Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional quartet by CD4+ T cells: a concerto of multiple cytokines

The differentiation of thymus-derived naive CD4+ T cells into distinct cell lineages upon activation enables them to provide help or to suppress other immune cells, thereby orchestrating varied immune responses against foreign and self antigens. The generation of two distinct subsets of CD4+ T helper (Th) cells (Th1 and Th2) was described over 20 years ago on the basis of different sets of cytokines secreted after activation and differentiation of naive CD4+ cells; each subset proved to mediate different patterns of immune responses [1]. Th1 cells secrete IFN-γ to protect against intracellular microbe infections, mediate organ-specific autoimmunity and eliminate cancer cells. In contradistinction, Th2 cells secrete IL-3, IL-4, IL-5 and IL-13 to regulate humoral immune responses, defend against parasites and mediate allergy and asthma. It was discovered that dendritic cells (DCs) recognize different pathogens via microbial pattern-recognition receptors (PRRs) and translate these signals into factors polarizing Th1 and Th2 cells [2]. Toll-like receptors (TLRs), which discriminate between different types of pathogens, are the most common PRRs involved in this process. For instance, the binding of TLRs with bacteria ligands, such as unmethylated CpG and lipopolysaccharide, turn immature DCs into IL-12-producing and Th1-promoting DCs (DC1). The PRRs that mediate Th2-promoting DCs (DC2) still need to be determined [2,3]. Cytokines that are secreted from DCs or other cells are critical for the polarization of Th1 and Th2 cells. For Th1 cell differentiation upon T-cell receptor (TCR) stimulation, IFN-γ activates signal transducer and activator of transcription (STAT)1, which in turn induces the transcription factor T-box expressed in T cells (T-bet). T-bet promotes IFN-γ production and expression of IL-12 receptor (IL-12Rβ2), facilitating IL-12-induced IFN-γ production and continuous development of Th1 cells. By contrast, Th2 differentiation is initiated by coordinate signaling through the TCR and IL-4 receptor/STAT6, which induce the expression of the zinc finger transcription factor GATA3; GATA3 is the master regulator that enables expression of Th2 cytokines [4]. Interestingly, Th1 and Th2 differentiation are mutually antagonistic. High levels of IFN-γ , IL-12 and Tbet inhibit GATA3 expression and Th2 differentiation [5], whereas increased levels of IL-4 and GATA3 downregulate T-bet expression and Th1 differentiation [6]. Therefore, IFN-γ and IL-4 serve as autocrines for Th1 and Th2 subsets, respectively, and are inhibitors to the opposite subsets. Owing to genetic imprinting, dividing committed subsets maintain polarization throughout the process of clonal expansion, which facilitates the development of more cells of the same subset for optimal effector function of desired immune responses.
In vivo studies on the positive control function of NifA: a conserved hydrophobic amino acid patch at the central domain involved in transcriptional activation

The eubacterial enhancer‐binding proteins activate transcription by binding to distant sites and, simultaneously, contacting the RNA polymerase σ54 promoter complex (Eσ54). The positive control function is located at the central domain of these proteins, but it is not know which specific region has the determinants for the interaction with Eσ54. Here, we present genetic evidence that a small region of hydrophobic amino acids, previously denominated C3, at the central domain of Bradyrhizobium japonicum NifA is involved in positive control. We obtained 26 missense mutants along this conserved region. Among these, only strains expressing the NifAF307→Y and NifAA310→S mutant proteins retained some of the transcriptional activity (< 20%), whereas those carrying NifAE298→D and NifAT308→S had very low but detectable activity (< 1.0%). The rest of the NifA mutants did not induce any measurable transcriptional activity. When expressed in the presence of wild‐type NifA, the great majority of the mutants displayed a dominant phenotype, suggesting that their oligomerization determinants were not altered. In vivo dimethyl‐sulphate footprinting experiments for a subset of the NifA mutants showed that they were still able to bind specifically to DNA. Analysis of intragenic supressors highlight the functional role of a hydroxyl group at position 308 to activate transcription.
Using the “reverse Warburg effect” to identify high-risk breast cancer patients

