Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Requirements for Expression of CD80/86 and CD40 on B Cells for T-Dependent Antibody Responses In Vivo

The CD80/86-CD28 and CD40-CD40 ligand costimulatory pathways are essential for Th cell-dependent B cell responses that generate high-affinity, class-switched Ab in vivo. Disruption of either costimulatory pathway results in defective in vivo humoral immune responses, but it remains unclear to what extent this is due to deficient activation of Th cells and/or of B cells. To address this issue, we generated mixed chimeras in which CD80/86- or CD40-deficient bone marrow-derived cells coexist with wild-type (WT) cells, thereby providing the functional T cell help and accessory cell functions required for fully competent B cell responses. We were then able to assess the requirement for CD80/86 or CD40 expression on B cells producing class-switched Ig in response to a T-dependent Ag. In CD80/86 WT plus CD80/86 double-knockout mixed chimeras, both WT- and CD80/86-deficient B cells produced IgG1 and IgE responses, indicating that direct signaling by CD80/86 is not essential for efficient B cell activation. In marked contrast, only WT IgG1 and IgE responses were detected in the chimeras containing CD40-deficient cells, demonstrating that CD40 expression on B cells is essential for class switching by those B cells. Thus, while disrupting either the CD80/86-CD28 or the CD40-CD40 ligand costimulatory pathway abrogates T-dependent B cell immune responses, the two pathways are nonredundant and mediated by distinct mechanisms.
Diagnostic performance of 3D TSE MRI versus 2D TSE MRI of the knee at 1.5 T, with prompt arthroscopic correlation, in the detection of meniscal and cruciate ligament tears*

Objective To compare the diagnostic performance of the three-dimensional turbo spin-echo (3D TSE) magnetic resonance imaging (MRI) technique with the performance of the standard two-dimensional turbo spin-echo (2D TSE) protocol at 1.5 T, in the detection of meniscal and ligament tears. Materials and Methods Thirty-eight patients were imaged twice, first with a standard multiplanar 2D TSE MR technique, and then with a 3D TSE technique, both in the same 1.5 T MRI scanner. The patients underwent knee arthroscopy within the first three days after the MRI. Using arthroscopy as the reference standard, we determined the diagnostic performance and agreement. Results For detecting anterior cruciate ligament tears, the 3D TSE and routine 2D TSE techniques showed similar values for sensitivity (93% and 93%, respectively) and specificity (80% and 85%, respectively). For detecting medial meniscal tears, the two techniques also had similar sensitivity (85% and 83%, respectively) and specificity (68% and 71%, respectively). In addition, for detecting lateral meniscal tears, the two techniques had similar sensitivity (58% and 54%, respectively) and specificity (82% and 92%, respectively). There was a substantial to almost perfect intraobserver and interobserver agreement when comparing the readings for both techniques. Conclusion The 3D TSE technique has a diagnostic performance similar to that of the routine 2D TSE protocol for detecting meniscal and anterior cruciate ligament tears at 1.5 T, with the advantage of faster acquisition.
Antibiogram, Adhesive Characteristics, and Incidence of Class 1 Integron in Aeromonas Species Isolated from Two South African Rivers

Aeromonas species are well distributed in freshwater environments, and their natural susceptibility to antimicrobials renders them interesting candidates for the survey of antimicrobial resistance in freshwater milieu. Water samples were collected from Kat and Tyume rivers in the Eastern Cape province of South Africa, and a total of 45 isolates identified as Aeromonas species were recovered from the two rivers. All Aeromonas isolates were resistant to oxacillin, penicillin, clindamycin, cephalothin, vancomycin, and rifamycin, while appreciable susceptibilities (89.3 : 94.1%, 82.1 : 94.1%, 85.7 : 88.2%, and 92.9 : 88.2%) were observed against ciprofloxacin, chloramphenicol, nitrofurantoin, and gentamicin from Kat and Tyume rivers, respectively. Multiple antibiotic resistance (MAR) indices ranged from 0.016 to 0.044 for the two rivers. Class 1 integron was detected in about 20% of the isolates, and all the isolates except one showed ability to produce biofilm in vitro as weak producers (53.33%), moderate producers (15.56%), and strong producers (28.9%). This investigation provides a baseline data on antibiotic resistance as well as the adhesive characteristics of Aeromonas isolates from Tyume and Kat rivers in the Eastern Cape province of South Africa.
DVS : Distributed Volatile Storage for low-latency read access

