Miracle-dz/UniFAR-FTUs huggingface dataset:
Coding Error Exponents for Asymmetric Two-User Discrete Memoryless Source-Channel Systems

Consider transmitting two discrete memoryless correlated sources, consisting of a common and a private source, over a discrete memoryless multi-terminal channel with two transmitters and two receivers. At the transmitter side, the common source is observed by both encoders but the private source can only be accessed by one encoder. At the receiver side, both decoders need to reconstruct the common source, but only one decoder needs to reconstruct the private source. We hence refer to this system by the asymmetric 2-user source-channel system. In this work, we derive a universally achievable joint source-channel coding (JSCC) error exponent pair for the 2-user system by using a technique which generalizes Csiszár’s method [8] for the point-to-point (single-user) discrete memoryless source-channel system. We next investigate the largest convergence rate of asymptotic exponential decay of the system (overall) probability of erroneous transmission, i.e., the system JSCC error exponent. We obtain lower and upper bounds for the exponent. As a consequence, we establish the JSCC theorem with single letter characterization.
Beyond Supersymmetry and Quantum Symmetry (an introduction to braided groups and braided matrices)

This is a systematic introduction for physicists to the theory of algebras and groups with braid statistics, as developed over the last three years by the author. There are braided lines, braided planes, braided matrices and braided groups all in analogy with superlines, superplanes etc. The main idea is that the bose-fermi $\pm1$ statistics between Grassmannn coordinates is now replaced by a general braid statistics $\Psi$, typically given by a Yang-Baxter matrix $R$. Most of the algebraic proofs are best done by drawing knot and tangle diagrams, yet most constructions in supersymmetry appear to generalise well. Particles of braid statistics exist and can be expected to be described in this way. At the same time, we find many applications to ordinary quantum group theory: how to make quantum-group covariant (braided) tensor products and spin chains, action-angle variables for quantum groups, vector addition on $q$-Minkowski space and a semidirect product q-Poincar\'e group are among the main applications so far. Every quantum group can be viewed as a braided group, so the theory contains quantum group theory as well as supersymmetry. There also appears to be a rich theory of braided geometry, more general than super-geometry and including aspects of quantum geometry. Braided-derivations obey a braided-Leibniz rule and recover the usual Jackson $q$-derivative as the 1-dimensional case.
Toward Addressing the Issues of Site Selection in District Effectiveness Research: A Two-Level Hierarchical Linear Growth Model

Purpose: District effectiveness research (DER) is an emerging field concerned with identifying the organizational structures, administration, and leadership practices at the school district level that help districts find success with all of their students across the schools within the system. This work has mirrored much of the early school effectiveness research (SER). However, to date across the DER literature, site selection for in-depth studies of districts deemed “effective” has been haphazard and nonsystematic. This is problematic given the long history of critiques centered on site selection in SER. The purpose of this study is to address and adapt the critiques from SER to a method of site selection for DER and test the method using a large multiyear data set to identify districts that are significantly unusual and effective. Research Design: A two-level hierarchical linear growth model that nests multiple time points per district (Level 1) within districts (Level 2) was used to predict gains in district achievement for all school districts in the state of Ohio during a 7-year period, 2001-2002 through 2007-2008. Findings: Districts that statistically significantly outperformed their predicted gains in achievement, controlling for background and demographic variables over the period, are identified as possible sites for in-depth qualitative studies for DER in comparison to districts performing at the norm. Conclusions: This study proposes and tests a method for district identification in DER that addresses the critiques from SER through controlling for achievement covariates, modeling district gains over time, and examining the population of districts within an entire state.
Ultrafast folding of WW domains without structured aromatic clusters in the denatured state

Ultrafast-folding proteins are important for combining experiment and simulation to give complete descriptions of folding pathways. The WW domain family comprises small proteins with a three-stranded antiparallel β-sheet topology. Previous studies on the 57-residue YAP 65 WW domain indicate the presence of residual structure in the chemically denatured state. Here we analyze three minimal core WW domains of 38–44 residues. There was little spectroscopic or thermodynamic evidence for residual structure in either their chemically or thermally denatured states. Folding and unfolding kinetics, studied by using rapid temperature-jump and continuous-flow techniques, show that each domain folds and unfolds very rapidly in a two-state transition through a highly compact transition state. Folding half-times were as short as 17 μs at 25°C, within an order of magnitude of the predicted maximal rate of loop formation. The small size and topological simplicity of these domains, in conjunction with their very rapid two-state folding, may allow us to reduce the difference in time scale between experiment and theoretical simulation.
The effect of randomised exposure to different types of natural outdoor environments compared to exposure to an urban environment on people with indications of psychological distress in Catalonia

