Miracle-dz/UniFAR-FTUs huggingface dataset:
MetaPath Online: a web server implementation of the network expansion algorithm

We designed a web server for the analysis of biosynthetic capacities of metabolic networks. The implementation is based on the network expansion algorithm and the concept of scopes. For a given network and predefined external resources, called the seed metabolites, the scope is defined as the set of products which the network is in principle able to produce. Through the web interface the user can select a variety of metabolic networks or provide his or her own list of reactions. The information on the organism-specific networks has been extracted from the KEGG database. By choosing an arbitrary set of seed compounds, the user can obtain the corresponding scopes. With our web server application we provide an easy to use interface to perform a variety of structural and functional network analyses. Problems that can be addressed using the web server include the calculation of synthesizing capacities, the visualization of synthesis pathways, functional analysis of mutant networks or comparative analysis of related species. The web server is accessible through http://scopes.biologie. hu-berlin.de.
Spectral Projected Gradient Descent for Efficient and Large Scale Generalized Multiple Kernel Learni

We address the problem of learning the kernel in a Support Vector Machine framework from training data. Learning diverse types of kernels has proved effective in different application areas. For instance, learning the kernel to be a sparse linear combination of given base kernels has proved useful in computer vision while more general kernel parameterizations, such as non-linear kernel combinations, have proved to be useful for feature selection. Similarly, various types of regularizers, such as those with varying levels of sparsity, have proved effective in different scenarios. However, each formulation typically necessitates the development of a specialized optimization algorithm. The lack of a general purpose optimizer capable of handling a wide range of formulations presents a significant challenge to those exploring new kernel parameterizations or regularizers. This problem was alleviated by the development of the Generalized Multiple Kernel Learning (GMKL) formulation which admits fairly general kernel parameterizations and regularizers subject to mild constraints. However, the projected gradient descent GMKL optimizer is inefficient as the computation of the step size and a reasonably accurate gradient direction are both expensive. We overcome these limitations by developing a Spectral Projected Gradient (SPG) descent optimizer which: a) takes into account second order information in selecting step sizes; b) employs a nonmonotone step size selection criterion requiring fewer function evaluations; c) is robust to gradient noise, and d) can take quick steps when far away from the optimum. We show that our proposed SPG-GMKL optimizer can be an order of magnitude faster than the state-of-the-art projected gradient descent implementations on even small and medium sized datasets. In some cases, SPG-GMKL can even outperform specialized optimization algorithms developed for a single MKL formulation. Furthermore, we demonstrate that SPG-GMKL can scale well beyond gradient descent to large problems involving a million kernels (on Sonar) or half a million data points (on Covertype which is a challenging Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Copyright 20XX ACM X-XXXXX-XX-X/XX/XX .$10.00. data set for even single kernel SVMs). We plan to make our code and implementation available publically.
Effect of Ocean Acidification on Iron Availability to Marine Phytoplankton

Ironed Out In large regions of the ocean, low levels of the essential nutrient, iron, limits primary productivity. Iron's chemistry and bioavailability are highly dependent on pH. Rising concentrations of atmospheric CO2 is leading to the acidification of the ocean. Shi et al. (p. 676, published online 14 January; see the Perspective by Sunda) show that the bioavailable fraction of iron dissolved in the ocean may decline as a result of the decrease in ocean pH, which affects the rate of iron uptake by diatoms and coccolithophores. Unless iron input to the oceans increases, these changes may lead to an increase in the iron stress of phytoplankton. Ocean acidification caused by anthropogenic carbon dioxide is changing the chemistry and bioavailability of iron in seawater. The acidification caused by the dissolution of anthropogenic carbon dioxide (CO2) in the ocean changes the chemistry and hence the bioavailability of iron (Fe), a limiting nutrient in large oceanic regions. Here, we show that the bioavailability of dissolved Fe may decline because of ocean acidification. Acidification of media containing various Fe compounds decreases the Fe uptake rate of diatoms and coccolithophores to an extent predicted by the changes in Fe chemistry. A slower Fe uptake by a model diatom with decreasing pH is also seen in experiments with Atlantic surface water. The Fe requirement of model phytoplankton remains unchanged with increasing CO2. The ongoing acidification of seawater is likely to increase the Fe stress of phytoplankton populations in some areas of the ocean.
Mortality Risk N Children with Epilepsy: The Dutch Study of Epilepsy in Childhood