We describe the design and implementation of DVS, a distributed, fault-tolerant in-memory storage system for fast random access to large datasets. The storage has a key-value interface and is optimized for read performance. It is used as a cache for static data stored on slower durable mediums to accelerate access to large datasets, such as those used in bioinformatics. The key problems that DVS solves are data location on and data distribution to a dynamic set of servers. We show that DVS can speed up a real bioinformatics application by more than 100%.
Social Media and the Social Good: How Nonprofits Use Facebook to Communicate with the Public

In this study, we examine the social networking practices of the 100 largest nonprofit organizations in the United States. More specifically, we develop a comprehensive classification scheme to delineate these organizations' use of Facebook as a stakeholder engagement tool. We find that there are 5 primary categories of Facebook "statuses", which can be aggregated into three key dimensions - "information", "community", and "action". Our analysis reveals that, though the "informational" use of Facebook is still significant, nonprofit organizations are better at using Facebook to strategically engage their stakeholders via "dialogic" and "community-building" practices than they have been with traditional websites. The adoption of social media seems to have engendered new paradigms of public engagement.
Updates in answer set programming: An approach based on basic structural properties

Abstract We have studied the update operator ⊕1 defined for update sequences by Eiter et al. without tautologies and we have observed that it satisfies an interesting property. This property, which we call Weak Independence of Syntax (WIS), is similar to one of the postulates proposed by Alchourrón, Gärdenfors, and Makinson (AGM); only that in this case it applies to nonmonotonic logic. In addition, we consider other five additional basic properties about update programs and we show that ⊕1 satisfies them. This work continues the analysis of the AGM postulates with respect to the ⊕1 operator under a refined view that considers N2 as a monotonic logic which allows us to expand our understanding of answer sets. Moreover, N2 helped us to derive an alternative definition of ⊕1 avoiding the use of unnecessary extra atoms.
Application of nanometer size of polypyrrole as a suitable adsorbent for removal of Cr(VI)

The objective of this work was to investigate the sorption characteristics of polypyrrole (PPy) for the removal of Cr(VI) from aqueous solutions. The sorption process was carried out by a dynamic batch method in order to determine the optimum conditions. For a sorbent dose of 0.6 g in 100 mL of a Cr(VI) solution, at a contact time of 15 min and a pH of 3, a removal efficiency of 84.5% was achieved. The Morris–Weber and Lagergren equations, as well as a pseudo‐second‐order equation were examined to explore the kinetics of the removal process. In addition, the Langmuir, Freundlich, and Dubinin–Radushkevich isotherm models were applied to estimate the capacity, intensity, and energy of the sorption process. It was found that increasing temperature showed a positive effect on the ion sorption efficiency. In summary, PPy was shown to be a suitable candidate for chromium(VI) ion removal from aqueous solutions at different concentrations. J. VINYL ADDIT. TECHNOL. , 2011. © 2011 Society of Plastics Engineers.
Relation between endothelial cell apoptosis and blood flow direction in human atherosclerotic plaques.

BACKGROUND Blood flow characteristics influence endothelial cell apoptosis. However, little is known about the occurrence of endothelial cell apoptosis in human atherosclerosis and its relation to blood flow. METHODS AND RESULTS A total of 42 human carotid atherosclerotic plaques were retrieved by endarterectomy; they were examined in the longitudinal axial direction. Plaques were included in this study when upstream and downstream parts were clearly visible, occlusion was absent, and immunostaining for luminal endothelium was present all along the plaque. Using these criteria, 13 plaques were processed for further immunohistochemical studies (using anti-CD31, anti-Ki-67, and anti-splicing factor antibodies) and in situ detection of apoptosis (terminal dUTP nick end-labeling and ligase assay). Eight plaques showed > or =1 apoptotic endothelial cell at the luminal surface. Quantitative analysis of endothelial cell apoptosis in these plaques showed a systematic preferential occurrence of apoptosis in the downstream parts of plaques, where low flow and low shear stress prevail, in comparison with the upstream parts (18.8+/-3.3% versus 2.7+/-1.2%, respectively, P<0.001). Endothelial cell apoptosis was barely detectable in plaque microvessels. CONCLUSIONS Our results suggest that in vivo local shear stress influences luminal endothelial cell apoptosis and may be a major determinant of plaque erosion and thrombosis.
Interleukin-10 downregulates protective immunity to Brucella abortus

