Miracle-dz/UniFAR-FTUs huggingface dataset:
Adipokines from local fat cells shape the macrophage compartment of the creeping fat in Crohn's disease

Objective The creeping fat in Crohn's disease (CD) is infiltrated by macrophages; local adipokine levels are increased. This study aimed to link these observations to define a role for macrophages in the pathology of human CD. Methods Human peripheral blood CD14 cells were polarised in vitro into M1 and M2 macrophages. The effects on adipokine receptors, phenotypic surface markers, cytokines and chemokines were assessed after treatment with leptin and adiponectin. Immunohistochemistry visualised macrophage subtypes in samples of mesenteric fat tissue from patients with CD. The chemotactic potential of secreted macrophage products was determined by T cell migration and chemokine production in vitro. Results Although both adipokines altered the phenotype and function of M1 and M2 macrophages, M2 macrophages were more susceptible. M1 responded to leptin by increased cytokine production, but the stronger effect was seen in M2 macrophages with high expression of interleukin (IL)-10, IL-6 and tumour necrosis factor α. Adiponectin exerted similar effects and led to upregulated mannose receptor expression by M2 macrophages. Large macrophage numbers within the mesenteric fat tissue of patients with CD comprise a unique infiltration predominantly of M2 macrophages, leading to an IL-10-rich environment. While leptin increased the potency of both subtypes to attract CD3 T cells, adiponectin only affected M2 macrophages. Conclusion The adipocyte-dependent microenvironment within the creeping fat of patients with CD modulates the local macrophage compartment to a preference for the M2 subtype. The findings in this study with human cells suggest a protective role for the mesenteric fat in CD in terms of an enveloping barrier with the potential to limit intestinal inflammation.
Alcohol consumption and marital status of French women in the GAZEL cohort: a longitudinal analysis between 1992 and 1996.

OBJECTIVE The purpose of this research was to describe women's consumption of alcoholic beverages as it related to their marital status over a 5-year period (1992 through 1996) and to study alcohol consumption around the time of marriage or divorce. METHOD The study sample comprised 4,782 women who worked for Electricité de France-Gaz de France and belonged to the GAZEL cohort. The relevant variables collected by five successive annual questionnaires included marital status and alcohol consumption characteristics. Marginal models were used, reflecting the fact that the data were not independent. RESULTS Divorcees and widows drank less than married women as measured in fewer glasses per day and fewer days per week drinking wine. Women in the oldest generation drank more than the younger women. Getting married was accompanied by an increased level of drinking, especially of wine, beginning a year before the wedding and lasting until 4 years after it. Consumption declined briefly during the year after a divorce. CONCLUSIONS These results may be useful for designing prevention programs aimed at groups of women in the general population in France.
Economic Mechanism Design for Computerized Agents

The field of economic mechanism design has been an active area of research in economics for at least 20 years. This field uses the tools of economics and game theory to design "rules of interaction" for economic transactions that will, in principle, yield some desired outcome. In this paper I provide an overview of this subject for an audience interested in applications to electronic commerce and discuss some special problems that arise in this context.
Identification of Outer Membrane and Exoproteins of Carbapenem-Resistant Multilocus Sequence Type 258 Klebsiella pneumoniae

