Miracle-dz/UniFAR-FTUs huggingface dataset:
Agonists binding nicotinic receptors elicit specific channel‐opening patterns at αγ and αδ sites

High‐resolution patch clamp currents evoked by epibatidine (Ebd), carbamylcholine (CCh) and acetylcholine (ACh) were compared. Ebd binds with 75‐fold higher affinity at αγ than at αδ sites, whereas CCh and ACh prefer αδ sites of nicotinic ACh receptor (nAChR) channels. Similar short (τO1), intermediate (τO2) and long (τO3) types of opening were observed. τO2 openings were maximally prevalent at low Ebd concentrations, binding at αγ sites, whereas τO1 openings appear to be generated at αδ sites. Short (∼0.75 ms) bursts of openings (τB1) arise from the αγ site, and long (>10 ms) bursts (τB2) arise from double liganded receptors. The duration of bursts and of openings within bursts depended on the agonist. Limited by the temporal resolution, the closings within bursts were invariant at 3 μs. Blocking αδ sites with α‐conotoxin M1 (CTx) eliminated both τO1 and τB2 and left only τO2 and the short τB1 bursts, as expected.
Temporal Development of Autoreactive Th1 Responses and Endogenous Presentation of Self Myelin Epitopes by Central Nervous System-Resident APCs in Theiler’s Virus-Infected Mice1

Theiler’s murine encephalomyelitis virus (TMEV)-induced demyelinating disease is a chronic-progressive, immune-mediated CNS demyelinating disease and a relevant model of multiple sclerosis. Myelin destruction is initiated by TMEV-specific CD4+ T cells targeting persistently infected CNS-resident APCs leading to activation of myelin epitope-specific CD4+ T cells via epitope spreading. We examined the temporal development of virus- and myelin-specific T cell responses and acquisition of virus and myelin epitopes by CNS-resident APCs during the chronic disease course. CD4+ T cell responses to virus epitopes arise within 1 wk after infection and persist over a >300-day period. In contrast, myelin-specific T cell responses are first apparent ∼50–60 days postinfection, appear in an ordered progression associated with their relative encephalitogenic dominance, and also persist. Consistent with disease initiation by virus-specific CD4+ T cells, CNS mononuclear cells from TMEV-infected SJL mice endogenously process and present virus epitopes throughout the disease course, while myelin epitopes are presented only after initiation of myelin damage (>50–60 days postinfection). Activated F4/80+ APCs expressing high levels of MHC class II and B7 costimulatory molecules and ingested myelin debris chronically accumulate in the CNS. These results suggest a process of autoimmune induction in which virus-specific T cell-mediated bystander myelin destruction leads to the recruitment and activation of infiltrating and CNS-resident APCs that process and present endogenous myelin epitopes to autoreactive T cells in a hierarchical order.
Evidence-based pediatric asthma interventions and outcome measures in a healthy homes program: An integrative review

ABSTRACT Objective: Asthma disproportionately impacts and has poorer outcomes in low-income, minority, and inner-city children. The home environment has a profound impact on a child's asthma. Home-based asthma visits have the potential to positively impact a child's asthma, especially in targeted populations. The purpose of this integrative review is 1. ) to explore the effectiveness of home-based education and environmental measures and 2. ) to explore specific indicators and tools to measure pediatric asthma control and program effectiveness. Data Sources: Medline, CINHAL, and Ovid databases were searched from 2010 to 2017 utilizing the keywords healthy homes AND asthma and home based interventions AND asthma. Study Selections: A total of 71 articles were retrieved of which 27 articles met the inclusion criteria of English language, human subjects, and the inclusion of pediatric populations. Three additional articles were hand-searched from previous references. In total, 30 articles were reviewed. A quality appraisal was conducted utilizing standardized appraisal tools. Results: Home-based asthma education and environmental interventions have proven to be effective. The programs reviewed varied in types of interventions, intensity and duration, the type of provider, length of follow-up, and outcome measures. Successful programs were patient-centered, included a home assessment and individualized education and interventions, and were collaborative. Multiple outcome indicators such as health care utilization, asthma control, missed days of school or productivity, asthma symptoms, and verification of environmental remediation have been utilized. Conclusion: Home-based asthma programs can be beneficial to children with poorly controlled asthma and have the potential to be cost-effective.
Modeling of transoceanic fiber-optic WDM communication systems

