Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a proton‐activated, outwardly rectifying anion channel

Anion channels are present in every mammalian cell and serve many different functions, including cell volume regulation, ion transport across epithelia, regulation of membrane potential and vesicular acidification. Here we characterize a proton‐activated, outwardly rectifying current endogenously expressed in HEK293 cells. Binding of three to four protons activated the anion permeable channels at external pH below 5.5 (50% activation at pH 5.1). The proton‐activated current is strongly outwardly rectifying, due to an outwardly rectifying single channel conductance and an additional voltage dependent facilitation at depolarized membrane potentials. The anion channel blocker 4,4′‐diisothiocyanostilbene‐2,2′‐disulphonic acid (DIDS) rapidly and potently inhibited the channel (IC50: 2.9 μm). Flufenamic acid blocked this channel only slowly, while mibefradil and amiloride at high concentrations had no effect. As determined from reversal potential measurements under bi‐ionic conditions, the relative permeability sequence of this channel was SCN−> I−> NO3−> Br−> Cl−. None of the previously characterized anion channel matches the properties of the proton‐activated, outwardly rectifying channel. Specifically, the proton‐activated and the volume‐regulated anion channels are two distinct and separable populations of ion channels, each having its own set of biophysical and pharmacological properties. We also demonstrate endogenous proton‐activated currents in primary cultured hippocampal astrocytes. The proton‐activated current in astrocytes is also carried by anions, strongly outwardly rectifying, voltage dependent and inhibited by DIDS. Proton‐activated, outwardly rectifying anion channels therefore may be a broadly expressed part of the anionic channel repertoire of mammalian cells.
Susceptibility Testing of Aspergillus flavus: Inoculum Dependence with Itraconazole and Lack of Correlation between Susceptibility to Amphotericin B In Vitro and Outcome In Vivo

ABSTRACT We have attempted to validate in Aspergillus flavus the main in vitro methodologies that have been used to detect resistance in Aspergillus fumigatus. We developed a murine model with two A. flavus isolates, one that was apparently resistant in vitro to amphotericin B (AFL5) and another that was resistant to itraconazole (AFL8). No correlation was found for amphotericin B in AFL5, since the in vivo response was compatible with a susceptible isolate. Modification of the in vitro susceptibility test methodology for amphotericin B was unsuccessful. Although AFL8 was apparently resistant to itraconazole in vitro, it was found to be susceptible in vivo. Additional in vitro work has detected weaknesses in the in vitro susceptibility methodology validated for A. fumigatus when applied to A. flavus. The principal problems are that changes in the inoculum have a large effect on the MICs of itraconazole for some A. flavus strains and that a trailing end point and spore sediment often appear when an inoculum with a higher colony count is used. We propose a modified method using a final inoculum of 2.5 × 104 CFU per ml of RPMI 1640 medium with 2% glucose buffered to pH 7.0 in a microtiter format, incubated for 48 h with no growth end point. Validation of this methodology requires one or more itraconazole-resistant A. flavus isolates, which have yet to be identified.
Sleep disordered breathing, daytime symptoms, and functional performance in stable heart failure.

STUDY OBJECTIVES To evaluate characteristics of sleep disordered breathing (SDB); clinical and demographic correlates of SDB; and the extent to which SDB explains functional performance and symptoms in stable heart failure patients receiving care in structured HF disease management programs. DESIGN Cross-sectional, observational study. SETTING Structured heart failure disease management programs. PARTICIPANTS 170 stable chronic heart failure patients (mean age = 60.3 +/- 16.8 years; n = 60 [35%] female; n = 50 [29%] African American; left ventricular ejection fraction mean = 32 +/- 14.6). INTERVENTIONS N/A. MEASUREMENTS AND RESULTS Full polysomnography was obtained for one night on participants in their homes. Participants completed the 6-minute walk, 3 days of actigraphy, MOS-SF 36, Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, Multi-Dimensional Assessment of Fatigue Scale, and the Centers for the Epidemiological Studies of Depression Scale. Fifty-one percent had significant SDB; Sixteen (9%) of the total sample had central sleep apnea. Severe SDB was associated with a 4-fold increase in the likelihood of poor self-reported physical function (OR = 4.15, 95%CI = 1.19-14.57) and CSA was associated with low levels of daytime mobility (OR = 4.09, 95%CI = 1.23-13.62) after controlling for clinical and demographic variables. There were no statistically significant relationships between SDB and daytime symptoms or self-reported sleep, despite poorer objective sleep quality in patients with SDB. CONCLUSIONS Severe SDB is associated with poor physical function in patients with stable HF but not with daytime symptoms or self-reported sleep, despite poorer objective sleep quality in patients with SDB.
Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