We have recently proposed a new model of cancer metabolism to explain the role of aerobic glycolysis and L-lactate production in fueling tumor growth and metastasis. In this model, cancer cells secrete hydrogen peroxide (H2O2), initiating oxidative stress and aerobic glycolysis in the tumor stroma. This, in turn, drives L-lactate secretion from cancer-associated fibroblasts. Secreted L-lactate then fuels oxidative mitochondrial metabolism (OXPHOS) in epithelial cancer cells, by acting as a paracrine onco-metabolite. We have previously termed this type of two-compartment tumor metabolism the “Reverse Warburg Effect,” as aerobic glycolysis takes place in stromal fibroblasts, rather than epithelial cancer cells. Here, we used MCT4 immuno-staining of human breast cancer tissue microarrays (TMAs; > 180 triple-negative patients) to directly assess the prognostic value of the “Reverse Warburg Effect. ” MCT4 expression is a functional marker of hypoxia, oxidative stress, aerobic glycolysis, and L-lactate efflux. Remarkably, high stromal MCT4 levels (score = 2) were specifically associated with decreased overall survival (< 18% survival at 10 y post-diagnosis). In contrast, patients with absent stromal MCT4 expression (score = 0), had 10-y survival rates of ~97% (p-value < 10−32). High stromal levels of MCT4 were strictly correlated with a loss of stromal Cav-1 (p-value < 10−14), a known marker of early tumor recurrence and metastasis. In fact, the combined use of stromal Cav-1 and stromal MCT4 allowed us to more precisely identify high-risk triple-negative breast cancer patients, consistent with the goal of individualized risk-assessment and personalized cancer treatment. However, epithelial MCT4 staining had no prognostic value, indicating that the “conventional” Warburg effect does not predict clinical outcome. Thus, the “Reverse Warburg Effect” or “parasitic” energy-transfer is a key determinant of poor overall patient survival. As MCT4 is a druggable-target, MCT4 inhibitors should be developed for the treatment of aggressive breast cancers, and possibly other types of human cancers. Similarly, we discuss how stromal MCT4 could be used as a biomarker for identifying high-risk cancer patients that could likely benefit from treatment with FDA-approved drugs or existing MCT-inhibitors (such as, AR-C155858, AR-C117977, and AZD-3965).
Computational design of membrane proteins using RosettaMembrane

Computational membrane protein design is challenging due to the small number of high‐resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high‐throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins. Herein, Rosetta is benchmarked for membrane protein design. We evaluate strategies to cope with the often reduced quality of experimental membrane protein structures. Further, we test the usage of symmetry in design protocols, which is particularly important as many membrane proteins exist as homo‐oligomers. We compare a soluble scoring function with a scoring function optimized for membrane proteins, RosettaMembrane. Both scoring functions recovered around half of the native sequence when completely redesigning membrane proteins. However, RosettaMembrane recovered the most native‐like amino acid property composition. While leucine was overrepresented in the inner and outer‐hydrophobic regions of RosettaMembrane designs, it resulted in a native‐like surface hydrophobicity indicating that it is currently the best option for designing membrane proteins with Rosetta.
Polymorphic Types in Functional Logic Programming

The rewriting logic CRWL has been proposed as a semantic frame- work for higher-order functional logic programming, using applicative rewriting systems as programs and lazy narrowing as the goal solving procedure. We present an extension of CRWL with a polymorphic type system, and we investigate the consequences of type discipline both at the semantic level and at the operational level. Semanti- cally, models must be extended to incorporate a type universe. Oper- ationally, lazy narrowing must maintain suitable type information in goals, in order to guarantee well-typed computed answers. ∗This research has been partially supported by the Spanish National Project TIC98- 0445-C03-02 “TREND” and the Esprit BRA Working Group EP-22457 “CCLII”. A pre- liminary version of the paper, much shorter and including no proofs, was published as [20].
Irreversible Electroporation in Medicine