Carbapenem-resistant Klebsiella pneumoniae strains have emerged as a cause of life-threatening infections in susceptible individuals (e.g., transplant recipients and critically ill patients). Strains classified as multilocus sequence type (ST) 258 are among the most prominent causes of carbapenem-resistant K. pneumoniae infections worldwide, but the basis for the success of this lineage remains incompletely determined. To gain a more comprehensive view of the molecules potentially involved in the success of ST258, we used a proteomics approach to identify surface-associated and culture supernatant proteins produced by ST258. Protein samples were prepared from varied culture conditions in vitro, and were analyzed by a combination of two-dimensional electrophoresis and liquid chromatography followed by tandem mass spectrometry (LC-MS/MS). We identified a total of 193 proteins in outer membrane preparations from bacteria cultured in Luria-Bertani broth (LB) or RPMI 1640 tissue culture media (RPMI). Compared with LB, several iron-acquisition proteins, including IutA, HmuR, HmuS, CirA, FepA, FitA, FoxA, FhuD, and YfeX, were more highly expressed in RPMI. Of the 177 proteins identified in spent media, only the fimbrial subunit, MrkA, was predicted to be extracellular, a finding that suggests few proteins (or a limited quantity) are freely secreted by ST258. Notably, we discovered 203 proteins not reported in previous K. pneumoniae proteome studies. In silico modeling of proteins with unknown function revealed several proteins with beta-barrel transmembrane structures typical of porins, as well as possible host-interacting proteins. Taken together, these findings contribute several new targets for the mechanistic study of drug-resistance and pathogenesis by ST258 K. pneumoniae isolates.
Treatment of Foot and Ankle Neuroma Pain With Processed Nerve Allografts

Background: Localized nerve pain in the foot and ankle can be a chronic source of disability after trauma and has been identified as the most common complication following operative interventions in the foot and ankle. The superficial location of the injured nerves and lack of suitable tissue for nerve implantation make this pain refractory to conventional methods of neuroma management. We describe a novel strategy for management using processed nerve allografts to bridge nerve gaps created by resection of both end neuromas and neuromas-in-continuity. Methods: A retrospective review of a prospectively maintained database was performed of all patients who received a processed nerve allograft for treatment of painful neuromas in the foot and ankle between May 2010 and June 2015. Patient demographic and operative information was obtained, as well as preoperative and postoperative pain assessments using a conventional ordinal scale and PROMIS (Patient Reported Outcomes Measurement Information System) Pain Behavior and Pain Interference assessments. Twenty-two patients were identified, with postoperative pain assessments occurring at a mean of 15.5 months after surgery. Results: Neuromas of the sural and superficial peroneal nerves were the most common diagnoses, with 3-cm nerve allografts being used as the interposition graft in the majority of cases. Eight patients had end neuromas and 18 patients had neuromas in continuity. Analysis of paired data demonstrated a mean ordinal pain score decrease of 2.6, with 24 and 31 percentage-point decreases in PROMIS Pain Behavior and Pain Interference measures, respectively. All changes were significant (P < .002). Conclusion: The painful sequelae of superficial nerve injuries in the foot and ankle was significantly improved with complete excision of the involved nerve segment followed by bridging of the resulting nerve gap with a processed nerve allograft. This approach limits surgery to the site of injury and reconstitutes the peripheral nerve anatomy. Level of Evidence: Level IV, retrospective case series.
The reconstitution of CD45RBhiCD4+ naive T cells is inversely correlated with donor age in murine allogeneic haematopoietic stem cell transplantation

A high incidence of opportunistic infections after unrelated bone marrow transplantation has been reported. Delayed lymphocyte recovery may be associated with opportunistic infections. Immune reconstitution is influenced by recipient age and graft‐vs‐host disease (GVHD). In fact, children develop GVHD less frequently than adults. However, the role of donor age is largely unknown. We examined the effect of donor age on lymphocyte reconstitution after transplant. Three‐month‐old BALB/c recipient mice were lethally irradiated and transplanted with allogeneic haematopoietic stem cells from A/J donor mice of different ages, ranging from 0 d to 12 months. The recovery of absolute lymphocyte counts and those of CD3+ T cells, CD4+ T cells and CD45RBhi CD4+ naive T cells in the early post‐transplant period correlated inversely with donor age. Recipient mice transplanted with haematopoietic stem cells from younger donors showed significantly higher survival rates and mitogenic responses than adult donors. As T cells, especially CD4+ naive T cells, play an important role in host defence, faster recovery of CD4+ naive T cells in younger donors may contribute to reduced mortality in the early post‐transplant period. The results suggest that it could be better to choose a younger donor if sufficient cell dose is available.
Comparative analysis of transverse intrafascicular multichannel, longitudinal intrafascicular and multipolar cuff electrodes for the selective stimulation of nerve fascicles