The rapid growth of long-haul wavelength-division multiplexing (WDM) fiber-optic telecommunications challenges lightwave system designers to increase the transmission capacity per fiber pair, while reducing the time to market. This makes it essential to have fast and accurate computer modeling tools to aid the systems design. There is a natural engineering tradeoff between simulation speed and accuracy; fast approximations tend to be inaccurate, while the exact treatment of the physical processes affecting transmission are nearly impossible to capture in a time-efficient algorithm. The proof of a successful tool development lies in the comparison of simulation results to transmission system measurements. In this paper, we discuss a new simulation technique based on careful evaluation of the key physical effects that produce system impairments. We show that this new approach can produce fast and accurate simulations of long-haul WDM transmission systems.
Sum-rate maximization for asynchronous two-way relay networks

This paper is on sum-rate maximization, under a total transmit power budget, for an asynchronous single-carrier bidirectional (two-way) relay network. Considering a two-way relay network where two single-antenna transceivers exchange information through multiple single-antenna amplify-and-forward (AF) relays, we assume that different transceiver-relay links cause significantly different propagation delays in the signal they convey. This asynchronous bidirectional network is not amenable to a frequency flat end-to-end channel model, rather a multi- path end-to-end channel model with multiple taps appears to be more realistic. Such multi-path channel causes inter-symbol- interference (ISI) at the two transceivers. Such an ISI results in inter-block interference (IBI) in a block transmission/reception scheme which in turn can result in the loss of sum-rate, if it is not properly taken into account in the process of power allocation and network beamforming. Assuming the transceivers' transmit powers as well as the relay beamforming weights as the design parameters, we rigorously prove that the sum-rate maximization problem of such a network leads to a relay selection scheme, where only those relays, which contribute to one of the taps of the end-to-end channel impulse response, are turned on and the rest of the relays are switched off. We present semi-closed-form solutions for the design parameters.
Treatment of polluted landscape lake water and community analysis of ammonia-oxidizing bacteria in constructed wetland

Three lab-scale horizontal subsurface flow constructed wetlands (HSSF CWs) were installed to demonstrate the use of constructed wetlands as a viable low-cost treatment option to purify the polluted scenery water. The goals of this study were to determine the effectiveness of the wetland treatment technology in reducing contaminants in polluted natural water body and to characterize bacterial composition present in 3 constructed wetlands. Water samples were collected periodically for 12 months from three wetlands to determine the efficiency of the treatment system in removal of chemical pollutants. The reduction by the treatment was greatest for chemical oxygen demand (COD), total nitrogen and total phosphorus, but the removal of nutrients obviously varied with seasons. Plant uptake was highly responsible for nitrogen and phosphorus removal. Denaturing gradient gel electrophoresis (DGGE) was used to study the diversity of microbial community in the constructed wetland. Changes in the total bacterial community and ammonia-oxidizing bacterial composition were examined by DGGE and sequencing of polymerase chain reaction (PCR)-amplified fragments of the gene carrying the ammonia monooxygenase subunit A gene (amoA) recovered from matrix samples and DGGE bands. DGGE analysis of wetlands samples revealed that seasonal change had an effect on the diversity and composition of microbial communities in constructed wetlands. The sequence analysis showed ammonia-oxidizing bacteria (AOB) in constructed wetlands were uncultivable and the population of AOB had a higher percentage of Nitrosomonas-like sequences from wetlands, while no Nitrosospira-like sequences were found.
Membrane-Type 6 Matrix Metalloproteinase Regulates the Activation-Induced Downmodulation of CD16 in Human Primary NK Cells

