Miracle-dz/UniFAR-FTUs huggingface dataset:
Antagonistic roles for the ubiquitin ligase Asr1 and the ubiquitin-specific protease Ubp3 in subtelomeric gene silencing

Significance Ubiquitylation is integral to a myriad of cellular processes, including protein destruction, cell cycle control, and regulation of gene activity. Here, we show that ubiquitylation plays a role in inactivating the expression of genes that are located close to telomeres. We present evidence that the ubiquitin ligase Asr1 associates with subtelomeric DNA and ubiquitylates RNA polymerase II to prevent it from transcribing genes at these locations. We also show that Asr1 interacts with Ubp3, an enzyme that reverses ubiquitylation, and that the two play antagonistic roles in silencing subtelomeric genes. These findings show how ubiquitylation of a core component of the transcriptional machinery impacts gene activity and reveal a mechanism for controlling the expression of telomere-proximal genes. Ubiquitin, and components of the ubiquitin–proteasome system, feature extensively in the regulation of gene transcription. Although there are many examples of how ubiquitin controls the activity of transcriptional regulators and coregulators, there are few examples of core components of the transcriptional machinery that are directly controlled by ubiquitin-dependent processes. The budding yeast protein Asr1 is the prototypical member of the RPC (RING, PHD, CBD) family of ubiquitin-ligases, characterized by the presence of amino-terminal RING (really interesting new gene) and PHD (plant homeo domain) fingers and a carboxyl-terminal domain that directly binds the largest subunit of RNA polymerase II (pol II), Rpb1, in response to phosphorylation events tied to the initiation of transcription. Asr1-mediated oligo-ubiquitylation of pol II leads to ejection of two core subunits of the enzyme and is associated with inhibition of polymerase function. Here, we present evidence that Asr1-mediated ubiquitylation of pol II is required for silencing of subtelomeric gene transcription. We show that Asr1 associates with telomere-proximal chromatin and that disruption of the ubiquitin-ligase activity of Asr1—or mutation of ubiquitylation sites within Rpb1—induces transcription of silenced gene sequences. In addition, we report that Asr1 associates with the Ubp3 deubiquitylase and that Asr1 and Ubp3 play antagonistic roles in setting transcription levels from silenced genes. We suggest that control of pol II by nonproteolytic ubiquitylation provides a mechanism to enforce silencing by transient and reversible inhibition of pol II activity at subtelomeric chromatin.
A multi-centre randomized controlled clinical trial on the treatment of intra-bony defects with enamel matrix derivatives/synthetic bone graft or enamel matrix derivatives alone: results after 12 months.

OBJECTIVES Comparison of the clinical and radiographic outcomes of a combination of enamel matrix derivatives (EMD) and a synthetic bone graft (EMD/SBG) with EMD alone in wide (≥2 mm) and deep (≥4 mm) one- and two- wall intra-bony defects 12 months after treatment. MATERIALS AND METHODS Seventy-three patients with chronic periodontitis and one wide (≥2 mm) and deep (≥4 mm) intra-bony defect were recruited in five centres in Germany. During surgery, defects were randomly assigned to EMD/SBG (test) or EMD (control). Assessments at baseline, after 6 and 12 months included bone sounding, attachment levels, probing pocket depths, bleeding on probing, and recessions. Changes in defect fill were recorded radiographically. RESULTS Both treatment modalities led to significant clinical improvements. In the EMD/SBG group a mean defect fill of 2.7 ± 1.9 mm was calculated, in the EMD group the defect fill was 2.8 ± 1.6 mm. A mean gain in clinical attachment of 1.7 ± 2.1 mm in the test group and 1.9 ± 1.7 mm in the control group after 1 year was observed. Radiographic analysis confirmed for both groups that deeper defects were associated with greater defect fill. CONCLUSION The results show comparable clinical and radiographic outcomes following both treatment modalities 12 months after treatment.
Automatic classification of Web queries using very large unlabeled query logs

