Miracle-dz/UniFAR-FTUs huggingface dataset:
MRI brain segmentation using hidden Markov random fields with alpha-stable distributions

A MRI brain image segmentation method using a hidden Markov random fields with heavy-tailed alpha-stable distributions is presented. Each brain tissue is modelled using an alpha-stable distribution. Then, a HMRF is used to include spatial information in the classification model. The Gaussian distribution has been widely used for the modelization of the cerebrospinal fluid, white matter and gray matter. Nevertheless, the alpha-stable distribution has been recently proposed as a more accurate alternative for this task. The alpha-stable distribution is more impulsive and is also able to model the asymmetry and heavy-tails of the histogram of the brain tissues. We have tested the proposed methodology in 18 MR images from the Internet Brain Segmentation Repository. The proposed methodology outperforms the segmentation results obtained when a Gaussian model for the histogram of the brain tissues is considered. Furthermore, as the Normal distribution is a particulaar case of alpha-stable distribution. Therefore, the proposed approach is also a generalization of the hidden Markov random field segmentation method with Gaussian distributions.
Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes

Blood stream infections can be caused by several pathogens such as viruses, fungi and bacteria and can cause severe clinical complications including sepsis. Delivery of appropriate and quick treatment is mandatory. However, it requires a rapid identification of the invading pathogen. The current gold standard for pathogen identification relies on blood cultures and these methods require a long time to gain the needed diagnosis. The use of in situ experiments attempts to identify pathogen specific immune responses but these often lead to heterogeneous biomarkers due to the high variability in methods and materials used. Using gene expression profiles for machine learning is a developing approach to discriminate between types of infection, but also shows a high degree of inconsistency. To produce consistent gene signatures, capable of discriminating fungal from bacterial infection, we have employed Support Vector Machines (SVMs) based on Mixed Integer Linear Programming (MILP). Combining classifiers by joint optimization constraining them to the same set of discriminating features increased the consistency of our biomarker list independently of leukocyte-type or experimental setup. Our gene signature showed an enrichment of genes of the lysosome pathway which was not uncovered by the use of independent classifiers. Moreover, our results suggest that the lysosome genes are specifically induced in monocytes. Real time qPCR of the identified lysosome-related genes confirmed the distinct gene expression increase in monocytes during fungal infections. Concluding, our combined classifier approach presented increased consistency and was able to “unmask” signaling pathways of less-present immune cells in the used datasets.
Combining greyvalue invariants with local constraints for object recognition

This paper addresses the problem of recognizing objects in large image databases. The method is based on local characteristics which are invariant to similarity transformations in the image. These characteristics are computed at automatically detected keypoints using the greyvalue signal. The method therefore works on images such as paintings for which geometry based recognition fails. Due to the locality of the method, images can be recognized being given part of an image and in the presence of occlusions. Applying a voting algorithm and semi-local constraints makes the method robust to noise, scene clutter and small perspective deformations. Experiments show an efficient recognition for different types of images. The approach has been validated on an image database containing 1020 images, some of them being very similar by structure, texture or shape.
t-Plausibility: Generalizing Words to Desensitize Text

De-identified data has the potential to be shared widely to support decision making and research. While significant advances have been made in anonymization of structured data, anonymization of textual information is in it infancy. Document sanitization requires finding and removing personally identifiable information. While current tools are effective at removing specific types of information (names, addresses, dates), they fail on two counts. The first is that complete text redaction may not be necessary to prevent re-identification, since this can affect the readability and usability of the text. More serious is that identifying information, as well as sensitive information, can be quite subtle and still be present in the text even after the removal of obvious identifiers. Observe that a diagnosis ``tuberculosis'' is sensitive, but in some situations it can also be identifying. Replacing it with the less sensitive term ``infectious disease'' also reduces identifiability. That is, instead of simply removing sensitive terms, these terms can be hidden by more general but semantically related terms to protect sensitive and identifying information, without unnecessarily degrading the amount of information contained in the document. Based on this observation, the main contribution of this paper is to provide a novel information theoretic approach to text sanitization and develop efficient heuristics to sanitize text documents.
Inhibitors of photophosphorylation and photoreduction.