CD16 (FcγRIIIa), the low-affinity receptor for IgG, expressed by the majority of human NK cells, is a potent activating receptor that facilitates Ab-dependent cell-mediated cytotoxicity (ADCC). ADCC dysfunction has been linked to cancer progression and poor prognosis for chronic infections, such as HIV; thus, understanding how CD16 expression is regulated by NK cells has clinical relevance. Importantly, CD16 cell-surface expression is downmodulated following NK cell activation and, in particular, exposure to stimulatory cytokines (IL-2 or IL-15), likely owing to the action of matrix metalloproteinases (MMPs). In this article, we identify membrane-type 6 (MT6) MMP (also known as MMP25) as a proteinase responsible for CD16 downmodulation. IL-2–induced upregulation of MT6/MMP25 cell-surface expression correlates with CD16 downmodulation. MT6/MMP25, sequestered in intracellular compartments in unstimulated NK cells, translocates to the cell surface after stimulation; moreover, it polarizes to the effector–target cell interface of the CD16-mediated immunological synapse. siRNA-mediated disruption of MT6/MMP25 expression enhances the ADCC capacity of NK cells, emphasizing the important functional role of MT6/MMP25 in the regulation of ADCC activity. Thus, this study uncovers a previously unknown role of MT6/MMP25 in human NK cells, and suggests that inhibition of MT6/MMP25 activity could improve ADCC efficacy of therapeutically administered NK cells that require IL-2 for culture and expansion.
A Self-Assembled Fibroblast-Endothelial Cell Co-Culture System That Supports in vitro Vasculogenesis by both Human Umbilical Vein Endothelial Cells and Human Dermal Microvascular Endothelial Cells

The construction of vascularized connective tissues is an important goal in tissue engineering in that the presence of a patent bio-engineered vasculature should facilitate vascularization of an implant. Fibroblasts play an essential role in the angiogenic process through their production of extracellular matrix molecules and through their release of essential growth factors. Therefore, the aim of this study is to develop a thin 3-dimensional model in which fibroblasts support endothelial cells in the formation of tube-like structures. Macro- and microvascular endothelial cells were seeded onto confluent lawns of human fibroblasts and were cultured in the presence of high levels of ascorbate 2-phosphate to create a tissue-like structure in which endothelial cell organized into tube-like structures. The process was visualized in the culture dish through labeling of cells with a long-lasting fluorescent vital dye. Intact sheet-like structures were created in which endothelial cell tube-like structures were encased by fibroblasts and were surrounded by a basement membrane. These structures appeared to contain a lumen and remained stable for up to 5 weeks in culture. This culture system provides an in vitro method to study fibroblast-endothelial cell interactions and to study the effects of pro- and anti-angiogenic factors on endothelial cell differentiation. This system also provides an experimental basis for developing vascularized tissue-engineered connective tissue.
Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities

ABSTRACT Single-nucleotide primer extension (SNuPE) is an emerging tool for parallel detection of DNA sequences of different target microorganisms. The specificity and sensitivity of the SNuPE method were assessed by performing single and multiplex reactions using defined template mixtures of 16S rRNA gene PCR products obtained from pure bacterial cultures. The mismatch discrimination potential of primer extension was investigated by introducing different single and multiple primer-target mismatches. The type and position of the mismatch had significant effects on the specificity of the assay. While a 3′-terminal mismatch has a considerable effect on the fidelity of the extension reaction, the internal mismatches influenced hybridization mostly by destabilizing the hybrid duplex. Thus, carefully choosing primer-mismatch positions should result in a high signal-to-noise ratio and prevent any nonspecific extension. Cyclic fluorescent labeling of the hybridized primers via extension also resulted in a significant increase in the detection sensitivity of the PCR. In multiplex reactions, the signal ratios detected after specific primer extension correlated with the original template ratios. In addition, reverse-transcribed 16S rRNA was successfully used as a nonamplified template to prove the applicability of SNuPE in a PCR-independent manner. In conclusion, this study demonstrates the great potential of SNuPE for simultaneous detection and typing of various nucleic acid sequences from both environmental and engineered samples.
Ion permeation and conduction in a human recombinant 5‐HT3 receptor subunit (h5‐HT3A)