Accurate topical classification of user queries allows for increased effectiveness and efficiency in general-purpose Web search systems. Such classification becomes critical if the system must route queries to a subset of topic-specific and resource-constrained back-end databases. Successful query classification poses a challenging problem, as Web queries are short, thus providing few features. This feature sparseness, coupled with the constantly changing distribution and vocabulary of queries, hinders traditional text classification. We attack this problem by combining multiple classifiers, including exact lookup and partial matching in databases of manually classified frequent queries, linear models trained by supervised learning, and a novel approach based on mining selectional preferences from a large unlabeled query log. Our approach classifies queries without using external sources of information, such as online Web directories or the contents of retrieved pages, making it viable for use in demanding operational environments, such as large-scale Web search services. We evaluate our approach using a large sample of queries from an operational Web search engine and show that our combined method increases recall by nearly 40% over the best single method while maintaining adequate precision. Additionally, we compare our results to those from the 2005 KDD Cup and find that we perform competitively despite our operational restrictions. This suggests it is possible to topically classify a significant portion of the query stream without requiring external sources of information, allowing for deployment in operationally restricted environments.
The Discrete Duality Finite Volume Method for Convection-diffusion Problems

In this paper we extend the discrete duality finite volume (DDFV) formulation to the steady convection-diffusion equation. The discrete gradients defined in DDFV are used to define a cell-based gradient for the control volumes of both the primal and dual meshes, in order to achieve a higher-order accurate numerical flux for the convection term. A priori analysis is carried out to show convergence of the approximation, and a global first-order convergence rate is derived. The theoretical results are confirmed by some numerical experiments.
Opportunistic sensing and detection of mild cognitive impairment

Dementia is a growing healthcare problem, and it has become necessary to find a way to reduce the prevalence of this disease. Mild cognitive impairment is a risk factor for dementia, and being able to detect the onset of mild cognitive impairment gives healthcare professionals the chance to reduce the effect of dementia on the society. In this paper, we propose a system that seeks to detect mild cognitive impairment in otherwise healthy persons. We are particularly interested in being able to gather data for monitoring without interfering with the subject's daily living.
Identification and evaluation of a novel sperm protamine abnormality in a population of infertile males.

BACKGROUND A significant relationship exists between an abnormally high sperm protamine-1 (P1)/protamine-2 (P2) ratio and male infertility. In this study we investigate whether a decreased P1/P2 ratio is also linked to male infertility and we attempt to describe, at the protein expression level, the underlying cause of sperm P1/P2 deregulation. METHODS P1 and P2 protein concentrations were quantified in sperm from 272 infertility patients and 87 fertile donors. P1/P2 ratios and protamine quantity were correlated with fertility status using semen analysis, sperm penetration capacity, and IVF data. RESULTS We identified four distinct groups in the study: normal P1/P2 fertile donors, normal P1/P2 patients, low P1/P2 patients, and high P1/P2 patients. P1 and P2 were both under-expressed in patients with a normal P1/P2 ratio, but not in fertile donors. In patients with a low P1/P2 ratio, P1 was under-expressed while P2 was over-expressed; in patients with a high P1/P2 ratio, P1 was normally expressed and P2 was under-expressed. Patients with abnormal P1/P2 ratios displayed significantly reduced semen quality and sperm penetration ability. CONCLUSIONS We have identified a novel population of infertile males with a reduced P1/P2 ratio. Aberrant P1/P2 ratios arise from an abnormal concentration of P1 and/or P2, either of which is associated with male infertility.
Domain decomposition by radial basis functions for time dependent partial differential equations

In the last years, there has been an increased investigation of efficient algorithms to solve problems of great scale. The main restriction of the traditional methods, like finite difference methods and finite element methods, is the mesh generation. In this work, we investigate the overlapping domain decomposition method applied to time dependent partial differential equations with unsymmetric radial basis function collocation method. Numerical experiments performed with thin-plate splines as kernel function, for an evolutionary problem in two dimensions, show a drastic time reduction as we increase the number of subdomains, high numerical accuracy and lower numerical diffusion. The numerical results suggest that the scheme proposed can be useful to tackle large scale time dependent problems.
Measurement of Arterial Geometry and Wall Composition in the Carotid Sinus Baroreceptor Area

The overall dimensions of the carotid sinus, the thicknesses of the individual layers within its wall, and the tissue composition of the tunica media were measured on histological sections of the carotid bifurcation fixed in vivo in anesthetized dogs, cats, and rabbits. The outstanding dimensional features of the carotid sinus as compared to the adjoining carotid segments are its thinned media-intima layer and increased ratio of internal radius to media-intima thickness. These differences carry a high level of significance statistically. There appears to be no marked increase in the ratio of radius to whole-wall thickness in the sinus portion of the carotid tree. The tunica media in the carotid sinus wall contains more than twice as much elastic tissue per unit volume (mean value 62.3% elastin) as the media in the carotid vessels adjoining the sinus; reciprocally, smooth muscle constitutes 16.4% of the tunica media in the sinus wall but approximately 50% or more of the media in the common, internal, and external carotid arteries caudal and cranial to the sinus (mean values in percent of total volume). Results are discussed in relation to the position of the baroreceptors within the sinus wall and mechanisms of stimulating them.
Atmospheric-hydrospheric mechanisms of climate anomalies in the western equatorial Indian Ocean

