiatan penyuluhan yang dilakukan berhasil meningkatkan pengetahuan masyarakat Batu Busuk mengenai arti penting pendaftaran varietas durian. Kegiatan demplot pembibitan durian dan demonstrasi teknik sambung meningkatkan pengetahuan dan keterampilan masyarakat mengenai propagasi durian. Kata kunci: Durian ungggul, Pendaftaran varietas, Teknologi tepat guna, Teknik sambung Development of Durian Batu Busuak, Lambung Bukit Village, Padang CityABSTRACT: Batu Busuk area, Lambung Bukit Village, Pauh Subdistrict, is one area of the centers of durian fruit production in West Sumatra. Although the Batu Busuk durian is already well-known and is sought after by durian lovers during the durian season, there is no attempt to lift the Batu Busuk durian to be known more widely. The first step to lifting the Batu Busuk durian is to fix the varieties identity of the Batu Busuk durian because until now the characteristics of the real Batu Busuk durian are not clear. Plants that have been characterized also need to be propagated so that in the future, the fruit produced by the Batu Busuk village is a fruit with certain superior characters. The community or farmers who plant durian also need to have the expertise to increase their superior durian. The application of science and technology conducted in community service activities uses several methods including counseling, demonstrations of applicationand demonstration plots of durian nurseries. The results of the activity showed the extension activities conducted succeeded in increasing the knowledge of the Batu Busuk community regarding the importance of registering durian varieties. The activities of the durian nursery demonstration plot and demonstration of connection techniques can increase the knowledge and skills of the community regarding the propagation of durian.Keywords: Superior durian, Varieties registration, Appropriate technology, Connection technique
Resilience of Core-Periphery Networks in the Case of Rich-Club

Core-periphery networks are structures that present a set of central and densely connected nodes, namely the core, and a set of non-central and sparsely connected nodes, namely the periphery. The rich-club refers to a set in which the highest degree nodes show a high density of connections. Thus, a network that displays a rich-club can be interpreted as a core-periphery network in which the core is made up by a number of hubs. In this paper, we test the resilience of networks showing a progressively denser rich-club and we observe how this structure is able to affect the network measures in terms of both cohesion and efficiency in information flow. Additionally, we consider the case in which, instead of making the core denser, we add links to the periphery. These two procedures of core and periphery thickening delineate a decision process in the placement of new links and allow us to conduct a scenario analysis that can be helpful in the comprehension and supervision of complex networks under the resilience perspective. The advantages of the two procedures, as well as their implications, are discussed in relation to both network effciency and node heterogeneity.
Digital forensic system profiling using context analysis

Conventional digital forensic investigations search digital devices for specific events or specific artefacts that indicate a crime has occurred. This does fulfil the investigative need to identify a crime, but it does not attribute the user of that digital device when the crime occurred. If a crime occurs frequently, such as accessing unlawful pornography, or is an isolated event but is co-located in time with other frequently occurring events, such as the one-off sending of a harassing message, then there may be investigative value in processing the history of the device to determine if there are patterns of repetitive behaviour present at the times of interest. This research project investigates the habitual use of a digital device by analysing the Internet history that can be recovered from the physical digital device, or from logs that are retained as the device is connected to a firewall or service provider. The presumption in this project is that there is zero-knowledge of the content of the web history, page content or even an accurate classification of the nature of the sites that are visited. We propose in this research that the patterns of usage themselves are a significant indicator of who the user is, or the type of usage that is being performed. We define context analysis as the investigation not of what is contained within the artefacts, but rather the investigation of the meta-data relating to that artefact and any other similar artefacts within a proximity, be it temporal, spatial or potentially spatio-temporal. Specifically, we show in this thesis that given suitable feature selection the context analysis we define is effective at identifying patterns of habitual behaviour, as evaluated in the case of Internet history artefacts. We present as our major contributions: the methods of analysing periods of Internet history in contextual groups of sessions; the novel approaches to feature selection for the Internet history sessions; and the display of the results on a network graph such that techniques such as community detection can be used to automatically cluster the Internet history.
A user-tunable approach to marketplace search