We expanded the knowledge base for Drosophila cell line transcriptomes by deeply sequencing their small RNAs. In total, we analyzed more than 1 billion raw reads from 53 libraries across 25 cell lines. We verify reproducibility of biological replicate data sets, determine common and distinct aspects of miRNA expression across cell lines, and infer the global impact of miRNAs on cell line transcriptomes. We next characterize their commonalities and differences in endo-siRNA populations. Interestingly, most cell lines exhibit enhanced TE-siRNA production relative to tissues, suggesting this as a common aspect of cell immortalization. We also broadly extend annotations of cis-NAT-siRNA loci, identifying ones with common expression across diverse cells and tissues, as well as cell-restricted loci. Finally, we characterize small RNAs in a set of ovary-derived cell lines, including somatic cells (OSS and OSC) and a mixed germline/somatic cell population (fGS/OSS) that exhibits ping-pong piRNA signatures. Collectively, the ovary data reveal new genic piRNA loci, including unusual configurations of piRNA-generating regions. Together with the companion analysis of mRNAs described in a previous study, these small RNA data provide comprehensive information on the transcriptional landscape of diverse Drosophila cell lines. These data should encourage broader usage of fly cell lines, beyond the few that are presently in common usage.
Fluorometric analysis of chlorophyll a as a representation of phytoplankton in phosphorus-limited media

Trends in data from recent years show movement toward eutrophication in Otsego Lake; these include increasing total phosphorus and resultant increasing chlorophyll a concentrations, decreasing Secchi transparency readings and decreasing hypolimnetic oxygen concentrations(Harman et al., 1997). The increase in phosphorus has triggered the changes in chlorophyll a, Secchi transparency, and dissolved oxygen levels. Of the total phosphorus entering Otsego Lake more than 80% is retained (Albright, 1996) and that which is available is consumed immediately by primary producers, particularly phytoplankton. Most phosphorus is associated with particulate material which sediments to the lake bottom. It has been suggested that this fraction may subsequently become available to algae following sediment resuspension (France and Albright, 1994; Bostrom ef al., 1982). According to studies that compare phosphorus levels to transparency, a quantity of phosphorus that doubles in size will be equivalent to a transparency reduction of 50% due to phytoplankton growth (Godfrey, 1977; Carlson, 1977; Albright, 1996). Oxygen-consuming bacteria decompose phytoplankton in the hypolimnion, thereby decreasing overall oxygen levels. The decrease in oxygen concentrations affects the entire food web in the lake by decreasing the habitat for cold water fish. These fish prey on alewives, so without them the already-significant alewife population would increase. This would further lead to a decrease in the zooplankton population and ultimately to higher standing crops of phytoplankton. More phytoplankton will cause a greater deficiency of oxygen by their decomposition (Harman et al., 1997).
Enhanced Dermal Regeneration using Modified Collagen Scaffolds: Experimental Porcine Study