Introduction Experimental studies have reported associations between short-term exposure to natural outdoor environments (NOE) and health benefits. However, they lack insight into mechanisms, often have low external and ecological validity, and have rarely focused on people with some psycho-physiological affection. The aim of this study was to use a randomized, case-crossover design to investigate: (i) the effects of unconstrained exposure to real natural and urban environments on psycho-physiological indicators of people with indications of psychological distress, (ii) the possible differential effects of 30 and 30+180 minutes exposures, and (iii) the possible mechanisms explaining these effects. Material and methods People (n = 26) with indications of psychological distress were exposed to green (Collserola Natural Park), blue (Castelldefels beach) and urban (Eixample neighbourhood) environments in Catalonia. They were exposed to all environments in groups for a period of 30+180 minutes between October 2013 and January 2014. During the exposure period, participants were instructed to do what they would usually do in that environment. Before, during (at 30 and 30+180 minutes) and after each exposure, several psycho-physiological measures were taken: mood (measured as Total Mood Disturbance, TMD), attention capacity (measured as backwards digit-span task), stress levels (measures as salivary cortisol), systolic and diastolic blood pressure, heart rate, autonomous nervous system (assessed as heart rate variability and the indicators: low frequency power (LF), high frequency power (HF), ratio between LF and HF (LF:HF), and coefficients of component variance of LF, HF, and LF:HF). We also measured several potential mediators: air pollution, noise, physical activity, social interactions, and self-perceived restoration experience. Results When compared with responses to urban environment, we found statistically significantly lower TMD [-4.78 (-7.77, -1.79) points difference], and salivary cortisol [-0.21 (-0.34, -0.08) log nmol/L] in the green exposure environment, and statistically significantly lower TMD [-4.53 (-7.57, -1.49) points difference], and statistically significant favourable changes in heart rate variability indicators (specifically LF:HF and CCV-LF:HF with around -0.20 points of difference of the indicators) in the blue exposure environment. Physical activity and self-perceived restoration experience partially mediated the associations between NOE and TMD. Physical activity and air pollution partially mediated the associations between NOE and heart rate variability. Discussion and conclusions This study extends the existing evidence on the benefits of NOE for people's health. It also suggests NOE potential as a preventive medicine, specifically focusing on people with indications of psychological distress. Trial registration Clinicaltrials.gov NCT02624921
Secure and scalable match: overcoming the universal circuit bottleneck using group programs

Abstract Confidential Content-Based Publish/Subscribe (C-CBPS) is an interaction model that allows parties to exchange content while protecting their security and privacy interests. In this paper we advance the state of the art in C-CBPS by showing how all predicate circuits in NC1 (logarithmic-depth, bounded fan-in) can be confidentially computed by a broker while guaranteeing perfect information-theoretic security. Previous work could handle only strictly shallower circuits (e.g. those with depth O(ℑ)). We present three protocols—UGP-Match, FSGP-Match and OFSGP-Match—based on 2-decomposable randomized encodings of group programs for circuits in NC1. UGP-Match is conceptually simple and has a clean proof of correctness but its running time is a polynomial with a high exponent and hence impractical. FSGP-Match uses a “fixed structure” construction that reduces the exponent drastically and achieves efficiency and scalability. OFSGP-Match optimizes the group programs further to shave off a linear factor.
Enasidenib in mutant IDH2 relapsed or refractory acute myeloid leukemia.

Recurrent mutations in isocitrate dehydrogenase 2 (IDH2) occur in ∼12% of patients with acute myeloid leukemia (AML). Mutated IDH2 proteins neomorphically synthesize 2-hydroxyglutarate resulting in DNA and histone hypermethylation, which leads to blocked cellular differentiation. Enasidenib (AG-221/CC-90007) is a first-in-class, oral, selective inhibitor of mutant-IDH2 enzymes. This first-in-human phase 1/2 study assessed the maximum tolerated dose (MTD), pharmacokinetic and pharmacodynamic profiles, safety, and clinical activity of enasidenib in patients with mutant-IDH2 advanced myeloid malignancies. We assessed safety outcomes for all patients and clinical efficacy in the largest patient subgroup, those with relapsed or refractory AML, from the phase 1 dose-escalation and expansion phases of the study. In the dose-escalation phase, an MTD was not reached at doses ranging from 50 to 650 mg per day. Enasidenib 100 mg once daily was selected for the expansion phase on the basis of pharmacokinetic and pharmacodynamic profiles and demonstrated efficacy. Grade 3 to 4 enasidenib-related adverse events included indirect hyperbilirubinemia (12%) and IDH-inhibitor-associated differentiation syndrome (7%). Among patients with relapsed or refractory AML, overall response rate was 40.3%, with a median response duration of 5.8 months. Responses were associated with cellular differentiation and maturation, typically without evidence of aplasia. Median overall survival among relapsed/refractory patients was 9.3 months, and for the 34 patients (19.3%) who attained complete remission, overall survival was 19.7 months. Continuous daily enasidenib treatment was generally well tolerated and induced hematologic responses in patients for whom prior AML therapy had failed. Inducing differentiation of myeloblasts, not cytotoxicity, seems to drive the clinical efficacy of enasidenib. This trial was registered at www.clinicaltrials. gov as #NCT01915498.
Transcriptional Factor PU.1 Regulates Decidual C1q Expression in Early Pregnancy in Human