Thle processes of eniergy transformation in mitochonidria and in chloroplasts have much in common, even though the energy obtained in mitochondria is derived from the oxidation of organic substrates, whereas energy is obtained from light in chloroplasts. A filnal product of both these transformations is ATP. The formationi of ATP is achieved with the participation of cytochromes and probably quinonies in each systemi. The use of inllibitors has been helpful in the study of oxidlative phosphorylation. Although the effects of a number of inhibitors on photop)hosphory'lation lby chloroplasts anld clhromllatophores also halve been examiinied (3, 4. 5. 6.7. 9, 11), imianly antibiotic inhibitors used in interpretilig oxi(latixve phospliorylation al(l electroll transport in mitochonidria have not been teste(d onl phiotophosphorylation by cliloroplasts. Photophosphorylation in chloroplasts is iniereased wvhen certaini re(lox dyes are adde(d to the systeiii as cofactors. Pheniazilne imiethosulfate (PMS) S was shown by jagendclorf anid Avron (10) to support very v-igorotus photophosphorylation. Gromiiet-Elhaniaii alnd Avron (8) also have tised 2,6-dichlorophenol indop)henol4 as a cofactor. It is active at a very low conicentration, alnd it is convenient to measure the amount of dye photoreduced. Thus these 2 cofactors are suitable for study of the actionl of inhibitors oni photophosphorylation. The present investigationis conicerned with determiiining what informationi can be gained with inhibitors of photophosphorylationi as vell as by examination of the comparative biochemistry of oxidative phosphorylationi alld p)hotophosp)horylation.
Inter-Sentence Segmentation of YouTube Subtitles Using Long-Short Term Memory (LSTM)

Recently, with the development of Speech to Text, which converts voice to text, and machine translation, technologies for simultaneously translating the captions of video into other languages have been developed. Using this, YouTube, a video-sharing site, provides captions in many languages. Currently, the automatic caption system extracts voice data when uploading a video and provides a subtitle file converted into text. This method creates subtitles suitable for the running time. However, when extracting subtitles from video using Speech to Text, it is impossible to accurately translate the sentence because all sentences are generated without periods. Since the generated subtitles are separated by time units rather than sentence units, and are translated, it is very difficult to understand the translation result as a whole. In this paper, we propose a method to divide text into sentences and generate period marks to improve the accuracy of automatic translation of English subtitles. For this study, we use the 27,826 sentence subtitles provided by Stanford University’s courses as data. Since this lecture video provides complete sentence caption data, it can be used as training data by transforming the subtitles into general YouTube-like caption data. We build a model with the training data using the LSTM-RNN (Long-Short Term Memory – Recurrent Neural Networks) and predict the position of the period mark, resulting in prediction accuracy of 70.84%. Our research will provide people with more accurate translations of subtitles. In addition, we expect that language barriers in online education will be more easily broken by achieving more accurate translations of numerous video lectures in English.
Did Hard Work Ever Kill Anyone

In February 2004 the Australian Government released the discussion papers Australia? s Demographic Challenges and A More Flexible and Adaptable Retirement Income System, which invited public submissions on proposals to encourage longer working lives. In Australia? s Demographic Challenges the Federal Treasurer, Peter Costello, announced policy initiatives aimed at increasing workforce participation to ensure future economic growth. These measures included encouraging people to delay retirement. The paper claimed that `paid work gives us the opportunity to develop personally, live independently, and interact socially? (Department of the Treasury, 2004b:7). In the same month the Australian Bureau of Statistics? (ABS) 2004 Year Book was released and it showed that in the past 20 years the average hours worked by employees had increased by three hours per week. The National Occupational Health and Safety Commission reported that the number of stressrelated workers? compensation claims had `substantially increased? over the past few years (Macken and Priest, 2004). The Government is promoting later retirement but is it possible that longer working lives could be detrimental to our health? In order to test whether there is any link between retirement age and age at death we have undertaken a study using data from a pension scheme for retired government employees.
Technological Change, Computerization, and the Wage Structure

1 Overall wage inequality and educational wage differentials have expanded substantially in the United States over the past two decades. This widening of the wage structure has coincided with the rapid computerization of the work place. Thus, it is not surprising that many labor market analysts have tried to draw a causal connection between rising earnings inequality and increases in growth rate of the relative demand for more-skilled workers driven by technological and organizational changes associated with the computer revolution (e. inferences follow a venerable and fruitful tradition extending back to Paul Douglas (1926) and Jan Tinbergen (1975) of viewing the evolution of the wage structure (at least partially) as depending on a race between technological development and educational advance. This hypothesis implies that improvements in access to post-secondary schooling and appropriate skills training may be necessary to allow the productivity benefits of the new technologies associated with the digital economy to be more widely shared. Two key pieces of evidence are often cited as being strongly suggestive of an integral role for skill-biased technological change in the recent rise in U.S. wage inequality. 1 The first is that the relative employment of more-educated workers and non-production workers has increased rapidly within detailed industries and within establishments in the United States during the 1980s and 1990s, despite the sharp rise in the relative wages of these groups within-industry demand shifts favoring the more skilled. Similar patterns of within-industry increases in the proportion of " skilled " workers are apparent in most other advanced nations (Berman, Bound, 1 Skill-biased technological change refers to any introduction of a new technology, change in production methods, or change in the organization of work that increases the demand for more-skilled labor (e.g., college graduates) relative to less-skilled labor (e.g., non-college workers) at fixed relative wages. 2 and Machin 1998; Machin and Van Reenen 1998). Skill-biased technological change (broadly interpreted to be associated with both new production technologies and organizational innovations) is a natural possibility for such unexplained within-sector growth in the demand for skill. 2 The second more direct evidence from both econometric and case-study research is that the relative utilization of more-skilled workers is strongly positively correlated with capital intensity and Levy and Murnane 1996). These findings imply that physical capital and new technologies are relative complements with more-skilled workers. Such evidence is certainly consistent with the view that the spread of computer technologies …
Who ’ s Afraid of Lifetime Electronic Medical Records ?