Atmosphere-ocean mechanisms of rainfall anomalies at the coast of eastern Africa are studied using long-term ship observations in the Indian Ocean, surface current measurements, subsurface casts, upper air analyses by the European Centre for Medium Range Weather Forecasts, rain gauge series in eastern Africa and India, and an index of the Southern Oscillation (SO), the high-SO phase being defined by anomalously high/low pressure at Tahiti/Darwin. The causalities of precipitation anomalies at the coast of eastern Africa differ for the two rainy seasons centered on April-May and October-November, and only the latter is strongly related to the SO. In the high-SO phase, April-May pressure is low over the entire Indian Ocean domain, whereas in October-November, pressure is high in the west and low in the east. Concomitantly, surface waters are anomalously cold in the west, and strong westerlies sweep the equatorial zone of the Indian Ocean. Eastern African rainfall anomalies are related to the SO through a combination of cooperative mechanisms that function most effectively in the boreal autumn rainy season of eastern Africa. (1) Equatorial westerly winds are conducive to lower tropospheric divergence over equatorial East Africa, and in the high-SO phase these are accelerated, especially in October-November, owing to the anomalous eastward pressure gradient. (2) The equatorial westerly winds drive the eastward equatorial jet in the upper hydrosphere, which entails cold-water upwelling in the western extremity of the basin where sea surface temperature further hydrostatically affects the zonal pressure gradient and thus feeds back into the equatorial westerly winds. (3) In addition, cold-water anomalies in the western Indian Ocean, most pronounced in October-November during the high-SO phase, also suppress convection. (4) In the high-SO phase, the Indian summer monsoon tends to be strong, leaving behind an anomalously cold western Indian Ocean, which in turn feeds into mechanisms 1 to 3. The eastward equatorial jet thus has a role to play in feedback mechanisms contributing to the anomalies of the boreal autumn rains at the coast of eastern Africa.
PATERNITY PROTECTION CAN PROVIDE A KICK‐START FOR THE EVOLUTION OF MALE‐ONLY PARENTAL CARE

Sperm competition and uncertainty of paternity hamper the evolution of male parental care. Thus, maternal care predominates in most taxa. What if males can, however, limit cuckoldry by guarding the eggs postmating? Here, we show that this provides a reason to reconsider an old and nowadays rather discredited hypothesis: that external fertilization is associated with male care because the parent who releases its gametes first can depart leaving the other in a “cruel bind,” having to care for the offspring. In our model, protection of paternity provides an additional incentive for the male to stay associated with its young. When we then assume that offspring survive better if guarded, paternity protection proves enough to kick‐start the evolution of male‐only parental care from a scenario with no care. This fits with data from fishes, where male‐only care is associated with external fertilization, whereas female‐only care almost always evolves after an initial transition to internal fertilization. Our model unifies disparate hypotheses regarding parental care roles and provides support for the idea that care roles can be influenced by sex differences in selection to be physically close to the offspring, including selection that is initially not based on offspring survival.
EventAction: Visual analytics for temporal event sequence recommendation

Recommender systems are being widely used to assist people in making decisions, for example, recommending films to watch or books to buy. Despite its ubiquity, the problem of presenting the recommendations of temporal event sequences has not been studied. We propose EventAction, which to our knowledge, is the first attempt at a prescriptive analytics interface designed to present and explain recommendations of temporal event sequences. EventAction provides a visual analytics approach to (1) identify similar records, (2) explore potential outcomes, (3) review recommended temporal event sequences that might help achieve the users' goals, and (4) interactively assist users as they define a personalized action plan associated with a probability of success. Following the design study framework, we designed and deployed EventAction in the context of student advising and reported on the evaluation with a student review manager and three graduate students.
How long can a hydrothermal system be sustained by a single intrusive event

Published numerical calculations show that the convective systems which produce near-surface geothermal systems or ore deposits are likely to cool their intrusion heat source in at most a few tens of thousands of years, even if the intrusion is large. Generally, hydrothermal circulation, near-surface geothermal activity, and magmatic intrusion should be closely tied in time and space. Long-lived ( approximately 1 m.y.) hydrothermal activity normally suggests multiple pulses of intrusion with associated pulses of hydrothermal circulation. However, if the permeability of the intruded environment is just above that which allows convection, and the volume of the intrusion is very large, calculations presented here show that a single episode of intrusion can sustain hydrothermal circulation and near-surface geothermal activity for approximately 800,000 yr. For a deep sill heat source, these unusually long-lived hydrothermal systems can vent through a few very widely separated discharge sites and have the potential to produce isolated massive sulfide deposits of unusually large size.
Text Segments as Constrained Formal Concepts