In vivo neutralization of interleukin-10 (IL-10) with an anti-IL-10 monoclonal antibody resulted in up to 10-fold fewer bacteria in the spleens of BALB/c mice infected with the virulent Brucella abortus strain 2308. In vitro neutralization of endogenous IL-10 in brucella antigen-stimulated cultures of splenocytes from infected mice resulted in increased gamma interferon production in these cultures, whereas exogenous recombinant IL-10 inhibited the ability of peptone-elicited peritoneal macrophages to control intracellular brucellae. These data suggest that IL-10 may be downregulating the immune response to B. abortus by affecting both macrophage effector function and the production of the protective Th1 cytokine gamma interferon.
Testing all six person-oriented principles in dynamic factor analysis

Abstract All six person-oriented principles identified by Sterba and Bauer's Keynote Article can be tested by means of dynamic factor analysis in its current form. In particular, it is shown how complex interactions and interindividual differences/intraindividual change can be tested in this way. In addition, the necessity to use single-subject methods in the analysis of developmental processes is emphasized, and attention is drawn to the possibility to optimally treat developmental psychopathology by means of new computational techniques that can be integrated with dynamic factor analysis.
Modeling the parameters for plasmodesmal sugar filtering in active symplasmic phloem loaders

Plasmodesmata (PD) play a key role in loading of sugars into the phloem. In plant species that employ the so-called active symplasmic loading strategy, sucrose that diffuses into their unique intermediary cells (ICs) is converted into sugar oligomers. According to the prevalent hypothesis, the oligomers are too large to pass back through PD on the bundle sheath side, but can pass on into the sieve element to be transported in the phloem. Here, we investigate if the PD at the bundle sheath-IC interface can indeed fulfill the function of blocking transport of sugar oligomers while still enabling efficient diffusion of sucrose. Hindrance factors are derived via theoretical modeling for different PD substructure configurations: sub-nano channels, slit, and hydrogel. The results suggest that a strong discrimination could only be realized when the PD opening is almost as small as the sugar oligomers. In order to find model parameters that match the in vivo situation, we measured the effective diffusion coefficient across the interface in question in Cucurbita pepo with 3D-photoactivation microscopy. Calculations indicate that a PD substructure of several sub-nano channels with a radius around 7 Å, a 10.4 Å-wide slit or a hydrogel with 49% polymer fraction would be compatible with the effective diffusion coefficient. If these configurations can accommodate sufficient flux of sucrose into the IC, while blocking raffinose and stachyose movement was assessed using literature data. While the slit-configuration would efficiently prevent the sugar oligomers from “leaking” from the IC, none of the configurations could enable a diffusion-driven sucrose flux that matches the reported rates at a physiologically relevant concentration potential. The presented data provides a first insight on how the substructure of PD could enable selective transport, but indicates that additional factors are involved in efficient phloem loading in active symplasmic loading species.
Interactive Authoring of Logical Forms for Multilingual Generation