The selection of a suitable nerve electrode for neuroprosthetic applications implies a trade-off between invasiveness and selectivity, wherein the ultimate goal is achieving the highest selectivity for a high number of nerve fascicles by the least invasiveness and potential damage to the nerve. The transverse intrafascicular multichannel electrode (TIME) is intended to be transversally inserted into the peripheral nerve and to be useful to selectively activate subsets of axons in different fascicles within the same nerve. We present a comparative study of TIME, LIFE and multipolar cuff electrodes for the selective stimulation of small nerves. The electrodes were implanted on the rat sciatic nerve, and the activation of gastrocnemius, plantar and tibialis anterior muscles was recorded by EMG signals. Thus, the study allowed us to ascertain the selectivity of stimulation at the interfascicular and also at the intrafascicular level. The results of this study indicate that (1) intrafascicular electrodes (LIFE and TIME) provide excitation circumscribed to the implanted fascicle, whereas extraneural electrodes (cuffs) predominantly excite nerve fascicles located superficially; (2) the minimum threshold for muscle activation with TIME and LIFE was significantly lower than with cuff electrodes; (3) TIME allowed us to selectively activate the three tested muscles when stimulating through different active sites of one device, both at inter- and intrafascicular levels, whereas selective activation using multipolar cuff (with a longitudinal tripolar stimulation configuration) was only possible for two muscles, at the interfascicular level, and LIFE did not activate selectively more than one muscle in the implanted nerve fascicle.
AMp: a highly parallel atomic multicast protocol

This paper deals with the problem of reliable group communication for distributed applications, in the context of the Reliable Broadcast class of protocols. An atomic multicast protocol for token passing Lans is presented. The actual implementation is on an 8802/4 Token-bus, although it is applicable to 8802/5 Token-rings and the FDDI Fibre-Optic network. The simplicity and efficiency of reliable broadcast protocols may be considerably improved, if the system fault model is restricted or convenient architectures are used. Fail-controlled communication components are used here to build an efficient reliable multicast protocol on top of the exposed MAC interface of a VLSI Lan controller. The architecture is built on standard Lans, in view of taking advantage of the availability of communications hardware and the possibility of coexistence with standard stations, in the same network. The service offered allows transparent multicasting inside logical groups, which are dynamically created and updated. The primitive is highly parallel and provides atomic agreement and consistent delivery order, respecting logical precedence. These features are an important contribution for the implementation of high performance distributed computing systems.
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs

The analysis of the sequence-structure relationship in RNA molecules is not only essential for evolutionary studies but also for concrete applications such as error-correction in next generation sequencing (NGS) technologies. The prohibitive sizes of the mutational and conformational landscapes, combined with the volume of data to process, require efficient algorithms to compute sequence-structure properties. In this article, we address the correction of NGS errors by calculating which mutations most increase the likelihood of a sequence to a given structure and RNA family. We introduce RNApyro, an efficient, linear time and space inside-outside algorithm that computes exact mutational probabilities under secondary structure and evolutionary constraints given as a multiple sequence alignment with a consensus structure. We develop a scoring scheme combining classical stacking base-pair energies to novel isostericity scores and apply our techniques to correct pointwise errors in 5s and 16s rRNA sequences. Our results suggest that RNApyro is a promising algorithm to complement existing tools in the NGS error-correction pipeline.
Knowledge Derived From Wikipedia For Computing Semantic Relatedness

Wikipedia provides a semantic network for computing semantic relatedness in a more structured fashion than a search engine and with more coverage than WordNet. We present experiments on using Wikipedia for computing semantic relatedness and compare it to WordNet on various benchmarking datasets. Existing relatedness measures perform better using Wikipedia than a baseline given by Google counts, and we show that Wikipedia outperforms WordNet on some datasets. We also address the question whether and how Wikipedia can be integrated into NLP applications as a knowledge base. Including Wikipedia improves the performance of a machine learning based coreference resolution system, indicating that it represents a valuable resource for NLP applications. Finally, we show that our method can be easily used for languages other than English by computing semantic relatedness for a German dataset.
The Presence and Role of the Tetrodotoxin-Resistant Sodium Channel Nav1.9 (NaN) in Nociceptive Primary Afferent Neurons