Ongoing research has achieved much progress towards the development of new artificial skin substitute products. However, effective implant material for correcting full-thickness defects (such as those arising from extensive burns, tumor resection, hereditary or congenital defects and chronic wounds) has not yet become available. Following split-thickness skin grafting, contraction and scar formation are unavoidable. These phenomena are believed to be due to poor dermis regeneration. Collagen dermis substitute has been developed for the treatment of deep, poorly vascularized tissue defects. However, their application is problematic, because scaffolds of this kind fail to adequately induce the neoangiogenesis needed for regeneration. To overcome these shortcomings a number of matrices have been chemically modified. Furthermore, these matrices first require implantation and follow-up by skin grafting 3 to 5 weeks later. In this article we describe new materials made of modified collagen which enhance dermal regeneration and neoangiogenesis. The procedure was applied in successfully dealing with full-thickness defects in pigs, with subsequent split-thickness skin grafting being performed immediately afterwards. Histological findings revealed that the neodermis obtained resembles a normal dermis structure. These scaffolds have the potential of serving as an off-the-shelf skin replacement in the reconstruction of deep wounds, thus supporting wound-healing processes.
SYNCRIP, a Member of the Heterogeneous Nuclear Ribonucleoprotein Family, Is Involved in Mouse Hepatitis Virus RNA Synthesis

ABSTRACT Several cellular proteins, including several heterogeneous nuclear ribonucleoproteins (hnRNPs), have been shown to function as regulatory factors for mouse hepatitis virus (MHV) RNA synthesis as a result of their binding to the 5′ and 3′ untranslated regions (UTRs) of the viral RNA. Here, we identified another cellular protein, p70, which has been shown by UV cross-linking to bind both the positive- and negative-strand UTRs of MHV RNA specifically. We purified p70 with a a one-step RNA affinity purification procedure with the biotin-labeled 5′-UTR. Matrix-assisted laser desorption ionization (MALDI)-mass spectrometry identified it as synaptotagmin-binding cytoplasmic RNA-interacting protein (SYNCRIP). SYNCRIP is a member of the hnRNP family and localizes largely in the cytoplasm. The p70 was cross-linked to the MHV positive- or negative-strand UTR in vitro and in vivo. The bacterially expressed SYNCRIP was also able to bind to the 5′-UTR of both strands. The SYNCRIP-binding site was mapped to the leader sequence of the 5′-UTR, requiring the UCUAA repeat sequence. To investigate the functional significance of SYNCRIP in MHV replication, we expressed a full-length or a C-terminally truncated form of SYNCRIP in mammalian cells expressing the MHV receptor. The overexpression of either form of SYNCRIP inhibited syncytium formation induced by MHV infection. Furthermore, downregulation of the endogenous SYNCRIP with a specific short interfering RNA delayed MHV RNA synthesis; in contrast, overexpression or downregulation of SYNCRIP did not affect MHV translation. These results suggest that SYNCRIP may be directly involved in MHV RNA replication as a positive regulator. This study identified an additional cellular hnRNP as an MHV RNA-binding protein potentially involved in viral RNA synthesis.
Does auditor-client distance matter to real earnings management? Evidence from China

ABSTRACT Using a large sample of Chinese listed firms and accounting firms during 2004–2013, this study investigates whether and how auditor-client distance affects corporate real earnings management (REM). We find that REM is positively associated with auditor-client distance, and the positive association is more pronounced in client firms with lower information transparency and higher business complexity, suggesting that information advantage arising from geographical proximity may facilitate auditors’ supervision over their client firms’ REM. Moreover, both marketization environment and ownership concentration significantly attenuate the positive association, thereby reflecting a substitution effect between external audit and the other two governance mechanisms.
Port rationalization and the evolution of regional port systems: the case of Norway