While technology and legal advancements now enable health consumers to have their medical records transmitted electronically, either to the web or to a personal device (e.g., smart card), ultimately resulting in a lifetime health record, many obstacles remain in the way of that vision. So who’s afraid of electronic medical records (EMR)? Healthcare providers would prefer that EMRs remain under their control. Many providers even claim to be the owners of those records and only submit copies of the records in accordance with a patient’s bill of rights. Providers are also concerned by a potential increase in the number of lawsuits based on the data recorded in patient-held EMRs. In addition, providers have considerations regarding the process of creating unified EMRs. This process may be accompanied by strict guidelines, which would be detrimental to the more “artistic'” parts of their work. As for the consumers, each of us is considered a health consumer, but is it really so? Some people may be reluctant to get hold of their EMR because they prefer “not to know too much” or even to deny certain conditions, which could have been defined as medical conditions had they been examined. What appears to be so natural, that is, managing your medical records in a “medical account” much like you manage your checking account, isn’t really all that simple. This paper reviews different approaches and models for the availability of clinical information and envisions the establishment of independent entities that facilitate a new consumer-oriented model. This model focuses on the consumers’ interests (where privacy is maintained by eliminating the need for a universal patient identifier), and at the same time proves advantageous to providers by reducing their costs.
Control of glutamate homeostasis in Bacillus subtilis: a complex interplay between ammonium assimilation, glutamate biosynthesis and degradation

Glutamate, the major amino group donor in anabolism, is synthesized by the combined action of the glutamine synthetase (GS) and the glutamate synthase (GOGAT) in Bacillus subtilis. The glutamate dehydrogenase (GDH) exclusively degrades glutamate. GS and GDH are both trigger enzymes, active in nitrogen metabolism and in controlling gene expression. Feedback‐inhibited GS (FBI‐GS) controls DNA‐binding activities of two transcription factors, the repressor GlnR and TnrA, the global regulator of nitrogen metabolism. FBI‐GS binds to and activates GlnR. This protein complex inhibits GS formation and thus glutamine synthesis. Moreover, FBI‐GS inhibits DNA‐binding activity of TnrA. Glutamate biosynthesis, the reaction linking carbon with nitrogen metabolism, is controlled by GDH. Together with glutamate GDH inhibits GltC, the transcription factor that activates expression of the GOGAT genes. Thus, GS and GDH control glutamine and glutamate synthesis, respectively, depending on the nitrogen status of the cell. B. subtilis lacking a functional GDH show a severe growth defect. Interestingly, the growth defect is suppressed by the rapid activation of an inactive GDH. Thus, maintenance of glutamate homeostasis is crucial for cellular vitality. This review covers the recent work on the complex control of glutamine and glutamate metabolism in the Gram‐positive model organism B. subtilis.
Detection of Bot Infected PCs Using Destination-Based IP and Domain Whitelists During a Non-Operating Term

Spam e-mails and distributed denial of service (DDoS) attacks have now become critical issues to the Internet. These attacks are considered to be sent from bot infected PCs. As a bot communicates with a malicious controller over an encrypted channel and updates its code frequently, it becomes difficult to detect infected personal computers (PCs) using pattern-based intrusion detection systems (IDSs) and antivirus systems (AVs). As sending attack and control packets from the bot process are independent of the user operation, a behavior monitor is effective to detect an anomaly communication. In this paper, we propose a bot detection technique that checks outbound packets with destination-based whitelists. If any outbound packets during the non-operating term do not match the whitelists, the PC is considered to be infected by the bot. The whitelists are a set of a destination IP address and/or domain names (DNs) that are listed by monitoring outbound packets from an un-infected PC. Because the many IPs and DNs are grouped into a few sub-networks and superior DNs, it is easier to maintain the destination-based whitelists than the pattern-based IDS/AV. We implement the proposal system as a host-based detector and evaluate false negative (FN) and false positive (FP) frequencies for detection of bot activities.
Base-flipping mutations of uracil DNA glycosylase: substrate rescue using a pyrene nucleotide wedge.