C1q is the first recognition subcomponent of the complement classical pathway, which in addition to being synthesized in the liver, is also expressed by macrophages and dendritic cells (DCs). Trophoblast invasion during early placentation results in accumulation of debris that triggers the complement system. Hence, both early and late components of the classical pathway are widely distributed in the placenta and decidua. In addition, C1q has recently been shown to significantly contribute to feto-maternal tolerance, trophoblast migration, and spiral artery remodeling, although the exact mechanism remains unknown. Pregnancy in mice, genetically deficient in C1q, mirrors symptoms similar to that of human preeclampsia. Thus, regulated complement activation has been proposed as an essential requirement for normal successful pregnancy. Little is known about the molecular pathways that regulate C1q expression in pregnancy. PU.1, an Ets-family transcription factor, is required for the development of hematopoietic myeloid lineage immune cells, and its expression is tissue-specific. Recently, PU.1 has been shown to regulate C1q gene expression in DCs and macrophages. Here, we have examined if PU.1 transcription factor regulates decidual C1q expression. We used immune-histochemical analysis, PCR, and immunostaining to localize and study the gene expression of PU.1 transcription factor in early human decidua. PU.1 was highly expressed at gene and protein level in early human decidual cells including trophoblast and stromal cells. Surprisingly, nuclear as well as cytoplasmic PU.1 expression was observed. Decidual cells with predominantly nuclear PU.1 expression had higher C1q expression. It is likely that nuclear and cytoplasmic PU.1 localization has a role to play in early pregnancy via regulating C1q expression in the decidua during implantation.
Perturbed Chloride Homeostasis and GABAergic Signaling in Human Temporal Lobe Epilepsy

Changes in chloride (Cl−) homeostasis may be involved in the generation of some epileptic activities. In this study, we asked whether Cl− homeostasis, and thus GABAergic signaling, is altered in tissue from patients with mesial temporal lobe epilepsy associated with hippocampal sclerosis. Slices prepared from this human tissue generated a spontaneous interictal-like activity that was initiated in the subiculum. Records from a minority of subicular pyramidal cells revealed depolarizing GABAA receptor-mediated postsynaptic events, indicating a perturbed Cl− homeostasis. We assessed possible contributions of changes in expression of the potassium–chloride cotransporter KCC2. Double in situ hybridization showed that mRNA for KCC2 was absent from ∼30% of CaMKIIα (calcium/calmodulin-dependent protein kinase IIα)-positive subicular pyramidal cells. Combining intracellular recordings with biocytin-filled electrodes and KCC2 immunochemistry, we observed that all cells that were hyperpolarized during interictal events were immunopositive for KCC2, whereas the majority of depolarized cells were immunonegative. Bumetanide, at doses that selectively block the chloride-importing potassium–sodium–chloride cotransporter NKCC1, produced a hyperpolarizing shift in GABAA reversal potentials and suppressed interictal activity. Changes in Cl− transporter expression thus contribute to human epileptiform activity, and molecules acting on these transporters may be useful antiepileptic drugs.
BAFF promotes regulatory T-cell apoptosis and blocks cytokine production by activating B cells in primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is a chronic and slowly progressive cholestatic liver disease of autoimmune etiology. A number of questions regarding its etiology are unclear. CD4+CD25+ regulatory T cells (Tregs) play a critical role in self-tolerance and, for unknown reasons, their relative number is reduced in PBC patients. B-cell-activating factor (BAFF) is a key survival factor during B-cell maturation and its concentration is increased in peripheral blood of PBC patients. It has been reported that activated B cells inhibit Treg cell proliferation and there are no BAFF receptors on Tregs. Therefore, we speculated that excessive BAFF may result in Treg reduction via B cells. To prove our hypothesis, we isolated Tregs and B cells from PBC and healthy donors. BAFF and IgM concentrations were then analyzed by ELISA and CD40, CD80, CD86, IL-10, and TGF-β expression in B cells and Tregs were measured by flow cytometry. BAFF up-regulated CD40, CD80, CD86, and IgM expression in B cells. However, BAFF had no direct effect on Treg cell apoptosis and cytokine secretion. Nonetheless, we observed that BAFF-activated B cells could induce Treg cell apoptosis and reduce IL-10 and TGF-β expression. We also showed that BAFF-activated CD4+ T cells had no effect on Treg apoptosis. Furthermore, we verified that bezafibrate, a hypolipidemic drug, can inhibit BAFF-induced Treg cell apoptosis. In conclusion, BAFF promotes Treg cell apoptosis and inhibits cytokine production by activating B cells in PBC patients. The results of this study suggest that inhibition of BAFF activation is a strategy for PBC treatment.
Uniform Signal Redundancy of Parasol and Midget Ganglion Cells in Primate Retina

