Miracle-dz/UniFAR-FTUs huggingface dataset:
Light‐Emitting Organic Solar Cells Based on a 3D Conjugated System with Internal Charge Transfer

Organic semiconductors (OSCs) such as linear p-conjugated systems are the focus of growing scientific and technological interest, motivated by their potential application in flexible and cost-effective (opto)electronic devices, for example, fieldeffect transistors (FETs), light-emitting diodes (LEDs), and solar cells. Each type of device requires active materials able to perform a specific function, such as charge transport, light-emission, or light harvesting. However, regardless of the expected function, the anisotropy of low-dimensional OSCs such as linear-conjugated systems is a major source of problems. Widely investigated OSCs, such as oligothiophenes or pentacene, reach high field-effect hole mobilities. However, this performance is obtained by controlling the orientation and interdistance of the molecules. A vertical orientation of conjugated molecules allows optimal charge transport across the conjugated-system channel in FETs, resulting in high charge-carrier mobilities. Conversely, such an orientation is detrimental for solar cells as it limits the absorption of incident light and the charge transport across the cell thickness. Finally, in LEDs, the emitting molecules must not interact too strongly to avoid luminescence quenching through nonradiative channels, but some intermolecular contacts are necessary for charge transport. In general, controlling the molecular orientation is a key issue to achieve optimal performance of organic devices based on low-dimensional conjugated systems. This control can be attained by optimizing the evaporation of small molecules or by post-processing treatments of spin-cast polymers. However, an interesting alternative to the pursuit of order could be the development of OSCs with isotropic charge-transport/optical properties and no grain boundaries. Isotropic OSCs are not only appealing in view of low-cost deposition techniques (e.g., roll-to-roll or jet printing) but might also lead to materials with different functions. To explore this possibility, we have recently synthesized 3D conjugated systems consisting of various cores carrying linear conjugated branches, and described some first examples of FETs and solar cells based on them. As a further step, here we describe thin-film diodes based on a glass-forming thienylenevinylenetriphenylamine functionalized with peripheral dicyanovinylene groups (TDCV-TPA, Fig. 1), which represent the first example of a single-molecule device that exhibits interesting dual photovoltaic (PV) and electroluminescent properties. Triphenylamines (TPAs) are well-known for their 3D propeller shape and glass-forming properties, and are widely used as hole-injecting/transporting or luminophore materials in LEDs. TDCV-TPA was designed as an isotropic material for solar cells for the following reasons: i) to obtain an electron donor and hole-transporting molecular glass; ii) to create an internal charge transfer (ICT) to better match the solar spectrum; while iii) preserving a high oxidation potential, and, C O M M U N IC A IO N S
ZBP1 regulates mRNA stability during cellular stress

An essential constituent of the integrated stress response (ISR) is a reversible translational suppression. This mRNA silencing occurs in distinct cytoplasmic foci called stress granules (SGs), which transiently associate with processing bodies (PBs), typically serving as mRNA decay centers. How mRNAs are protected from degradation in these structures remains elusive. We identify that Zipcode-binding protein 1 (ZBP1) regulates the cytoplasmic fate of specific mRNAs in nonstressed cells and is a key regulator of mRNA turnover during the ISR. ZBP1 association with target mRNAs in SGs was not essential for mRNA targeting to SGs. However, ZBP1 knockdown induced a selective destabilization of target mRNAs during the ISR, whereas forced expression increased mRNA stability. Our results indicate that although targeting of mRNAs to SGs is nonspecific, the stabilization of mRNAs during cellular stress requires specific protein–mRNA interactions. These retain mRNAs in SGs and prevent premature decay in PBs. Hence, mRNA-binding proteins are essential for translational adaptation during cellular stress by modulating mRNA turnover.
Maximal termsets as a query structuring mechanism