PURPOSE: We describe first unprovoked seizures and newly diagnosed epilepsies at initial presentation, with a special emphasis on epilepsy syndromes, in a large cohort recruited in the mid-1990s in France. METHODS: The French Foundation for Research on Epilepsy set up a network to conduct a prospective study of patients with newly diagnosed unprovoked seizures. Information was provided by 243 child or adult neurologists. Four neurologists classified each case according to the International League Against Epilepsy (ILAE) criteria. First-seizure patients and patients with previously undiagnosed seizures were compared. RESULTS: Between May 1, 1995, and June 30, 1996, 1,942 patients aged from 1 month to 95 years were identified: 926 (47.7%) with a single seizure and 1,016 (52.3%) with newly diagnosed epilepsy. All but 17 patients had EEGs. In the first-seizure and newly-diagnosed-epilepsy groups, neuroimaging studies were performed in 78.2 and 68.3% of patients, and medication prescribed in 54.1 and 89.6%, respectively. There were significant differences between the two groups with respect to age at onset and diagnosis, sex, etiology, several specific syndromes, as well as the type and presentation of initial seizure. In patients for whom the first seizure was convulsive, only sex, multiple seizures in a day or status epilepticus, and cryptogenic localizationrelated syndrome differed between the two groups. CONCLUSIONS: Approximately half of patients who first came to attention for an unprovoked seizure already met epidemiologic criteria for epilepsy. There were significant differences between the types of patients with a first seizure and those with newly diagnosed epilepsy. One or several seizures at diagnosis did not influence the diagnostic assessment of the patients but had a strong influence on the initiation of treatment.
Crystal structure of gingipain R: an Arg‐specific bacterial cysteine proteinase with a caspase‐like fold

Gingipains are cysteine proteinases acting as key virulence factors of the bacterium Porphyromonas gingivalis, the major pathogen in periodontal disease. The 1.5 and 2.0 Å crystal structures of free and D‐Phe‐Phe‐Arg‐chloromethylketone‐inhibited gingipain R reveal a 435‐residue, single‐polypeptide chain organized into a catalytic and an immunoglobulin‐like domain. The catalytic domain is subdivided into two subdomains comprising four‐ and six‐stranded β‐sheets sandwiched by α‐helices. Each subdomain bears topological similarities to the p20‐p10 heterodimer of caspase‐1. The second subdomain harbours the Cys‐His catalytic diad and a nearby Glu arranged around the S1 specificity pocket, which carries an Asp residue to enforce preference for Arg‐P1 residues. This gingipain R structure is an excellent template for the rational design of drugs with a potential to cure and prevent periodontitis. Here we show the binding mode of an arginine‐containing inhibitor in the active‐site, thus identifying major interaction sites defining a suitable pharmacophor.
Individuality of numerals

The analysis of handwritten documents from the view-pointof determining their writership has great bearing onthe criminal justice system. In many cases, only a limitedamount of handwriting is available and sometimes it consistsof only numerals. Using a large number of handwrittennumeral images extracted from about 3000 samples writtenby 1000 writers, a study of the individuality of numerals foridentification/verification purposes was conducted. The individualityof numerals was studied using cluster analysis.Numerals discriminability was measured for writer verification.The study shows that some numerals present a higherdiscriminatory power and that their performances for theverification/identification tasks are very different.
A Low-Cost UWB-RFID System Utilizing Compact Circularly Polarized Chipless Tags

In this letter, circularly polarized (CP) chipless tags for a ultrawideband radio-frequency identification (UWB-RFID) system are demonstrated for the first time. Different from conventional linearly polarized tags, CP tags not only help to significantly reduce the mutual coupling between the transmitting and receiving antennas in a UWB-RFID reader, but also greatly lessen the signal ratio between structural and antenna modes to improve system performance. In addition, short delay line is adopted to make the chipless CP tag with compact size. Nevertheless, a short delay line usually results in the structural and antenna modes being overlapped. To separate these signals, a time-domain processing scheme is then proposed and validated. Measured results and system demonstration show that the compact chipless CP tag is a very promising candidate for low-cost UWB-RFID applications.
From the Editor's Desk

During my first full year as editor-in-chief of ACM Transations on Computing Education (TOCE), the editorial board and I took the following four steps to improve the journal's ability to serve the growing community of computing education researchers: (1) We streamlined the peer review process, (2) we established a new partnership with the ACM Special Interest Group on Computer Science Education Conference, (c) we transitioned to a double-blind review process, and (4) we recruited guest editors for two new special issues that address timely research topics. In this editorial, I present key statistics on TOCE's review process and submissions during the 2016 calendar year, discuss and reflect on the positive steps we took to improve the journal during 2016, and describe steps we will consider in the coming year in order to ensure that ACM TOCE continues on its positive trajectory. These include forging additional partnerships with professional conferences, altering the review criteria to make the journal more welcoming to a broader range of research, especially within the K-12 space, and developing a set of evidence standards for research published in the journal.
Enhanced Progression of Early Carotid Atherosclerosis Is Related to Chlamydia pneumoniae (Taiwan Acute Respiratory) Seropositivity

