Miracle-dz/UniFAR-FTUs huggingface dataset:
A Gly-Zipper Motif Mediates Homodimerization of the Transmembrane Domain of the Mitochondrial Kinase ADCK3

Interactions between α-helices within the hydrophobic environment of lipid bilayers are integral to the folding and function of transmembrane proteins; however, the major forces that mediate these interactions remain debated, and our ability to predict these interactions is still largely untested. We recently demonstrated that the frequent transmembrane association motif GASright, the GxxxG-containing fold of the glycophorin A dimer, is optimal for the formation of extended networks of Cα–H hydrogen bonds, supporting the hypothesis that these bonds are major contributors to association. We also found that optimization of Cα–H hydrogen bonding and interhelical packing is sufficient to computationally predict the structure of known GASright dimers at near atomic level. Here, we demonstrate that this computational method can be used to characterize the structure of a protein not previously known to dimerize, by predicting and validating the transmembrane dimer of ADCK3, a mitochondrial kinase. ADCK3 is involved in the biosynthesis of the redox active lipid, ubiquinone, and human ADCK3 mutations cause a cerebellar ataxia associated with ubiquinone deficiency, but the biochemical functions of ADCK3 remain largely undefined. Our experimental analyses show that the transmembrane helix of ADCK3 oligomerizes, with an interface based on an extended Gly-zipper motif, as predicted by our models. The data provide strong evidence for the hypothesis that optimization of Cα–H hydrogen bonding is an important factor in the association of transmembrane helices. This work also provides a structural foundation for investigating the role of transmembrane association in regulating the biological activity of ADCK3.
DIGITAL TEXTS FOR LEARNING FINNISH: SHARED RESOURCES AND EMERGING PRACTICES

Recent studies in the field of new literacies have indicated that a remarkable change in the way we access, consume, and produce information has taken place. The boundaries between concepts such as authorship and ownership have become blurred. This paper will deal with using digital texts in teaching reading comprehension on a university-level course with a special focus on Finnish as a second language. Furthermore, the benefits and challenges of teaching L2 reading comprehension in a multimodal learning environment will be discussed. The three main perspectives utilized are meaningfulness, sharing, and adaptivity. The students attending the course described in the paper were advanced university students from various European countries, who studied Finnish as a second language. The study examines the literacy practices that take place when learners of Finnish as a second language engage in reading and writing blogs in a reading comprehension course. The results of this study indicate that sharing, meaningfulness and adaptivity promote learners’ engagement with reading as a social practice and thus support the claim that using blogs represents opportunities to enhance L2 reading comprehension skills.
Steadied-bubbles: combining techniques to address pen-based pointing errors for younger and older adults

Tablet PCs are gaining popularity but many older adults still struggle with pointing, particularly with two error types: missing, landing and lifting outside the target bounds; and slipping, landing on the target, but slipping off before lifting. To solve these problems, we examined the feasibility of extending and combining existing techniques designed for younger users and the mouse, focusing our investigation on the Bubble cursor and Steady Clicks techniques. Through a laboratory experiment with younger and older adults, we showed that both techniques can be adapted for use in a pen interface, and that combining the two techniques provides greater support than either technique on its own. Though our results were especially pertinent to the older group, both ages benefited from the designs. We also found that technique performance depended on task context. From these findings we established guidelines for technique selection.
Manual Stimulation of the Suprahyoid-Sublingual Region Diminishes Polynnervation of the Motor Endplates and Improves Recovery of Function After Hypoglossal Nerve Injury in Rats

Background. Using the rat facial nerve axotomy model, the authors recently showed that manual stimulation of denervated whiskerpad muscles reduced the posttransectional polyinnervation at the neuromuscular junctions and promoted full recovery of vibrissal whisking. Objective. Prompted by implications for rehabilitation therapy, the authors examined whether manual stimulation of denervated supra- and infrahyoid muscles would also improve recovery after unilateral lesion on the hypoglossal nerve. Methods. Adult rats underwent transection of the right hypoglossal nerve. Half of the animals received no postoperative treatment, and the other half were subjected to daily manual stimulation of the suprahyoid/sublingual region for 2 months. Recovery was assessed by measuring the angle of tongue-tip deviation from the midline, degree of collateral axonal branching at the lesion site (counts after retrograde labeling with 2 fluorescent dyes), synaptic input to the hypoglossal motoneurons using synaptophysin immunocytochemistry, tongue-muscles motor representation in the cerebral cortex after c-Fos immunocytochemistry, and portion of polyinnervated neuromuscular junctions. Results. In animals receiving manual stimulation, the tongue-tip deviation was 37.0 ± 49.37°, whereas values in control nonstimulated rats were significantly higher (50.1 ± 9.01°; P < .05; mean ± SD). Improved recovery was not associated with reduced collateral axonal branching; there were also no differences in tongue-muscles representation in the motor cortex. However, manual stimulation restored the total synaptic input to levels in intact animals and reduced the proportion of polyinnervated neuromuscular junctions compared with nonstimulated animals. Conclusion. The data show that manual stimulation of denervated muscles improves functional outcome following peripheral nerve injury. This suggests immediate potential for enhancing clinical rehabilitation strategies.
Controlling for Gene Expression Changes in Transcription Factor Protein Networks*