We recently introduced a new substrate rescue tool for investigating enzymatic base flipping by uracil DNA glycosylase (UDG) in which a bulky pyrene nucleotide wedge (Y) was placed opposite a uracil in duplex DNA (i.e., a U/Y pair), thereby preorganizing the target base in an extrahelical conformation [Jiang, Y. L. , et al. (2001) J. Biol. Chem. 276, 42347-54]. The pyrene wedge completely rescued the large catalytic defects resulting from removal of the natural Leu191 wedge, presumably mimicking the pushing and plugging function of this group. Here we employ the pyrene rescue method in combination with transient kinetic approaches to assess the functional roles of six conserved enzymatic groups of UDG that have been implicated in the "pinch, push, plug, and pull" base-flipping mechanism (see the preceding paper in this issue). We find that a U/Y base pair increases the apparent second-order rate constant for damaged site recognition by L191G pushing mutation by 45-fold as compared to a U/A pair, thereby fully rescuing the kinetic effects of the mutation. Remarkably, the U/Y pair also allows L191G to proceed through the conformational docking step that is severely comprised with the normal U/A substrate, and allows the active site of UDG to clamp around the extrahelical base. Thus, pyrene also fulfills the plugging role of the Leu191 side chain. Preorganization of uracil in an extrahelical conformation by pyrene allows diffusion-controlled damage recognition by all of these base-flipping mutants, and allows the UDG conformational change to proceed as rapidly as the rate of uracil flipping with the natural U/A base pair. Thus, the pyrene wedge substrate allows UDG to recognize uracil by a lock-and-key mechanism, rather than the natural induced-fit mechanism. Unnatural pyrene base pairs may provide a general strategy to promote site-specific targeting of other enzymes that recognize extrahelical bases.
Compensating for the keeper current of CMOS domino logic using a well designed NMOS transistor

Domino CMOS logic finds a wide variety of applications due to their high speed and low device count. However, this type of logic has the drawback of low noise immunity especially when compared to complementary CMOS logic. This is due to the leakage current and charge sharing. So, a PMOS keeper must be used in order to compensate for this leakage. However, the use of a keeper in the conventional domino circuit degrades the speed of the circuit or results in an erroneous output due to the contention current. In this paper, a novel technique that acts to speed up the operation of domino logic and to improve its noise immunity using a weak keeper is proposed. In this technique, a well designed NMOS transistor will be connected to the dynamic node in order to draw the contention current during the evaluation phase. The term “well designed” will be illustrated through the paper. A modification to the proposed technique will also be presented in which the precharge device need not be increased in size. Simulation will be carried out for the 0.13 µm technology with VDD=1.2 V for the case of AND gate with two inputs. Simulation results show that the speed improves by a factor of approximately 33% and the noise margin increases from only 100 mV to 600 mV in case the dynamic node is to be at logic “0” for the same transistor aspect ratios at the cost of adding only one NMOS transistor and increasing the size of the precharge device, or instead connecting two serially connected NMOS transistors to the dynamic node and keeping the size of the precharge device the same.
Linguistic factors conditioning glottal constriction in Nicaraguan Spanish

This paper provides the first quantitative exploration of the linguistic factors conditioning glottal constriction in Nicaraguan Spanish, an allophone of word-final, intervocalic /s/, e.g. [ma. 'al.to] for mas alto ‘higher’. To date the variant has only been mentioned in passing in dialectal surveys (Quesada Pacheco 1996; Rosales Solis 2010) or described as a contact feature in other dialects of Spanish, i.e. Philipino (Lipski 2000), Yucatan (Lope Blanch 1987: 108-124), Argentinian/Paraguayan (Sanicky 1989; Thon 1989), and Puerto Rican Spanish (Valentin-Marquez 2006). However, the Spanish spoken in Managua is not in contact with any other languages, and I argue that glottal constriction in this dialect is a phonetically motivated, language-internal phenomenon. After a statistical analysis of 3,701 tokens from 36 Managuan participants, I conclude that glottal constriction serves to 1)strengthen prosodically strong positions due to its likelihood before word-initial, stressed vowels and 2) avoid postlexical hiatus, being more likely after longer words with high rates of /s/ deletion
Calorie restriction: Decelerating mTOR-driven aging from cells to organisms (including humans)

Although it has been known since 1917 that calorie restriction (CR) decelerates aging, the topic remains highly controversial. What might be the reason? Here I discuss that the anti-aging effect of CR rules out accumulation of DNA damage and failure of maintenance as a cause of aging. Instead, it suggests that aging is driven in part by the nutrient-sensing TOR (target of rapamycin) network. CR deactivates the TOR pathway, thus slowing aging and delaying diseases of aging. Humans are not an exception and CR must increase both maximal and healthy lifespan in humans to the same degree as it does in other mammals. Unlike mice, however, humans benefit from medical care, which prolongs lifespan despite accelerated aging in non-restricted individuals. Therefore in humans the effect of CR may be somewhat blunted. Still how much does CR extend human lifespan? And could this extension be surpassed by gerosuppressants such as rapamycin?