In this paper we address the problem of segmenting (and summarizing) a text by Formal Concept Analysis (FCA) using Lexical Chains established for the text. The first proposed method relies on the Conceptual hierarchy (Concept lattice) derived for a formal context expressing the map of Lexical Chains to the text. The second one offers a conceptual view for a segmentation, using a conceptual clustering of sentences. At least at our knowledge there are not previous attempts to solve the segmentation (and the summarization) of a text by FCA.
An ASIC design of an optimized multiplication using twin precision

A binary multiplier is an electronic circuit used in digital electronics, such as computer, to multiply two binary numbers. A binary computer does exactly the same, but with binary numbers. In binary encoding each long number is multiplied by one digit (either 0 or 1) and that's much easier than in decimal, as the product by 0 or 1 is just 0 or same number. Therefore the multiplication of two binary numbers comes down to the process of calculating the partial products(which are 0 or the first number), shifting them left and the adding them together. Twin precision can be efficiently used to attain double output in multipliers and this method is simulated in signed multipliers. Twin precision is defined as one of the coherent method to attain double throughput in the multipliers. Twin precision is implemented using Modified Booth multiplier. The added advantage of reduced partial product is the reason for using Modified Booth multiplier. The possibility of combining N & N/2 bit multiplication in the same N bit tree multiplier is called as TP multiplier, where N is the bit of the multiplier. Since the partial product generation of MB multiplication is based on the encoding and decoding logic, it is not possible to use the results of full precision(N bit) for narrow width(N/2 bit) MB multiplication. Therefore MB algorithm reduces N number of partial product rows to N/2 rows. Multiplexers are needed to select the approximate partial products for N and N/2 multiplications. When more number of multiplexers are used area increases. Here in this paper, TP implementation it is done using an extra logic block for obtaining double throughput. Optimized TP multiplier gave a way for overall reduction in power, delay & area. This is then implemented in floating point multiplication and is taken as application study. It is observed that the speed of the floating point multiplier to genrate product is found faster than the present multipliers. Simulations and evaluations are done in Cadence RTL compiler using TSMC 90nm library.
Finding keyword from online broadcasting content for targeted advertising

Content targeted advertising has been a successful way of delivering ads, as effective technologies were developed to find keywords from the webpage a user is browsing. However, existing technologies cannot be easily applied to find keywords from online broadcasting content, which usually contain more specific phrases and wordings in certain communities than in general webpage content. In this paper, motivated by some existing research works on information extraction field, we suggest a sequential pattern mining-based method to discover language patterns from online broadcasting content. With selected keyword seeds, iteratively applying the language pattern mining and keyword extraction, the proposed technique avoids any tedious labeling work for this task. Our experiments on real-world data show that the proposed keyword extraction algorithm significantly outperforms the baseline method.
Emotion word processing: does mood make a difference?

Visual emotion word processing has been in the focus of recent psycholinguistic research. In general, emotion words provoke differential responses in comparison to neutral words. However, words are typically processed within a context rather than in isolation. For instance, how does one's inner emotional state influence the comprehension of emotion words? To address this question, the current study examined lexical decision responses to emotionally positive, negative, and neutral words as a function of induced mood as well as their word frequency. Mood was manipulated by exposing participants to different types of music. Participants were randomly assigned to one of three conditions—no music, positive music, and negative music. Participants' moods were assessed during the experiment to confirm the mood induction manipulation. Reaction time results confirmed prior demonstrations of an interaction between a word's emotionality and its frequency. Results also showed a significant interaction between participant mood and word emotionality. However, the pattern of results was not consistent with mood-congruency effects. Although positive and negative mood facilitated responses overall in comparison to the control group, neither positive nor negative mood appeared to additionally facilitate responses to mood-congruent words. Instead, the pattern of findings seemed to be the consequence of attentional effects arising from induced mood. Positive mood broadens attention to a global level, eliminating the category distinction of positive-negative valence but leaving the high-low arousal dimension intact. In contrast, negative mood narrows attention to a local level, enhancing within-category distinctions, in particular, for negative words, resulting in less effective facilitation.