1 A human recombinant homo‐oligomeric 5‐HT3 receptor (h5‐HT3A) expressed in a human embryonic kidney cell line (HEK 293) was characterized using the whole‐cell recording configuration of the patch clamp technique. 2 5‐HT evoked transient inward currents (EC50= 3.4 μM; Hill coefficient = 1.8) that were blocked by the 5‐HT3 receptor antagonist ondansetron (IC50= 103 pM) and by the non‐selective agents metoclopramide (IC50= 69 nM), cocaine (IC50= 459 nM) and (+)‐tubocurarine (IC50= 2.8 μM). 3 5‐HT‐induced currents rectified inwardly and reversed in sign (E5‐HT) at a potential of −2.2 mV. N‐Methyl‐D‐glucamine was finitely permeant. Permeability ratios PNa/PCs and PNMDG/PCs were 0.90 and 0.083, respectively. 4 Permeability towards divalent cations was assessed from measurements of E5‐HT in media where Ca2+ and Mg2+ replaced Na+. PCa/PCs and PMg/PCs were calculated to be 1.00 and 0.61, respectively. 5 Single channel chord conductance (γ) estimated from fluctuation analysis of macroscopic currents increased with membrane hyperpolarization from 243 fS at −40 mV to 742 fS at −100 mV. 6 Reducing [Ca2+]o from 2 to 0.1 mM caused an increase in the whole‐cell current evoked by 5‐HT. A concomitant reduction in [Mg2+]o produced further potentiation. Fluctuation analysis indicates that a voltage‐independent augmentation of γ contributes to this phenomenon. 7 The data indicate that homo‐oligomeric receptors composed of h5‐HT3A subunits form inwardly rectifying cation‐selective ion channels of low conductance that are permeable to Ca2+ and Mg2+.
Depressive symptoms predict postoperative disability among patients with lumbar spinal stenosis: A two-year prospective study comparing two age groups

Purpose. To examine the importance of preoperative and recovery phase depressive symptoms in two age groups of patients with lumbar spinal stenosis (LSS) with respect to surgery outcome 2 years postoperatively. Method. Ninety-six patients with symptomatic LSS underwent decompressive surgery. Data were collected with self-report questionnaires before surgery and 3 months, 6 months, 1 year and 2 years postoperatively. Depression was assessed with the Beck Depression Inventory (BDI). Depressive burden was examined by compiling the sum of preoperative, 3-month and 6-month BDI scores. Physical functioning and pain were assessed with the Oswestry Disability Index, Walking ability and VAS. In the analyses, the subjects were divided into two groups according to the median age (62 years). Results. Depressive burden was a strong predictor of disability at the 2-year postoperative phase both in younger and elderly patients with LSS. A notable proportion (20%) of the younger patients had considerable depressive symptomatology 2 years after the surgery, whereas in the older age group this proportion was 8%. Conclusion. The results suggest that there is a strong relationship between depressive symptoms and disability among postoperative patients with LSS. Identifying and treating patients with preoperative and postoperative depressive symptoms may be a useful strategy for improving LSS surgery outcomes.
Structure‐function studies of nerve growth factor: functional importance of highly conserved amino acid residues.

Selected amino acid residues in chicken nerve growth factor (NGF) were replaced by site‐directed mutagenesis. Mutated NGF sequences were transiently expressed in COS cells and the yield of NGF protein in conditioned medium was quantified by Western blotting. Binding of each mutant to NGF receptors on PC12 cells was evaluated in a competition assay. The biological activity was determined by measuring stimulation of neurite outgrowth from chick sympathetic ganglia. The residues homologous to the proposed receptor binding site of insulin (Ser18, Met19, Val21, Asp23) were substituted by Ala. Replacement of Ser18, Met19 and Asp23 did not affect NGF activity. Modification of Val21 notably reduced both receptor binding and biological activity, suggesting that this residue is important to retain a fully active NGF. The highly conserved Tyr51 and Arg99 were converted into Phe and Lys respectively, without changing the biological properties of the molecule. However, binding and biological activity were greatly impaired after the simultaneous replacement of both Arg99 and Arg102 by Gly. The three conserved Trp residues at positions 20, 75 and 98 were substituted by Phe. The Trp mutated proteins retained 15‐60% of receptor binding and 40‐80% of biological activity, indicating that the Trp residues are not essential for NGF activity. However, replacement of Trp20 significantly reduced the amount of NGF in the medium, suggesting that this residue may be important for protein stability.
Ground beetles (Coleoptera: Carabidae) of rice field banks and restored habitats in an agricultural area of the Po Plain (Lombardy, Italy)