The collective representation of visual space in high resolution visual pathways was explored by simultaneously measuring the receptive fields of hundreds of ON and OFF midget and parasol ganglion cells in isolated primate retina. As expected, the receptive fields of all four cell types formed regular mosaics uniformly tiling the visual scene. Surprisingly, comparison of all four mosaics revealed that the overlap of neighboring receptive fields was nearly identical, for both the excitatory center and inhibitory surround components of the receptive field. These observations contrast sharply with the large differences in the dendritic overlap between the parasol and midget cell populations, revealing a surprising lack of correspondence between the anatomical and functional architecture in the dominant circuits of the primate retina.
Herpes Simplex Virus Immediate-Early ICP0 Protein Inhibits Toll-Like Receptor 2-Dependent Inflammatory Responses and NF-κB Signaling

ABSTRACT The discovery of the Toll-like receptors (TLRs) and their importance in the regulation of host responses to infection raised attention to the complex interplay between viral gene products and the host innate immune responses in determining the outcome of virus infection. Robust inflammatory cytokine responses are observed in herpes simplex virus (HSV)-infected animals and cells. Our studies have demonstrated that Toll-like receptor 2 (TLR2) activation by HSV results in NF-κB activation with concomitant inflammatory cytokine production and that TLR2 activation plays a critical role in HSV-induced pathology and mortality. Here we demonstrate that the HSV-1 immediate-early ICP0 protein reduces the TLR2-mediated inflammatory response to HSV 1 (HSV-1) infection. Expression of ICP0 alone is sufficient to block TLR2-driven responses to both viral and nonviral ligands at or downstream of the MyD88 adaptor and upstream of p65. ICP0 alone can also reduce the levels of MyD88 and Mal (TIRAP). In HSV-infected cells, the E3 ligase function of ICP0 and cellular proteasomal activity are required for the inhibitory activity. Our results argue for a model in which ICP0 promotes the degradation of TLR adaptor molecules and inhibition of the inflammatory response, much as it inhibits the interferon response by sequestration and degradation of interferon regulatory factor 3 (IRF-3).
Age-related deficit in a bimanual joint position matching task is amplitude dependent

The cognitive load associated with joint position sense increases with age but does not necessarily result in impaired performance in a joint position matching task. It is still unclear which factors interact with age to predict matching performance. To test whether movement amplitude and direction are part of such predictors, young and older adults performed a bimanual wrist joint position matching task. Results revealed an age-related deficit when the target limb was positioned far from (25°) the neutral position, but not when close to (15°, 5°) the neutral joint position, irrespective of the direction. These results suggest that the difficulty associated with the comparison of two musculoskeletal states increases towards extreme joint amplitude and that older adults are more vulnerable to this increased difficulty.
JOURNAL OF NEUROCHEMISTRY | 2009 | 110 | 1014–1027 doi: 10.1111/j.1471-4159.2009.06192.x

*Department of Medicine, University of Wisconsin and Geriatric Research, Education and Clinical Center, Veterans Administration Hospital, Madison, Wisconsin, USA Mammary Biology and Tumorigenesis Laboratory, National Cancer Institute, Bethesda, Maryland, USA Department of Biology, Tuskegee University, Tuskegee, Alabama, USA §OTB Research, Raleigh, North Carolina, USA ¶Institute of Pathology, Case Western Reserve University, Cleveland, Ohio, USA **School of Exercise, Biomedical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

Background The miniaturised and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. Results After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries was sufficient to study two mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Conclusions Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108) permitted to retrieve the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimising base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.
Procoagulant potential of platelet α granules

In this brief review of the literature it is pointed out that during platelet activation and degranulation platelet α granules leave the platelet interior through blebs in platelet plasma membrane and through the tips of the pseudopods, and then accumulate in the external milieu. There they undergo disintegration and secondary adhesion to the platelet plasma membranes. During their disintegration they expose their tightly packed GPIIb–IIIa complexes, annexin V stainable aminophospholipids, factor V, and the membrane markers CD62 and CD63. There is also demasking of lysosomal acid phosphatase activity and microvesicle formation. Lysosomal nature of platelet α granules is mentioned. It is suggested that platelet α granules are the sole source of platelet procoagulant activity and platelet microparticles (MP) or microvesicles (MV). The implications of this concept for antiplatelet therapy are discussed. A relationship of this process to tissue factor exposure and apoptosis is suggested.