This is a brief introduction to the emerging field of irreversible electroporation in medicine. Certain electrical fields when applied across a cell can have as a sole effect the permeabilization of the cell membrane, presumable through the formation of nanoscale defects in the cell membrane. Sometimes this process leads to cell death, primarily when the electrical fields cause permanent permeabilization of the membrane and the consequent loss of cell homeostasis, in a process known as irreversible electroporation. This is an unusual mode of cell death that is not understood yet. While the phenomenon of irreversible electroporation may have been known for centuries it has become only recently rigorously considered in medicine for various applications of tissue ablation. A brief historical perspective of irreversible electroporation is presented and recent studies in the field are discussed.
Sequence-independent and reversible photocontrol of transcription/expression systems using a photosensitive nucleic acid binder

To understand non-trivial biological functions, it is crucial to develop minimal synthetic models that capture their basic features. Here, we demonstrate a sequence-independent, reversible control of transcription and gene expression using a photosensitive nucleic acid binder (pNAB). By introducing a pNAB whose affinity for nucleic acids is tuned by light, in vitro RNA production, EGFP translation, and GFP expression (a set of reactions including both transcription and translation) were successfully inhibited in the dark and recovered after a short illumination at 365 nm. Our results indicate that the accessibility of the protein machinery to one or several nucleic acid binding sites can be efficiently regulated by changing the conformational/condensation state of the nucleic acid (DNA conformation or mRNA aggregation), thus regulating gene activity in an efficient, reversible, and sequence-independent manner. The possibility offered by our approach to use light to trigger various gene expression systems in a system-independent way opens interesting perspectives to study gene expression dynamics as well as to develop photocontrolled biotechnological procedures.
Specific adaptive humoral response against a gp41 motif inhibits CD4 T-cell sensitivity to NK lysis during HIV-1 infection

Objective:We have recently found that during HIV-1 infection, CD4 T cells overexpress a ligand of the NK activating receptor NKp44 (NKp44L) and are sensitized to NK lysis. Expression of NKp44L is triggered by a motif (3S) from the gp41, highly conserved in all HIV-1 clades. The objectives were to determine whether anti-3S antibodies were produced, could counteract 3S-CD4 interactions and were correlated to CD4 cell count and NKp44L expression in HIV-infected patients. Design:Anti-3S antibodie production was studied in HIV-infected patients at various stages of the disease, including a longitudinal study in Asymptomatiques à Long Terme (ALT) patients. Methods:Specimens from 193 HIV-1 infected patients were examined. Anti-3S antibodies were detected by ELISA, and NKp44L expression was analysed by flow cytometry. NK cytotoxicity against CD4NKp44L cells was determined in the presence of anti-3S antibodies. Results:Anti-3S antibodies were detected in 28.5% of HIV-infected patients. They were positively correlated to CD4 cell counts (P = 0.01) and inversely correlated to NKp44L expression (P = 0.007). Particularly, in ALT patients, a longitudinal study revealed that the CD4 cell count slope differed according to the presence or absence of anti-3S antibodies (−0.98 cells/month versus −7.48 cells/month, P > 0.001). In addition, a clear inhibition of CD4NKp44L NK lysis was observed in relationship to anti-3S antibodies titres. Conclusions:These results strongly suggested that anti-3S antibodies might affect disease course in inhibiting NKp44L expression and CD4 sensitivity to NK lysis. In linking specific adaptive immunity to the innate immunity induced by the 3S motif, this study may have important implications for therapeutic vaccines against AIDS.
CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti.