Abstract An entomological investigation was carried out in an agricultural area, mainly rice fields, of the Po river plain, located in the municipalities of Lacchiarella (MI) and Giussago (PV) (Lombardy, Italy). In 2009 and 2010, ground beetles (Coleoptera: Carabidae) were sampled along rice field banks and in restored habitats, by means of pitfall traps. The area appeared as species-rich, compared to other anthropogenic habitats in the Po river pain. Most of the collected Carabids were species with a wide distribution in the Paleartic region, eurytopic and common in European agroecosystems. The assemblages were dominated by small-medium, macropterous species, with summer larvae. No endemic species were found. Species with southern distribution, rarely found north of the Po river, were also sampled. Amara littorea is recorded for the first time in Italy.
Cystatin F Affects Natural Killer Cell Cytotoxicity

Cystatin F is a cysteine peptidase inhibitor which, unlike other cystatin family members, is targeted to endosomal/lysosomal compartments. It is synthesized as an inactive disulfide-linked dimer which is then converted to an active monomer by proteolytic cleavage of 15 N-terminal residues. Cystatin F has been suggested to regulate the cytotoxicity of natural killer (NK) cells by inhibiting the major granzyme convertases, cathepsins C and H. To test this hypothesis, we prepared variants of cystatin F and analyzed their uptake, subcellular trafficking, and peptidase inhibition, as well as their impact on the cytotoxicity of NK-92 cells and primary NK cells. The N-glycosylation pattern is responsible for the secretion, uptake, and subcellular sorting of cystatin F in HeLa and Hek293 cells, whereas the legumain binding site had no effect on these processes. Active, N-terminally truncated, monomeric cystatin F can also be internalized by recipient cells and targeted to endo/lysosomes, affecting also cells lacking the activating peptidase. Cystatin F mutants capable of cell internalization and trafficking through the endo/lysosomal pathway significantly decreased cathepsin C and H activities, both in situ, following transfection and in trans, using conditioned media. Further, incubation of IL-2 stimulated NK-92 and primary NK cells with full-length and N-terminally truncated cystatin F mutants led to suppression of their granule-mediated cytotoxicity. This effect was most significant with the N-terminally truncated mutants. These results suggest that cystatin F can be an important mediator within tumor microenvironment affecting the cytotoxicity of NK cells and consequently antitumor immune response.
Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation

Electron transfer dissociation (ETD) is a recently introduced mass spectrometric technique which has proven to be an excellent tool for the elucidation of labile post-translational modifications such as phosphorylation and O-GlcNAcylation of serine and threonine residues. However, unlike collision induced dissociation (CID), which has been studied for decades, the intricacies of ETD-based fragmentation have not yet been firmly established or systematically addressed. In this analysis, we have systematically compared the CID and ETD fragmentation patterns for the large majority of the peptides that do not contain such labile modifications. Using a standard 48 protein mix, we were able to measure false-positive rates for the experiments and also assess a large number of peptides for a detailed comparison of CID and ETD fragmentation pattern. Analysis of ∼19 000 peptides derived from both standard proteins and complex protein samples revealed that (i) CID identified 50% more peptides than ETD; (ii) ETD resulted in ∼20% increase in amino acid sequence coverage over CID; and (iii) combining CID and ETD fragmentation increased the sequence coverage for an average tryptic peptide to 92%. Interestingly, our analysis revealed that nearly 60% of all ETD-identified peptides carried two positive charges, which is in sharp contrast to what has been generally accepted. We also present a novel strategy for automatic validation of peptide assignments based on identification of a peptide by consecutive CID and ETD fragmentation in an alternating mode.
Block-Parallel IDA* for GPUs

We investigate GPU-based parallelization of Iterative-Deepening A* (IDA*). We show that straightforward thread-based parallelization techniques which were previously proposed for massively parallel SIMD processors perform poorly due to warp divergence and load imbalance. We propose Block-Parallel IDA* (BPIDA*), which assigns the search of a subtree to a block (a group of threads with access to fast shared memory) rather than a thread. On the 15-puzzle, BPIDA* on a NVIDIA GRID K520 with 1536 CUDA cores achieves a speedup of 4.98 compared to a highly optimized sequential IDA* implementation on a Xeon E5-2670 core.