We present an authoring system for logical forms encoded as conceptual graphs (CG). The system belongs to the family of WYSIWYM (What You See Is What You Mean) text generation systems: logical forms are entered interactively and the corresponding linguistic realization of the expressions is generated in several languages. The system maintains a model of the discourse context corresponding to the authored documents. The system helps users author documents formulated in the CG format. In a first stage, a domainspecific ontology is acquired by learning from example texts in the domain. The ontology acquisition module builds a typed hierarchy of concepts and relations derived from the WordNet and Verbnet. The user can then edit a specific document, by entering utterances in sequence, and maintaining a representation of the context. While the user enters data, the system performs the standard steps of text generation on the basis of the authored logical forms: reference planning, aggregation, lexical choice and syntactic realization – in several languages (we have implemented English and Hebrew and are exploring an implementation using the Bliss graphical language). The feedback in natural language is produced in real-time for every single modification performed by the author. We perform a cost-benefit analysis of the application of NLG techniques in the context of authoring cooking recipes in English and Hebrew. By combining existing large-scale knowledge resources (WordNet, Verbnet, the SURGE and HUGG realization grammars) and techniques from modern integrated software development environment (such as the Eclipse IDE), we obtain an efficient tool for the generation of logical forms, in domains where content is not available in the form of databases. ∗Research supported by the Israel Ministry of Science Knowledge Center for Hebrew Computational Linguistics and by the Frankel Fund
Language, executive function and social cognition in the diagnosis of frontotemporal dementia syndromes

Abstract Frontotemporal dementia (FTD) represents a spectrum of non-Alzheimer's degenerative conditions associated with focal atrophy of the frontal and/or temporal lobes. Frontal and temporal regions of the brain have been shown to be strongly involved in executive function, social cognition and language processing and, thus, deficits in these domains are frequently seen in patients with FTD or may even be hallmarks of a specific FTD subtype (i.e. relatively selective and progressive language impairment in primary progressive aphasia). In this review we have attempted to delineate how language, executive function, and social cognition may contribute to the diagnosis of FTD syndromes, namely the behavioural variant FTD as well as the language variants of FTD including the three subtypes of primary progressive aphasia (PPA): non-fluent/agrammatic, semantic and logopenic. This review also addresses the extent to which deficits in these cognitive areas contribute to the differential diagnosis of FTD versus Alzheimer’s disease (AD). Finally, early clinical determinants of pathology are briefly discussed and contemporary challenges to the diagnosis of FTD are presented.
The Power of Depth 2 Circuits over Algebras

We study the problem of polynomial identity testing (PIT) for depth 2 arithmetic circuits over matrix algebra. We show that identity testing of depth 3 (SPS) arithmetic circuits over a field F is polynomial time equivalent to identity testing of depth 2 (PS) arithmetic circuits over U2(F), the algebra of upper-triangular 2 2 matrices with entries from F. Such a connection is a bit surprising since we also show that, as computational models, PS circuits over U2(F) are strictly ‘weaker’ than SPS circuits over F. The equivalence further implies that PIT of SPS circuits reduces to PIT of width-2 commutative Algebraic Branching Programs(ABP). Further, we give a deterministic polynomial time identity testing algorithm for a PS circuit of size s over commutative algebras of dimension O(log s/ log log s) over F. Over commutative algebras of dimension poly(s), we show that identity testing of PS circuits is at least as hard as that of SPS circuits over F.
Continuum Theory for Strain‐Softening

In heterogeneous materials such as concretes or rocks, failure occurs by progressive distributed damage during which the material exhibits strain‐softening, i.e., a gradual decline of stress at increasing strain. It is shown that strain‐softening which is stable within finite‐size regions and leads to a nonzero energy dissipation by failure can be achieved by a new type of nonlocal continuum called the imbricate continuum. Its theory is based on the hypothesis that the stress depends on the change of distance between two points lying a finite distance apart. This continuum is a limit of a discrete system of imbricated (regularly overlapping) elements which have a fixed length, l, and a cross‐section area that tends to zero as the discretization is refined. The principal difference from the existing nonlocal continuum theory is that the equation of motion involves not only the averaging of strains but also the averaging of stress gradients. This assures that the finite element stiffness matrices are symmet.
Side effects of treatment with benzodiazepines.