Background —Chlamydia pneumoniae (Cp) infection has been associated with atherosclerosis and has been proposed as a possible additional cardiovascular risk factor. However, the relationship between Cp seropositivity and the progression of early carotid atherosclerosis is not unequivocally clarified. Methods and Results —We evaluated the association between serological detection of Cp IgG and/or IgA antibodies and the progression of the intima-media thickness (IMT) of the common carotid artery using duplex ultrasonography in a prospective study with a follow-up of 3 years in 272 consecutive patients with cerebrovascular disease. Cp-seropositive patients showed a significantly enhanced progression of the IMT even after adjustment for other cardiovascular risk factors (0.12 mm/y [95% CI 0.11 to 0.14] versus 0.07 mm/y [0.05 to 0.09];P <0.005). Patients with increased C-reactive protein (≥0.5 mg/dL) and Cp seropositivity showed the most pronounced IMT progression. Multivariate regression analysis revealed Cp seropositivity to be an independent risk factor for progression of early carotid atherosclerosis. Cox proportional-hazard regression analysis demonstrated a significantly increased rate of cerebrovascular and cardiovascular events in patients with Cp seropositivity, particularly in patients with increased C-reactive protein levels. Conclusions —Our data support the importance of chronic inflammation and infection for the early stages of atherosclerotic development.
Reconstitution of ‘floral quartets’ in vitro involving class B and class E floral homeotic proteins

Homeotic MADS box genes encoding transcription factors specify the identity of floral organs by interacting in a combinatorial way. The ‘floral quartet model’, published several years ago, pulled together several lines of evidence suggesting that floral homeotic proteins bind as tetramers to two separated DNA sequence elements termed ‘CArG boxes’ by looping the intervening DNA. However, experimental support for ‘floral quartet’ formation remains scarce. Recently, we have shown that the class E floral homeotic protein SEPALLATA3 (SEP3) is sufficient to loop DNA in floral-quartet-like complexes in vitro. Here, we demonstrate that the class B floral homeotic proteins APETALA3 (AP3) and PISTILLATA (PI) do only weakly, at best, form floral-quartet-like structures on their own. However, they can be incorporated into such complexes together with SEP3. The subdomain K3 of SEP3 is of critical importance for the DNA-bound heterotetramers to be formed and is capable to mediate floral quartet formation even in the sequence context of AP3 and PI. Evidence is presented suggesting that complexes composed of SEP3, AP3 and PI form preferentially over other possible complexes. Based on these findings we propose a mechanism of how target gene specificity might be achieved at the level of floral quartet stability.
Light-at-night, circadian disruption and breast cancer: assessment of existing evidence.

BACKGROUND Breast cancer incidence is increasing globally for largely unknown reasons. The possibility that a portion of the breast cancer burden might be explained by the introduction and increasing use of electricity to light the night was suggested >20 years ago. METHODS The theory is based on nocturnal light-induced disruption of circadian rhythms, notably reduction of melatonin synthesis. It has formed the basis for a series of predictions including that non-day shift work would increase risk, blind women would be at lower risk, long sleep duration would lower risk and community nighttime light level would co-distribute with breast cancer incidence on the population level. RESULTS Accumulation of epidemiological evidence has accelerated in recent years, reflected in an International Agency for Research on Cancer (IARC) classification of shift work as a probable human carcinogen (2A). There is also a strong rodent model in support of the light-at-night (LAN) idea. CONCLUSION If a consensus eventually emerges that LAN does increase risk, then the mechanisms for the effect are important to elucidate for intervention and mitigation. The basic understanding of phototransduction for the circadian system, and of the molecular genetics of circadian rhythm generation are both advancing rapidly, and will provide for the development of lighting technologies at home and at work that minimize circadian disruption, while maintaining visual efficiency and aesthetics. In the interim, there are strategies now available to reduce the potential for circadian disruption, which include extending the daily dark period, appreciate nocturnal awakening in the dark, using dim red light for nighttime necessities, and unless recommended by a physician, not taking melatonin tablets.
A novel resource allocation scheme based on multi-satellite terminals in MF-TDMA satellite systems

The future satellite communication systems should be able to accommodate the integrated services with a variety of applications and fulfill Quality of Service requirements. Regarding to the limited and costly resources, a novel resource allocation in a multi-frequency time-division multiple access (MF-TDMA) is proposed. In order to optimize packing performance, the users with more time slots are packed first. The algorithm's performance of delay and channel utilization can be validated through the simulation for different types of traffic. We further compare the performances of classical schemes. The theoretical analysis and simulation results show that that new algorithm can efficiently improve channel utilization in satellite resource allocation, especially when the number of satellite terminals is large. The algorithm is simple and easy to implement in satellite communication system.
Using neuro-fuzzy techniques based on a two-stage mapping model for concept-based image database indexing