The development of affinity purification technologies combined with mass spectrometric analysis of purified protein mixtures has been used both to identify new protein–protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we investigated whether ectopic expression of an affinity tagged transcription factor as bait in affinity purification mass spectrometry experiments perturbs gene expression in cells, resulting in the false positive identification of bait-associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA sequencing, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then co-purify non-specifically and be misidentified as bait-associated proteins. Therefore, typical controls should be sufficient, and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFκB1, NFκB2, Rel, RelB, IκBα, IκBβ, and IκBε). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFκB family transcription factors. This work therefore provides a conceptual and experimental framework for analyzing transcription factor protein interactions.
The proportional lack of archaeal pathogens: Do viruses/phages hold the key?

Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease‐causing Archaea is due, in part, to mutually‐exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control.
Rethinking the paradigms that inform behavioral treatment research for substance use disorders.

AIMS Over the last three decades, the randomized controlled trial or 'psychotherapy technology' approach has been the dominant model of inquiry in research on addiction treatment. This period has yielded impressive discoveries, but recent failures to confirm core research hypotheses such as occurred in Project MATCH and the Cocaine Collaborative Treatment Study have raised questions about future research directions. The paper identifies several testable assumptions of the psychotherapy technology model. METHODS A review is conducted on four substance use disorder behavioral interventions--motivational interviewing, cognitive-behavioral treatment, behavioral couples treatment and 12-Step-oriented treatment--to determine whether these assumptions are supported by research findings. RESULTS Overall, the review suggests weak support for the technology model of psychotherapy research. Lack of support is interpreted as indicating flaws in several model assumptions about how to conceptualize and measure patient responsivity and the interaction of non-specific and specific therapeutic factors. The paper offers alternative strategies for addressing these issues drawn from the general psychotherapy process literature and provides illustrative examples of how these could be used to spur innovation in addiction treatment research. CONCLUSIONS The addiction treatment research field is coming up against the limitations of the psychotherapy technology model as the dominant paradigm guiding treatment research. It is important for addiction treatment researchers to explore alternative conceptualizations and methodologies in order to understand more clearly how treatment works.
Nominal wage rigidity in the European Countries: evidence from the Europanel

This paper analyses wage dynamics at individual level using the ECHP data. We compare yearly wage changes of employees in twelve European countries during the 1994-96 time-period. In all the European countries we find evidence of nominal and not real wage rigidity. At the same time, in none of the countries considered wages are completely downwardly rigid. We also compare nominal wage changes of employees staying with the same employer to movers and find that, despite movers distributions are generally more flexible than stayers, surprisingly enough they also have a spike at zero. Explanations of the above results with institutional features of the countries considered are given.
Flexural Bending Fatigue of Raw and Chemically Treated Jute

Flexural bending fatigue of raw, mercerized, and sodium chlorite (Textone) bleached jute fiber was studied. Mercerized jute fiber could withstand a greater number of flex cycles before rupture compared to raw jute, while the modal height of the fatigue cycle histogram showed a sharp fall with bleaching of jute fibers.
Affect Computation Models from Textual Aspect: A Brief Survey

emotions are outcome of the subjective evaluation of events that occur in the environment. There are various affect theories in psychology to understand human emotion. To make Human-Computer-Interaction (HCI) intelligent, affect theory are to be incorporated. In this paper, discussion of various affect theories and affect computation models have been presented. General Terms Data mining, text mining, emotion detection, sentiment analysis
Peritoneal Resorption Capacity for Lipopolysaccharide and Interleukin-6 in Acute Zymosan-Induced Chemical Peritonitis