BACKGROUND The use of benzodiazepine anxiolytics and hypnotics continues to excite controversy. Views differ from expert to expert and from country to country as to the extent of the problem, or even whether long-term benzodiazepine use actually constitutes a problem. Although as a class benzodiazepines act rapidly and are well tolerated, their use presents clinical issues such as dependence, rebound anxiety, memory impairment, and discontinuation syndrome. The aim of this article is to review literature regarding different side effects associated with treatment with benzodiazepines - effects on cognition, treatment with benzodiazepines during pregnancy, dependence on benzodiazepines and risk of falling. CONTENT ANALYSIS OF LITERATURE Literature research included structured searches of Medline and other publications on the subject of treatment with benzodiazepines, particularly effects on cognition, risk of falls, benzodiazepine dependence and treatment with benzodiazepines during pregnancy. CONCLUSION Results of investigations have revealed different side effects associated with treatment with benzodiazepines. Previous investigations showed that treatment with benzodiazepines may induce anterograde amnesia. Also, previous studies confirmed occurrence of physical dependence in high percentage of patients in long term treatment with benzodiazepines at therapeutic dosages. Some investigation suggested higher risk of oral cleft, the floppy infant syndrome, or marked neonatal withdrawal symptoms when using benzodiazepines during pregnany. Investigations have shown increased risk of falling in elderly persons taking benzodiazepines.
Modulation of Nitro-fatty Acid Signaling

Background: Nitroalkenes are electrophilic anti-inflammatory mediators that signal via Michael addition and are metabolized in vivo. Results: Prostaglandin reductase-1 is identified as a nitroalkene reductase. Conclusion: Prostaglandin reductase-1 reduces fatty acid nitroalkenes to nitroalkanes, inactivating electrophilic reactivity. Significance: A mammalian enzyme is identified that metabolizes fatty acid nitroalkenes in vivo to silence their signaling reactions. Inflammation, characterized by the activation of both resident and infiltrated immune cells, is accompanied by increased production of oxidizing and nitrating species. Nitrogen dioxide, the proximal nitrating species formed under these conditions, reacts with unsaturated fatty acids to yield nitroalkene derivatives. These electrophilic products modulate protein function via post-translational modification of susceptible nucleophilic amino acids. Nitroalkenes react with Keap1 to instigate Nrf2 signaling, activate heat shock response gene expression, and inhibit NF-κB-mediated signaling, inducing net anti-inflammatory and tissue-protective metabolic responses. We report the purification and characterization of a NADPH-dependent liver enzyme that reduces the nitroalkene moiety of nitro-oleic acid, yielding the inactive product nitro-stearic acid. Prostaglandin reductase-1 (PtGR-1) was identified as a nitroalkene reductase by protein purification and proteomic studies. Kinetic measurements, inhibition studies, immunological and molecular biology approaches as well as clinical analyses confirmed this identification. Overexpression of PtGR-1 in HEK293T cells promoted nitroalkene metabolism to inactive nitroalkanes, an effect that abrogated the Nrf2-dependent induction of heme oxygenase-1 expression by nitro-oleic acid. These results situate PtGR-1 as a critical modulator of both the steady state levels and signaling activities of fatty acid nitroalkenes in vivo.
Regulation of the Expression of Acetylcholinesterase by Muscular Activity in Avian Primary Cultures

Abstract: Primary cultures of avian muscle cells express both globular and asymmetric molecular forms of acetylchoiinesterase (AChE) when grown in a simple defined culture medium. Under these conditions, we analyzed the role of various agents interfering with muscular activity: tetrodotoxin (TTX) and veratridine, as well as a depolarizing concentration of KC1. These treatments caused the complete cessation of contractions in mature myotubes. We observed no influence on cellular AChE activity. The paralyzing treatments induced different effects on AChE secretion: TTX increased the secretion by ∼25%, whereas KC1 and veratridine reduced it by ∼30%. The proportions of secreted molecular forms (mostly hydrophilic G4 and G2) were not modified significantly. TTX did not affect the pattern of molecular forms of cellular AChE (in particular, the proportion of A forms was not changed). Depolarization by veratridine or KC1 induced an increase in the proportion of A forms in mature myotubes by a factor of 2–3. Similar results were obtained with quail myotubes cultured under the same conditions. This study shows that, in avian muscle cultures, the ionic balance across myotube membranes, rather than muscular activity per se, can regulate the level of A forms and the rate of AChE secretion. These results do not exclude the possible involvement of other factors, such as Ca2+ and/or peptidic factors. In addition, taking together our results and data from the literature, we conclude that the expression of AChE molecular forms depends both on the species and on the culture conditions used.