We present a two-stage mapping model (TSMM), which is intended to minimise the semantic gap for content-based image retrieval (CBIR) by reducing recognition errors during the image indexing stage. This model is composed of a feature extraction module based on our image segmentation and feature extraction algorithm, a colour and texture classification modules based on support vector machines (SVMs), and an inference module based on fuzzy logic to make final decisions as high level concepts from the colour and texture concepts. The experimental results show that the proposed method outperforms general approaches by using one single SVM classifier as direct mapping between the combined colour and texture feature vectors and high level concepts directly.
The physical user interface profile (PUIP): modelling mobile interactions with the real world

So far the field of model based user interface development has focused mostly on the usage of one device, such as a Personal Computer, by one person. New interaction techniques emerge in which the user interacts with the surrounding world while using the mobile phone as a mediator for physical interactions and as communication tool to interact with services and other users. Here several devices or physical elements are used for input and output, and more than one user might be involved. These new settings require description models to support the analysis, design and implementation of systems that take such interaction techniques into account. We present the new UML 2.0 Physical User Interface Profile (PUIP) that is based on the UML 2.0 Profile for Context-Sensitive User Interface (CUP, [24]) to support the modelling of this kind of interactions. We show the feasibility of our approach through the modelling of an existing physical mobile interaction and discuss its suitability.
Irreversible effects of neonatal exposure to p-tert-octylphenol on the reproductive tract in female rats.

It has been known for many years that administration of androgens or estrogens at critical periods of development in mammals causes severe long-term effects on the endocrine/genital systems. The environmental pollutant p-tert-octylphenol (OP) possesses a weak but clear estrogen agonist activity in in vitro and in vivo studies. In the present study, effects of neonatal exposure to OP on the reproductive tract of female rats were investigated. Newborn female pups were injected with 100 mg/kg OP subcutaneously within 24 h after birth. Administration was repeated every other day until postnatal day 15 (total of eight doses). Before weaning, serum follicle-stimulating hormone (FSH) and luteinizing hormone (LH) remained at low levels during OP exposure, although the serum FSH peak and the high LH level were obvious in the controls. Histologically, inhibition of uterine gland genesis was apparent. The day of vaginal opening was about 4 days earlier in OP-treated animals than in controls. Persistent estrus was consistently observed in OP-treated animals. Atrophic and polycystic ovaries without corpora lutea showed anovulation. In the endometrium, cell-proliferative activity and cell-death were increased and decreased, respectively, and expression of estrogen receptor alpha mRNA was apparent by in situ hybridization. Unexpectedly, endometrial hyperplasias appeared at 8 weeks of age. After ovariectomy, vaginal smears immediately became of castration type and the uterus was atrophied. These results suggested that neonatal exposure to a high dose of OP alters developmental hormonal secretion presumably due to a hypothalamo-pituitary-ovarian disorder, with accelerated vaginal opening, subsequent persistent estrus, and uterine endometrial hyperplasia. The changes in the uterus and vagina are ovary-dependent.
Wideband injection-locked divide-by-3 frequency divider design with regenerative second-harmonic feedback technique

This paper presents an integration of wideband injection-locked divide-by-3 frequency divider with regenerative second-harmonic feedback technique. By using the proposed feedback technique, a divider with a wide input locking range over 10% can be achieved at Ka-band, which performs near the device maximum oscillation frequency (fMAX) in a CMOS 0.18- μm process. The divider can operate from 33.9 GHz to 37.7 GHz with an input injection power of 0 dBm. The measured input locking range is 3.8 GHz (10.6%). The chip area of the divider core is 0.22 mm2. The core power consumption is 11.9 mW at a supply voltage of 0.9 V. At an offset frequency of 200 KHz, the measured output phase noise under lock is -121 dBc/Hz as the input signal with phase noise of -111.5 dBc/Hz is applied. The difference of 9.5 dB in phase noise is close to the theoretical value predicted by the theorem of division-by-3.
Understanding and evaluating cooperative games

Cooperative design has been an integral part of many games. With the success of games like Left4Dead, many game designers and producers are currently exploring the addition of cooperative patterns within their games. Unfortunately, very little research investigated cooperative patterns or methods to evaluate them. In this paper, we present a set of cooperative patterns identified based on analysis of fourteen cooperative games. Additionally, we propose Cooperative Performance Metrics (CPM). To evaluate the use of these CPMs, we ran a study with a total of 60 participants, grouped in 2-3 participants per session. Participants were asked to play four cooperative games (Rock Band 2, Lego Star Wars, Kameo, and Little Big Planet). Videos of the play sessions were annotated using the CPMs, which were then mapped to cooperative patterns that caused them. Results, validated through inter-rater agreement, identify several effective cooperative patterns and lessons for future cooperative game designs.