Aim: To evaluate peritoneal resorption capacity for lipopolysaccharide (LPS) and interleukin-6 (IL-6) in a model of chemical peritonitis. Methods: Zymosan peritonitis was induced in anesthetized rats. LPS was injected intraperitoneally to different groups at 4 h (n = 10), 8 h (n = 9), 12 h (n = 9), and 24 h (n = 9) after peritonitis and to a control group (n = 8). Similarly, IL-6 was injected intraperitoneally to different groups at 4 h (n = 9), 8 h (n = 10), 12 h (n = 10), and 24 h (n = 10) after peritonitis, and to a control group (n = 10). Plasma levels of LPS or IL-6 were measured immediately after intraperitoneal injections of LPS or IL-6, respectively, and at 5, 15, 30, 45, and 60 min later. Results: There was no change over time in plasma LPS levels in the groups receiving LPS intraperitoneally (p = 0.4). There was highly significant change over time in the IL-6 level in the studied time periods in the groups receiving IL-6 intraperitoneally (p < 0.0001). There was an increase in the plasma IL-6 level when sampled at 4 h after peritonitis. Conclusion: There was a reduction of resorption capacity of inflamed peritoneum for inflammatory mediators in acute chemical peritonitis.
Metamorphosis of Polyhedral Surfaces using Decomposition

This paper describes an algorithm for morphing polyhedral surfaces based on their decompositions into patches. The given surfaces need neither be genus‐zero nor two‐manifolds. We present a new algorithm for decomposing surfaces into patches. We also present a new projection scheme that handles topologically cylinder‐like polyhedral surfaces. We show how these two new techniques can be used within a general framework and result with morph sequences that maintain the distinctive features of the input models.
Coding Dojo: An Environment for Learning and Sharing Agile Practices

A Coding Dojo is a meeting where a group of programmers gets together to learn, practice, and share experiences. This report describes the authors' experience of creating and running an active Coding Dojo in Sao Paulo, Brazil, sharing the lessons learned from the experience. The role of the Dojo in the learning process is discussed, showing how it creates an environment for fostering and sharing agile practices such as test-driven development, refactoring and pair programming, among others.
The Development and Evolution of TREC and DUC

The Text REtrieval Conference (TREC) has been running for 11 years now, with 93 participants in the last round of evaluation. This paper chronicles the changes in TREC over that time, emphasizing the evolution in the tasks that were evaluated rather than discussing the results of the specific evaluations. The development of the new Document Understanding Conference (DUC) is also discussed, including the evaluation issues that have surfaced during its first two years.
Organic Bionics: A New Dimension in Neural Communications

The term “bionics” is synonymous with the term “biomimetics” and in this context refers to the integration of human engineered devices to take advantage of functional mechanisms and structures resident in nature. The use of electrical conductors to transmit charge into and out of biological systems to affect biological processes has been the source of great scientific interest. This has inspired many to explore the possible use of electrical stimulation in promoting positive health outcomes. Advances in medical bionics technology are dependent upon eliciting precise control of the electrical energy to deliver beneficial health outcomes. The advent of carbon‐based organic conductors now provides the platform for unprecedented possibilities by which the electrical energy can be used to modulate the function of medical devices. The use of organic conductors in the field of bionics, and in particular medical bionics, as that involved with the development of devices that enable the effective integration of biology (nature) and electronics to achieve a targeted functional outcome is explored.
Drug resistant-Mycobacterium leprae--results of mouse footpad studies from a laboratory in south India.

Out of 265 biopsies of leprosy patients received at the Experimental Pathology Laboratory of Schieffelin Leprosy Research and Training Centre from 1987 to 1997 for evaluating resistant strains of M. leprae, using the mouse footpad technique, 49 showed resistant strains of M leprae to varying concentrations of dapsone, rifampicin and clofazimine. 23 (47%) of these were from a control area. With 369 skin-smear positive multibacillary (MB) patients as the risk group (denominator), 23 (6.23%) were resistant to one or more drugs. 18 (4.88%) had dapsone resistance, 5 (1.36%) were resistant to rifampicin and 9 (2.44%) had resistance to low concentrations of clofazimine (0.0001%). Out of the 23 biopsies with drug resistance from the control area, primary dapsone resistance was seen in 7 (30%) biopsies and secondary dapsone resistance in 11 (48%). Primary rifampicin resistance was seen in 4 (17.4%) patients, secondary rifampicin resistance in 1 (4.35%) and primary clofazimine resistance in 7 (30%). 3 (13%) of the strains showed secondary clofazimine resistance. One biopsy had resistant strains to all the three drugs. In a control area where properly supervised effective multidrug therapy (MDT) was regularly administered over the years, the emergence of drug resistance is negligible. It may not be the case if the content, duration and regularity of the drug regimen were not satisfactory. Aware of the possible shortcomings in mass administration of MDT, it is emphasized that mouse footpad studies on drug resistance should be made available at least in endemic areas where the incidence of the disease has not changed despite good MDT coverage in order to monitor the emergence of drug resistance. Research into molecular biological identification of drug resistant-M.leprae should be intensified. These steps would help to institute timely measures to check the spread of any drug-resistant organisms in the community.
Panel and Speech Balloon Extraction from Comic Books