Search engines process queries conjunctively to restrict the size of the answer set. Further, it is not rare to observe a mismatch between the vocabulary used in the text of Web pages and the terms used to compose the Web queries. The combination of these two features might lead to irrelevant query results, particularly in the case of more specific queries composed of three or more terms. To deal with this problem we propose a new technique for automatically structuring Web queries as a set of smaller subqueries. To select representative subqueries we use information on their distributions in the document collection. This can be adequately modeled using the concept of maximal termsets derived from the formalism of association rules theory. Experimentation shows that our technique leads to improved results. For the TREC-8 test collection, for instance, our technique led to gains in average precision of roughly 28% with regard to a BM25 ranking formula.
Harvesting in a two-prey one-predator fishery: a bioeconomic model

A multispecies harvesting model with interference is proposed. The model is based on Lotka-Volterra dynamics with two competing species which are affected not only by harvesting but also by the presence of a predator, the third species. In order to understand the dynamics of this complicated system, we choose to model the simplest possible predator response function in which the feeding rate of the predator increases linearly with prey density. We derive the conditions for global stability of the system using a Lyapunov function. The possibility of existence of a bioeconomic equilibrium is discussed. The optimal harvest policy is studied and the solution is derived in the equilibrium case using Pontryagin's maximal principle. Finally, some numerical examples are discussed.
Effect of ribavirin, levovirin and viramidine on liver toxicological gene expression in rats

The ribavirin/interferon‐α combination is currently the standard therapy for patients with chronic hepatitis C. However, ribavirin causes hemolytic anemia as a signiﬁcant side‐effect. Levovirin, an l‐enantiomer of ribavirin, possesses similar immunomodulatory activity to ribavirin but lacks direct antiviral activity or hemolytic anemia. Viramidine is a liver‐targeting prodrug of ribavirin with much less potential for hemolytic anemia. The aim of the present study is to proﬁle the hepatic toxicological gene response to ribavirin, levovirin and viramidine. Rats were dosed orally with 120 mg kg−1 day−1 of ribavirin and viramidine and 2000 mg kg−1 day−1 of levovirin for 8 days. Ribavirin did not cause any signiﬁcant change (> threefold) in gene expression as analyzed by the Affymetrix GeneChip technique. Levovirin decreased the mRNA level of CYP7A1 by fourfold but did not affect the expression of CYP27/CYP7B1 that functions as an alternative pathway for cholesterol metabolism. Viramidine down‐regulated both expressed sequence tag 233569 and heat shock protein 86 genes threefold. The changes at mRNA level of these genes were conﬁrmed by the reverse transcription competitive polymerase chain reaction technique. None of the compounds changed the liver/body weight ratio, the major cytochrome P‐450 protein levels or enzyme activities. The data indicated that a high dose of ribavirin, levovirin or viramidine did not cause signiﬁcant change at the transcription level of most of the liver toxicological genes. Copyright © 2003 John Wiley & Sons, Ltd.
Seismic evidence of nonlinear crustal deformation during a large slow slip event in Mexico

Repeated cross‐correlations of ambient seismic noise indicate a long‐term seismic velocity change associated with the 2006 M7.5 slow‐slip event (SSE) in the Guerrero region, Mexico. Because the SSE does not radiate seismic waves, the measured velocity change cannot be associated with the response of superficial soil layers to strong shaking as observed for regular earthquakes. The perturbation observed maximized at periods between 7 s and 17 s, which correspond to surface waves with sensitivity to the upper and middle crust. The amplitude of the relative velocity change (∼10−3) was much larger than the volumetric deformation (∼10−6) at the depths probed (∼5–20 km). Moreover, the time dependence of the velocity perturbation indicated that it was related to the strain rate rather than the strain itself. This suggests that during strong slow‐slip events, the deformation of the overlying crust shows significant nonlinear elastic behavior.
Novel Compression Tool to Prevent Hematomas and Skin Erosions After Device Implantation.