The notion of relevance is key to the performance of search engines as they interpret the user queries and respond with matching results. Online search engines have used other features beyond pure IR features to return relevant matching documents. However, over-emphasis on relevance could lead to redundancy in search results. In document search, diversity is simply the variety of documents that span the result set. In an online marketplace the diversity in the result set is represented by items for sale by different sellers at different prices with different sales options. For such a marketplace, in order to minimize query abandonment and the risk of dissatisfaction to the average user, several factors like diversity, trust and value need to be taken into account. Previous work in this field [4] has shown an impossibility result that there exists no such function that can optimize for all these factors. Since these factors and the measures associated with the factors could be subjective we take an approach of giving the control back to the user. In this paper we describe an interface which enables users to have more control over the optimization function used to present the results. We demonstrate this for search on eBay - one of the largest online marketplaces with a vibrant user community and dynamic inventory. We use an algorithm based on bounded greedy selection [5] to construct the result set based on parameters specified by the user.
Frequency domain connectivity identification: An application of partial directed coherence in fMRI

Functional magnetic resonance imaging (fMRI) has become an important tool in Neuroscience due to its noninvasive and high spatial resolution properties compared to other methods like PET or EEG. Characterization of the neural connectivity has been the aim of several cognitive researches, as the interactions among cortical areas lie at the heart of many brain dysfunctions and mental disorders. Several methods like correlation analysis, structural equation modeling, and dynamic causal models have been proposed to quantify connectivity strength. An important concept related to connectivity modeling is Granger causality, which is one of the most popular definitions for the measure of directional dependence between time series. In this article, we propose the application of the partial directed coherence (PDC) for the connectivity analysis of multisubject fMRI data using multivariate bootstrap. PDC is a frequency domain counterpart of Granger causality and has become a very prominent tool in EEG studies. The achieved frequency decomposition of connectivity is useful in separating interactions from neural modules from those originating in scanner noise, breath, and heart beating. Real fMRI dataset of six subjects executing a language processing protocol was used for the analysis of connectivity. Hum Brain Mapp, 2009. © 2007 Wiley‐Liss, Inc.
Homeostatic mechanisms may shape the type and duration of oscillatory modulation

Neural oscillations are observed ubiquitously in the mammalian brain, but their stability is known to be rather variable. Some oscillations are tonic and last for seconds or even minutes. Other oscillations appear as unstable bursts. Likewise, some oscillations rely on excitatory AMPAergic synapses, but others are GABAergic and inhibitory. Why this diversity exists is not clear. We hypothesized Ca 2+ -dependent homeostasis could be important in finding an explanation. We tested this hypothesis in a highly simplified model of hippocampal neurons. In this model homeostasis profoundly alters the modulatory effect of neural oscillations. Under homeostasis, tonic AMPAergic oscillations actually decrease excitability and desynchronize firing. Tonic oscillations that are synaptically GABAergic–like those in real hippocampus–don’t provoke a homeostatic response, however. If our simple model is correct, homeostasis can explain why the theta rhythm in the hippocampus is synaptically inhibitory: GABA has little to no intrinsic homeostatic response, and so can preserve the pyramidal cell’s natural dynamic range. Based on these results we can also speculate that homeostasis may explain why AMPAergic oscillations in cortex, and hippocampus, often appear as bursts. Bursts do not interact with the slow homeostatic time constant, and so retain their normal excitatory effect. New and Noteworthy The intricate interplay of neuromodulators, like acetylcholine, with homeostasis is well known. The interplay between oscillatory modulation and homeostasis is not. We studied oscillatory modulation and homeostasis for the first time using a simplified model of hippocampus. We report a paradoxical result: Ca-mediated homeostasis causes AMPAergic oscillations to become effectively inhibitory. This result, along with other new observations, means homeostasis might be just as complex and important for oscillations as it is for other neuromodulators.
Prediction-based Dynamic Energy Management in Wireless Sensor Networks

Energy consumption is a critical constraint in wireless sensor networks. Focusing on the energy efficiency problem of wireless sensor networks, this paper proposes a method of prediction-based dynamic energy management. A particle filter was introduced to predict a target state, which was adopted to awaken wireless sensor nodes so that their sleep time was prolonged. With the distributed computing capability of nodes, an optimization approach of distributed genetic algorithm and simulated annealing was proposed to minimize the energy consumption of measurement. Considering the application of target tracking, we implemented target position prediction, node sleep scheduling and optimal sensing node selection. Moreover, a routing scheme of forwarding nodes was presented to achieve extra energy conservation. Experimental results of target tracking verified that energy-efficiency is enhanced by prediction-based dynamic energy management.