Comic books represent an important cultural heritage in many countries. However, few researches have been done in order to analyse the content of comics such as panels, speech balloons or characters. At first glance, the structure of a comic page may appear easy to determine. In practice, the configuration of the page, the size and the shape of the panels can be different from one page to the next. Moreover, authors often draw extended contents (speech balloon or comic art) that overlap two panels or more. In some situations, the panel extraction can become a real challenge. Speech balloons are other important elements of comics. Full text indexing is only possible if the text can be extracted. However the text is usually embedded among graphic elements. Moreover, unlike newspapers, the text layout in speech balloons can be irregular. Classic text extraction method can fail. We propose, in this paper, a method based on region growing and mathematical morphology to extract automatically the panels of a comic page and a method to detect speech balloons. Our approach is compared with other methods find in the literature. Results are presented and discussed.
Chart-Based Transfer Rule Application in Machine Translation

Transfer-based Machine Translation systems require a procedure for choosing the set of transfer rules for generating a target language translation from a given source language sentence. In an MT system with many competing transfer rules, choosing the best set of transfer rules for translation may involve the evaluation of an explosive number of competing sets. We propose a solution to this problem based on current best-first chart parsing algorithms.
Using field data to assess model predictions of surface and ground fuel consumption by wildfire in coniferous forests of California

Inventories of greenhouse gas (GHG) emissions from wildfire provide essential information to the state of California, USA, and other governments that have enacted emission reductions. Wildfires can release a substantial amount of GHGs and other compounds to the atmosphere, so recent increases in fire activity may be increasing GHG emissions. Quantifying wildfire emissions however can be difficult due to inherent variability in fuel loads and consumption and a lack of field data of fuel consumption by wildfire. We compare a unique set of fuel data collected immediately before and after six wildfires in coniferous forests of California to fuel consumption predictions of the first‐order fire effects model (FOFEM), based on two different available fuel characterizations. We found strong regional differences in the performance of different fuel characterizations, with FOFEM overestimating the fuel consumption to a greater extent in the Klamath Mountains than in the Sierra Nevada. Inaccurate fuel load inputs caused the largest differences between predicted and observed fuel consumption. Fuel classifications tended to overestimate duff load and underestimate litter load, leading to differences in predicted emissions for some pollutants. When considering total ground and surface fuels, modeled consumption was fairly accurate on average, although the range of error in estimates of plot level consumption was very large. These results highlight the importance of fuel load input to the accuracy of modeled fuel consumption and GHG emissions from wildfires in coniferous forests.
Special Section on Processing Natural Speech Variability for Improved Verbal Human-Computer Interaction Acoustic Model Adaptation for Speech Recognition

Statistical speech recognition using continuous-density hidden Markov models (CDHMMs) has yielded many practical applications. However, in general, mismatches between the training data and input data significantly degrade recognition accuracy. Various acoustic model adaptation techniques using a few input utterances have been employed to overcome this problem. In this article, we survey these adaptation techniques, including maximum a posteriori (MAP) estimation, maximum likelihood linear regression (MLLR), and eigenvoice. We also present a schematic view called the adaptation pyramid to illustrate how these methods relate to each other. key words: speech recognition, acoustic model adaptation, hidden Markov models
A case study on diurnal and seasonal variation in pavement temperature

An empirical numerical model was established for analysing the temperature variation of pavements in Xi'an area of China. This model can consider the influence of solar radiation, atmospheric temperature and humidity. It was verified by comparing the calculated and measured temperature of the natural ground surface. The effect of seasonal variations of temperature on asphalt and concrete pavement surfaces were then calculated. The temperature distribution of both asphalt and concrete pavements in January and July was investigated using the model. For each type of pavement, four groups of different pavement materials were considered to investigate the influence of thermal parameters for pavement materials on the temperature distribution. Furthermore, the diurnal variation of pavement temperature was analysed and discussed based on the normal climate characteristics in Xi'an. The results of the analysis showed that the diurnal variation of pavement temperature is very significant and must be considered in the design of a pavement.