BACKGROUND The incidence of hematoma formation following implantation of a cardiovascular implantable electronic device (CIED) is estimated to be 5% even if a pressure dressing is applied. It is unclear whether a pressure dressing can really compress the pocket in different positions. Furthermore, the adhesive tape for fixing pressure dressings can tear the skin. We developed a new compression tool for preventing hematomas and skin erosions. METHODS AND RESULTS We divided 46 consecutive patients receiving anticoagulation therapy who underwent CIED implantation into 2 groups (Group I: conventional pressure dressing, Group II: new compression tool). The pressure on the pocket was measured in both the supine and standing positions. The incidence of hematomas was compared between the 2 groups. The pressure differed between the supine and standing positions in Group I, but not in Group II (Group I: 14.8±7.1 mmHg vs. 11.3±9.9 mmHg, P=0.013; Group II: 13.5±2.8 mmHg vs. 13.5±3.5 mmHg, P=0.99). The incidence of hematomas and skin erosions was documented in 2 (8.7%) and 3 (13%) Group I patients, respectively. No complications were documented in Group II. CONCLUSIONS The new compression tool can provide adequate continuous pressure on the pocket, regardless of body position. This device may reduce the incidence of hematomas and skin erosions after CIED implantation.
Preventing shilling attacks in online recommender systems

Collaborative filtering techniques have been successfully employed in recommender systems in order to help users deal with information overload by making high quality personalized recommendations. However, such systems have been shown to be vulnerable to attacks in which malicious users with carefully chosen profiles are inserted into the system in order to push the predictions of some targeted items. In this paper we propose several metrics for analyzing rating patterns of malicious users and evaluate their potential for detecting such shilling attacks. Building upon these results, we propose and evaluate an algorithm for protecting recommender systems against shilling attacks. The algorithm can be employed for monitoring user ratings and removing shilling attacker profiles from the process of computing recommendations, thus maintaining the high quality of the recommendations.
Proteomics Based Identification of Cell Migration Related Proteins in HBV Expressing HepG2 Cells

Proteomics study was performed to investigate the specific protein expression profiles of HepG2 cells transfected with mutant HBV compared with wildtype HBV genome, aiming to identify the specific functions of SH3 binding domain (proline rich region) located in HBx. In addition to the cell movement and kinetics changes due to the expression of HBV genome we have observed previously, here we further targeted to explore the specific changes of cellular proteins and potential intracellular protein interactions, which might provide more information of the potential cellular mechanism of the differentiated cell movements. Specific changes of a number of proteins were shown in global protein profiling in HepG2 cells expressing wildtype HBV, including cell migration related proteins, and interestingly the changes were found recovered by SH3 binding domain mutated HBV. The distinctive expressions of proteins were validated by Western blot analysis.
CRISPR adaptive immune systems of Archaea

CRISPR adaptive immune systems were analyzed for all available completed genomes of archaea, which included representatives of each of the main archaeal phyla. Initially, all proteins encoded within, and proximal to, CRISPR-cas loci were clustered and analyzed using a profile–profile approach. Then cas genes were assigned to gene cassettes and to functional modules for adaptation and interference. CRISPR systems were then classified primarily on the basis of their concatenated Cas protein sequences and gene synteny of the interference modules. With few exceptions, they could be assigned to the universal Type I or Type III systems. For Type I, subtypes I-A, I-B, and I-D dominate but the data support the division of subtype I-B into two subtypes, designated I-B and I-G. About 70% of the Type III systems fall into the universal subtypes III-A and III-B but the remainder, some of which are phyla-specific, diverge significantly in Cas protein sequences, and/or gene synteny, and they are classified separately. Furthermore, a few CRISPR systems that could not be assigned to Type I or Type III are categorized as variant systems. Criteria are presented for assigning newly sequenced archaeal CRISPR systems to the different subtypes. Several accessory proteins were identified that show a specific gene linkage, especially to Type III interference modules, and these may be cofunctional with the CRISPR systems. Evidence is presented for extensive exchange having occurred between adaptation and interference modules of different archaeal CRISPR systems, indicating the wide compatibility of the functionally diverse interference complexes with the relatively conserved adaptation modules.
Coarse-to-Fine Inference and Learning for First-Order Probabilistic Models