BACKGROUND Polymorphisms in CYP2B6 are known to predict increased steady-state plasma concentrations of efavirenz. We characterized relationships between genetic polymorphisms and plasma efavirenz concentrations among 45 Haitians who initiated antiretroviral therapy in Port-au-Prince. METHODS An observational study characterized relationships between clinical factors, pharmacokinetics, and treatment response among antiretroviral-naive patients initiating once-daily treatment with efavirenz plus twice-daily treatment with zidovudine and lamivudine. Plasma drug concentrations were determined at weeks 2 and 4. Drug doses were directly observed by field workers or designated family members. We retrospectively characterized relationships between efavirenz concentrations and 50 single-nucleotide polymorphisms in CYP2B6 and several polymorphisms in CYP2A6, CYP3A4, CYP3A5, and ABCB1. RESULTS Plasma specimens for efavirenz analysis were obtained from study participants a mean (+/- standard deviation) of 13.9 +/- 1.6 h after they received the dose. As expected, CYP2B6 516G-->T was associated with increased plasma efavirenz concentrations (Spearman rho = 0.71; P < .001), as were 10 polymorphisms in linkage disequilibrium with 516G-->T. Distinct CYP2B6 polymorphisms were associated with decreased plasma efavirenz concentrations (greatest absolute rho = 0.48; P = .001). Associations were replicated by results from a recent pharmacokinetic study involving 34 healthy, human immunodeficiency virus-negative African Americans. CONCLUSIONS Relatively frequent CYP2B6 polymorphisms may predict decreased plasma efavirenz exposure in patients of African descent. If replicated in other cohorts, the implications of these novel associations for treatment response warrant further study.
Barriers to the initiation of, and persistence with, insulin therapy*

ABSTRACT Objectives: Many patients with Type 2 diabetes mellitus (DM) delay and/or discontinue the use of insulin. This study determined patient-perceived barriers to the initiation of, and persistence with, insulin therapy. Research design and methods: Patients ≥ 18 years with Type 2 DM and ≥ 1 elevated HbA1c test result (≥ 9%) were identified from computerized laboratory test results within a single healthcare system, a study limitation. Insulin use patterns were characterized by automated pharmacy claims data, and patients were classified into those who discontinued insulin use (discontinuers) or those who did not initiate insulin use (non-initiators). Telephone interviews were conducted to determine the barriers to initiation of, and persistence with, insulin therapy. Results: Response rates were 80.0% (73/91) for discontinuers and 82.0% (129/157) for non-initiators. Pharmacy claims data indicated that discontinuers stopped filling prescriptions for insulin; 46.6% of patients self-reported discontinuing insulin. The average time between first and last prescription for insulin among discontinuers was 4.9 years (SD = 4.4). The most common reasons for discontinuation were related to insulin injection (74.0%) and a doctor's advice not to use insulin (47.1%). In the non-initiator group, 86.1% were never advised by a healthcare provider to take insulin. Conclusions: These findings suggest that issues related to insulin injection are the primary reason patients with Type 2 DM discontinue insulin therapy. Understanding these patterns is important to develop interventions to overcome barriers to treatment and improve the medical outcomes of patients with Type 2 DM.
High-order Zames-Falb multiplier analysis using linear matrix inequalities

This paper proposes an algorithm for stability analysis of systems containing slope-restricted nonlinearities using high-order Zames-Falb multipliers. The main innovation in this paper is the use of a new congruence transformation which enables multipliers of twice the order of the linear part of the system to be used in a linear-matrix-inequality (LMI) framework for stability analysis. Although the use of such high-order multipliers increases computational requirements, various numerical examples show that the resulting stability bounds are sometimes less conservative than using other similar approaches.
Building an Inclusive Entrepreneurial Culture

The process through which entrepreneurial firms plan and achieve strategic growth and innovation often reflects a complex set of internal organizational challenges and opportunities. This paper specifically focuses on how entrepreneurs build internal cultures in order to stimulate and drive innovation and improve organizational effectiveness. Drawing upon both strategic-management and entrepreneurial-dynamics perspectives, the authors argue that sustained innovation requires moving beyond the characteristics of the entrepreneur towards an organization that will support a firm's growth by eliciting and directing additive contributions from the individuals working for these ventures. Results revealed that entrepreneurs were more likely to create high-performance and innovative ventures if they were able systematically to involve employees in the idea and opportunity-development stages of the firm. Implications for the strategic management of innovation in emerging entrepreneurial firms are further discussed.
A digital output piezoelectric accelerometer using CMOS-compatible AlN thin film