This is the first examination of sensory receptive properties and associated electrophysiological properties in vivo of dorsal root ganglion (DRG) neurons that express the TTX-resistant sodium channel Nav1.9 (NaN). Intracellular recordings in lumbar DRGs in Wistar rats enabled units with dorsal root C-, Aδ-, or Aα/β-fibers to be classified as nociceptive, low-threshold mechanoreceptive (LTM), or unresponsive. Intracellular dye injection enabled subsequent immunocytochemistry for Nav1.9-like immunoreactivity (Nav1.9-LI). Nav1.9-LI was expressed selectively in nociceptive-type (C- and A-fiber nociceptive and C-unresponsive) units. Of the nociceptive units, 64, 54, and 31% of C-, Aδ-, and Aα/β-fiber units, respectively, were positive for Nav1.9-LI. C-unresponsive units were included in the nociceptive-type group on the basis of their nociceptor-like membrane properties; 91% were positive. Nav1.9-LI was undetectable in Aδ- or Aα/β-fiber LTM units and in one C-LTM unit. Nav1.9-LI intensity was correlated negatively with soma size and conduction velocity in nociceptive units and with conduction velocity in C-fiber units. There was a positive correlation with action potential rise time in nociceptive-type units with membrane potentials equal to or more negative than –50 mV. The data provide direct evidence that Nav1.9 is expressed selectively in (but not in all) C- and A-fiber nociceptive-type units and suggest that Nav1.9 contributes to membrane properties that are typical of nociceptive neurons.
Selective Capability of SynCAM and Neuroligin for Functional Synapse Assembly

Synaptic cell adhesion is central for synapse formation and function. Recently, the synaptic cell adhesion molecules neuroligin 1 (NL1) and SynCAM were shown to induce presynaptic differentiation in cocultured neurons when expressed in a non-neuronal cell. However, it is uncertain how similar the resulting artificial synapses are to regular synapses. Are these molecules isofunctional, or do all neuronal cell adhesion molecules nonspecifically activate synapse formation? To address these questions, we analyzed the properties of artificial synapses induced by NL1 and SynCAM, compared the actions of these molecules with those of other neuronal cell adhesion molecules, and examined the functional effects of NL1 and SynCAM overexpression in neurons. We found that only NL1 and SynCAM specifically induced presynaptic differentiation in cocultured neurons. The induced nerve terminals were capable of both spontaneous and evoked neurotransmitter release, suggesting that a full secretory apparatus was assembled. By all measures, SynCAM- and NL1-induced artificial synapses were identical. Overexpression in neurons demonstrated that only SynCAM, but not NL1, increased synaptic function in immature developing excitatory neurons after 8 d in vitro. Tests of chimeric molecules revealed that the dominant-positive effect of SynCAM on synaptic function in developing neurons was mediated by its intracellular cytoplasmic tail. Interestingly, morphological analysis of neurons overexpressing SynCAM or NL1 showed the opposite of the predictions from electrophysiological results. In this case, only NL1 increased the synapse number, suggesting a role for NL1 in morphological synapse induction. These results suggest that both NL1 and SynCAM act similarly and specifically in artificial synapse induction but that this process does not reflect a shared physiological function of these molecules.
Literature Survey : Non-Negative Matrix Factorization

This article surveys recent research on Non-Negative Matrix Factorization (NNMF), a relatively new technique for dimensionality reduction. It is based on the idea that in many data-processing tasks, negative numbers are physically meaningless. The NNMF technique addresses this problem by placing non-negativity constraints on the data model. I discuss the applications of NNMF, the algorithms and the qualitative results. Since many of the algorithms proposed for NNMF seem to lack a firm theoretical foundation, this article also surveys techniques for proving that iterative algorithms converge. It concludes with a description of additional investigations which are presently underway.
lacP1 Promoter with an Extended – 10 Motif