Coarse-to-fine approaches use sequences of increasingly fine approximations to control the complexity of inference and learning. These techniques are often used in NLP and vision applications. However, no coarse-to-fine inference or learning methods have been developed for general first-order probabilistic domains, where the potential gains are even higher. We present our Coarse-to-Fine Probabilistic Inference (CFPI) framework for general coarse-to-fine inference for first-order probabilistic models, which leverages a given or induced type hierarchy over objects in the domain. Starting by considering the inference problem at the coarsest type level, our approach performs inference at successively finer grains, pruning high- and low-probability atoms before refining. CFPI can be applied with any probabilistic inference method and can be used in both propositional and relational domains. CFPI provides theoretical guarantees on the errors incurred, and these guarantees can be tightened when CFPI is applied to specific inference algorithms. We also show how to learn parameters in a coarse-to-fine manner to maximize the efficiency of CFPI. We evaluate CFPI with the lifted belief propagation algorithm on social network link prediction and biomolecular event prediction tasks. These experiments show CFPI can greatly speed up inference without sacrificing accuracy.
Strategy for Identifying Dendritic Cell-Processed CD4+ T Cell Epitopes from the HIV Gag p24 Protein

Mass Spectrometry (MS) is becoming a preferred method to identify class I and class II peptides presented on major histocompability complexes (MHC) on antigen presenting cells (APC). We describe a combined computational and MS approach to identify exogenous MHC II peptides presented on mouse spleen dendritic cells (DCs). This approach enables rapid, effective screening of a large number of possible peptides by a computer-assisted strategy that utilizes the extraordinary human ability for pattern recognition. To test the efficacy of the approach, a mixture of epitope peptide mimics (mimetopes) from HIV gag p24 sequence were added exogenously to Fms-like tyrosine kinase 3 ligand (Flt3L)-mobilized splenic DCs. We identified the exogenously added peptide, VDRFYKTLRAEQASQ, and a second peptide, DRFYKLTRAEQASQ, derived from the original exogenously added 15-mer peptide. Furthermore, we demonstrated that our strategy works efficiently with HIV gag p24 protein when delivered, as vaccine protein, to Flt3L expanded mouse splenic DCs in vitro through the DEC-205 receptor. We found that the same MHC II-bound HIV gag p24 peptides, VDRFYKTLRAEQASQ and DRFYKLTRAEQASQ, were naturally processed from anti-DEC-205 HIV gag p24 protein and presented on DCs. The two identified VDRFYKTLRAEQASQ and DRFYKLTRAEQASQ MHC II-bound HIV gag p24 peptides elicited CD4+ T-cell mediated responses in vitro. Their presentation by DCs to antigen-specific T cells was inhibited by chloroquine (CQ), indicating that optimal presentation of these exogenously added peptides required uptake and vesicular trafficking in mature DCs. These results support the application of our strategy to identify and characterize peptide epitopes derived from vaccine proteins processed by DCs and thus has the potential to greatly accelerate DC-based vaccine development.
Leveraging Structure in Activity Recognition: Context and Spatiotemporal Dynamics