We have developed the digital output piezoelectric accelerometer using CMOS-compatible AlN thin films. The AlN thin films were deposited by sputtering. The multilayer of Pt/Ti/AlN/Pt/Ti/SiO2 has been fabricated into the piezoelectric accelerometers, where the patterned AlN thin films are arrayed in parallel and electrically connected in series. The sensitivity of the fabricated accelerometer reaches 184 mV/g, which is about 6 times larger than that of the accelerometer using Pb(Zr,Ti)O3 thin films. The results indicate that AlN thin film is more promising compared to PZT thin films to realize the digital output piezoelectric accelerometer.
Human immunodeficiency virus type 1 infection of human macrophages modulates the cytokine response to Pneumocystis carinii

The present studies examined production of the cytokines tumor necrosis factor alpha (TNF-alpha), interleukin-1 beta (IL-1 beta), and IL-6 by human monocyte-derived macrophages exposed to Pneumocystis carinii in vitro and the impact of concurrent macrophage infection with human immunodeficiency virus type 1 (HIV-1) on these cytokine responses. Macrophages were infected with the HIV-1 BaL monocytotropic strain for 10 to 14 days and then exposed to P. carinii. At various times following P. carinii treatment, culture supernatants were harvested to assess the cytokine profile. Addition of P. carinii to HIV-uninfected macrophages resulted in augmented production of IL-6, TNF-alpha, and IL-1 beta protein. By contrast, in HIV-infected macrophages exposed to P. carinii, only the release of IL-6 was increased compared with that for HIV-uninfected macrophages, while the levels of TNF-alpha and IL-1 beta decreased. This altered response was confirmed at the molecular level for TNF-alpha mRNA. Preventing physical contact between P. carinii and macrophages by a membrane filter inhibited all cytokine release. Substituting P. carinii with a preparation of P. carinii 95- to 115-kDa major membrane glycoprotein A yielded a response similar to that obtained by addition of intact P. carinii. These results suggest that HIV-1 infection of human macrophages modulates cytokine responses to P. carinii.
New insights into carbon acquisition and exchanges within the coral–dinoflagellate symbiosis under NH4+ and NO3− supply

Anthropogenic nutrient enrichment affects the biogeochemical cycles and nutrient stoichiometry of coastal ecosystems and is often associated with coral reef decline. However, the mechanisms by which dissolved inorganic nutrients, and especially nitrogen forms (ammonium versus nitrate) can disturb the association between corals and their symbiotic algae are subject to controversial debate. Here, we investigated the coral response to varying N : P ratios, with nitrate or ammonium as a nitrogen source. We showed significant differences in the carbon acquisition by the symbionts and its allocation within the symbiosis according to nutrient abundance, type and stoichiometry. In particular, under low phosphate concentration (0.05 µM), a 3 µM nitrate enrichment induced a significant decrease in carbon fixation rate and low values of carbon translocation, compared with control conditions (N : P = 0.5 : 0.05), while these processes were significantly enhanced when nitrate was replaced by ammonium. A combined enrichment in ammonium and phosphorus (N : P = 3 : 1) induced a shift in nutrient allocation to the symbionts, at the detriment of the host. Altogether, these results shed light into the effect of nutrient enrichment on reef corals. More broadly, they improve our understanding of the consequences of nutrient loading on reef ecosystems, which is urgently required to refine risk management strategies.
Development and preliminary validation of a pain measure specific to neuropathic pain

Article abstract-Neuropathic pain syndromes are commonly seen in clinical practice and are frequently used as pain models in testing new therapies. However, no pain scale exists with the primary purpose to measure pain in neuropathic syndromes. This paper describes the development and preliminary validation of the Neuropathic Pain Scale (NPS), which is designed to assess distinct pain qualities associated with neuropathic pain. Results support the discriminant and predictive validity of the NPS items. Moreover, the NPS items appear to be sensitive to treatments known to impact neuropathic pain. These findings provide support for the further development of the NPS. NEUROLOGY 1997;48: 332-338
Redefining pain

Medicine defines pain as a signal of physical injury to the body, despite evidence contradicting the tight linkage and despite the exclusion of vast numbers of sufferers who experience psychological pain. By broadening the definition to include both functionalist (or objectivist) and phenomenological (or subjectivist) features of pain, we would not only better accommodate the basic science of pain but would also recognize what is already appreciated by the layperson, that pain from diverse sources – physical and psychological – share an underlying felt structure.