The cyclic AMP receptor protein (CRP), which activates transcription from the wild-type lacP1 promoter and most of its mutants, represses productive RNA synthesis from a lacP1 promoter variant that contains an extended -10 element, although CRP enhances RNA polymerase binding as well as open complex formation in both promoters. Moreover, abortive RNA synthesis, which is already higher in the extended -10 variant compared with the parent promoter, was further enhanced by CRP. These results, together with the observed decrease in productive RNA synthesis, indicate that CRP, while facilitating the earlier steps of initiation, inhibits transcription from the extended -10 lacP1 by hindering promoter clearance. We propose that CRP decreases energetic barriers to RNA polymerase binding, isomerization, and abortive RNA synthesis but stabilizes the abortive RNA initiating complex, which results in increasing the activation energy of the transition state before the elongation complex. The results demonstrate for the first time that a DNA-binding regulatory protein acts as an activator or a repressor in different steps of the transcription initiation pathway because of the energetic differences of the intermediate complex in the same promoter.
Induction of DNA Strand Breaks in Peripheral Lymphocytes by Soluble Chromium Compounds

1 Incubation of human lymphocytes with sodium dichromate (CrVI) at 37°C for 3 h resulted in a dose-dependent increase in DNA strand breaks without concurrent cytotoxicity. In contrast, chromium acetate hydroxide (CrIII) failed to induce DNA strand breaks at sub-cytotoxic concentrations. 2 DNA strand breaks were also detected in the peripheral lymphocytes of Wistar rats, 24 h after intratracheal instillation of sodium dichromate (1.3 and 2.5 mg kg-1 ). Instillation of chromium acetate hydroxide (up to 21.8 mg kg -1) failed to induce DNA strand breaks in peripheral lymphocytes. In accord with previous studies, hexavalent chromium was found to be more readily absorbed from the lungs into the peripheral blood than chromium in its trivalent form. 3 The results of this study indicate that fluorometric analysis of DNA unwinding (FADU) in peripheral lymphocytes might be a convenient method of measuring an important biological effect of chromium in occupationally-exposed workers.
Semidefinite Programming Approach to Gaussian Sequential Rate-Distortion Trade-Offs

Sequential rate-distortion (SRD) theory provides a framework for studying the fundamental trade-off between data-rate and data-quality in real-time communication systems. In this paper, we consider the SRD problem for multi-dimensional time-varying Gauss-Markov processes under mean-square distortion criteria. We first revisit the sensor-estimator separation principle, which asserts that considered SRD problem is equivalent to a joint sensor and estimator design problem in which data-rate of the sensor output is minimized while the estimator's performance satisfies the distortion criteria. We then show that the optimal joint design can be performed by semidefinite programming. A semidefinite representation of the corresponding SRD function is obtained. Implications of the obtained result in the context of zero-delay source coding theory and applications to networked control theory are also discussed.
Quantifying the Microvascular Origin of BOLD-fMRI from First Principles with Two-Photon Microscopy and an Oxygen-Sensitive Nanoprobe

The blood oxygenation level-dependent (BOLD) contrast is widely used in functional magnetic resonance imaging (fMRI) studies aimed at investigating neuronal activity. However, the BOLD signal reflects changes in blood volume and oxygenation rather than neuronal activity per se. Therefore, understanding the transformation of microscopic vascular behavior into macroscopic BOLD signals is at the foundation of physiologically informed noninvasive neuroimaging. Here, we use oxygen-sensitive two-photon microscopy to measure the BOLD-relevant microvascular physiology occurring within a typical rodent fMRI voxel and predict the BOLD signal from first principles using those measurements. The predictive power of the approach is illustrated by quantifying variations in the BOLD signal induced by the morphological folding of the human cortex. This framework is then used to quantify the contribution of individual vascular compartments and other factors to the BOLD signal for different magnet strengths and pulse sequences.