Title of dissertation: LEVERAGING STRUCTURE IN ACTIVITY RECOGNITION: CONTEXT AND SPATIOTEMPORAL DYNAMICS Sameh Khamis, Doctor of Philosophy, 2015 Dissertation directed by: Larry S. Davis Department of Computer Science Activity recognition is one of the fundamental problems of computer vision. An activity recognition system aims to identify the actions of humans from an image or a video. This problem has been historically approached in isolation, and typically as part of a multi-stage system, where tracking for instance is another part. However, recent work sheds light on how activity recognition is in fact entangled with other fundamental problems in the field. Tracking is one such instance, where the identity of each person is maintained across a video sequence. Scene classification is another example, where scene properties are identified from image data. Affordance reasoning is yet another, where the objects in the scene are assigned labels representing what types of actions can be performed upon them. In this thesis we build a joint formulation for activity recognition, modeling the aforementioned coupled problems as latent variables. Optimizing the objective function for this formulation allows us to recover a more accurate solution to activity recognition and simultaneously solutions to problems like tracking or scene classification. We first introduce a model that jointly solves tracking and activity recognition from videos. Instead of establishing tracks in a preprocessing step, the model solves a joint optimization problem, recovering actions and identities for every person in a video sequence. We then extend this model to include frame-level cues, where activity labels assigned to people in the same scene are inter-compatible through a scene-level label. In the second half of the thesis we look at an alternative formulation of the same problem, based on probabilistic logic. This new model leverages the same cues, temporal and spatial, through soft logic rules. This joint formulation can be efficiently solved, recovering both action labels and tracks. We finally introduce another model that reformulates action recognition in the multi-label setting, where each person can be performing more than one action at the same time. In this setting, a joint formulation can solve for all the likely actions of a person through explicit modeling of action label correlations. Finally, we conclude with a discussion of several challenges and how they can motivate viable future extensions. LEVERAGING STRUCTURE IN ACTIVITY RECOGNITION: CONTEXT AND SPATIOTEMPORAL DYNAMICS
Automatic Construction of Polarity-Tagged Corpus from HTML Documents

This paper proposes a novel method of building polarity-tagged corpus from HTML documents. The characteristics of this method is that it is fully automatic and can be applied to arbitrary HTML documents. The idea behind our method is to utilize certain layout structures and linguistic pattern. By using them, we can automatically extract such sentences that express opinion. In our experiment, the method could construct a corpus consisting of 126,610 sentences.
On 2-moment completeness of non pre-emptive, non anticipative work conserving scheduling policies in some single class queues

Completeness of some scheduling policies with mean waiting time performance measure is used quiet extensively in literature for dynamic control of multi-class queues due to its wide range of applications in computers, communication networks and manufacturing systems. For a single class queue, we introduce the idea of 2-moment completeness of a parametrized class of policies that also have to be non pre-emptive, non anticipative and work conserving. Significance of this idea lies in the importance of variance (or second moment) of waiting time in any queuing system. Some parametrized classes of policies are identified and shown to be 2-moment complete for M/M/1 queues. Some well known queue disciplines viz random order of service (ROS), Random Assigned Priority (RAP), etc., turn out to be 2-moment incomplete. We introduce a parametrized priority scheme that also turns out to be 2-moment incomplete. Further, few preemptive and anticipative scheduling disciplines are shown to have second moment beyond the achievable region of non pre-emptive, non anticipative and work conserving scheduling policies. Some optimal control problems are discussed to illustrate the possible applications of 2-moment complete parametrized set of policies.
Effects of the twin-arginine translocase on secretion of virulence factors, stress response, and pathogenesis

A novel secretion pathway originally found in plants has recently been discovered in bacteria and termed TAT, for “twin-arginine translocation,” with respect to the presence of an Arg-Arg motif in the signal sequence of TAT-secreted products. However, it is unknown whether the TAT system contributes in any way to virulence through the secretion of factors associated with pathogenesis or stress response. We found that the opportunistic pathogen Pseudomonas aeruginosa produces several virulence factors that depend on the TAT system for proper export to the periplasm, outer membrane, or extracellular milieu. We identified at least 18 TAT substrates of P. aeruginosa and characterized the pleiotropic phenotypes of a tatC deletion mutant. The TAT system proved essential for the export of phospholipases, proteins involved in pyoverdine-mediated iron-uptake, anaerobic respiration, osmotic stress defense, motility, and biofilm formation. Because all these traits have been associated with virulence, we studied the role of TAT in a rat lung model. A tatC mutant did not cause the typical multifocal pulmonary abscesses and did not evoke a heavy inflammatory host response compared with wild type, indicating that tatC mutant cells are attenuated for virulence. Because the TAT apparatus is well conserved among important bacterial pathogens yet absent in mammalian cells, it represents a potential target for novel antimicrobial compounds.