ABSTRACT This paper explores container port system evolution and port choice from the perspective of a regional or secondary (feeder and short sea) system. Theory predicts that large-scale container port systems tend towards concentration, rationalizing the number of ports, followed by deconcentration. By contrast, regional port systems remain under-researched. Such systems tend to retain their large number of small ports, as the alternative would be serving their long coastlines, small islands and sparse populations by long overland routes or not at all. Norway is a classic feeder and short sea market with a long coastline and dispersed population served by many small ports. The methodology utilizes concentration analysis and semi-structured interviews to explore if the Norwegian system conforms to theories of port concentration and port choice, including issues of regional port governance. Findings show that the Norwegian system demonstrates the same process of concentration and then deconcentration as major port ranges. However, its number of ports has not been rationalized, suggesting that such regional systems may indeed evolve differently to major port ranges. Nevertheless, ongoing discussion of reform in Norway towards regional port governance, similar to other European countries, may eventually result in such rationalization.
Hitting the bull's eye: Novel directed cancer therapy through helicase‐targeted synthetic lethality

Designing strategies for anti‐cancer therapy have posed a significant challenge. One approach has been to inhibit specific DNA repair proteins and their respective pathways to enhance chemotherapy and radiation therapy used to treat cancer patients. Synthetic lethality represents an approach that exploits pre‐existing DNA repair deficiencies in certain tumors to develop inhibitors of DNA repair pathways that compensate for the tumor‐associated repair deficiency. Since helicases play critical roles in the DNA damage response and DNA repair, particularly in actively dividing and replicating cells, it is proposed that the identification and characterization of synthetic lethal relationships of DNA helicases will be of value in developing improved anti‐cancer treatment strategies. In this review, we discuss this hypothesis and current evidence for synthetic lethal interactions of eukaryotic DNA helicases in model systems. J. Cell. Biochem. 106: 758–763, 2009. Published 2009 Wiley‐Liss, Inc.
Distributed adaptive consensus protocols for linear multi-agent systems: An integrated design approach

This paper considers the consensus problem of multi-agent systems. It is pointed out that the existing consensus protocols decouple the effects of the agent and protocol dynamics of the consensus stability from that of the communication topology. In this paper, an integrated design approach is presented, under which a novel distributed adaptive consensus protocol is proposed to achieve consensus of multi-agent systems with undirected graphs. For the case there exist bounded external disturbances, by using the s modification technique, a distributed robust adaptive consensus protocol is presented to ensure the ultimate boundedness of the consensus error. Both of the proposed adaptive protocols are fully distributed, depending on only relative states of neighboring agents.
A novel type of class I gene organization in vertebrates: a large family of non‐MHC‐linked class I genes is expressed at the RNA level in the amphibian Xenopus.

A Xenopus class I cDNA clone, isolated from a cDNA expression library using antisera, is a member of a large family of non‐classical class I genes (class Ib) composed of at least nine subfamilies, all of which are expressed at the RNA level. The subfamilies are well conserved in their immunoglobulin‐like alpha 3 domains, but their peptide‐binding regions (PBRs) and cytoplasmic domains are very divergent. In contrast to the great allelic diversity found in the PBR of classical class I genes, the alleles of one of the Xenopus non‐classical subfamilies are extremely well conserved in all regions. Several of the invariant amino acids essential for the anchoring of peptides in the classical class I groove are not conserved in some subfamilies, but the class Ib genes are nevertheless more closely related in the PBR to classical and non‐classical genes linked to the MHC in mammals and birds than to any other described class I genes like CD1 and the neonatal rat intestinal Fc receptor. Comparison with the Xenopus MHC‐linked class Ia protein indicate that amino acids presumed to interact with beta 2‐microglobulin are identical or conservatively changed in the two major class I families. Genomic analyses of Xenopus species suggest that the classical and non‐classical families diverged from a common ancestor before the emergence of the genus Xenopus over 100 million years ago; all of the non‐classical genes appear to be linked on a chromosome distinct from the one harboring the MHC. We hypothesize that this class Ib gene family is under very different selection pressures from the classical MHC genes, and that each subfamily may have evolved for a particular function.
A 2.5-GHz InGaP/GaAs differential cross-coupled self-oscillating mixer (SOM) IC

This letter presents a monolithic differential cross-coupled self-oscillating mixer (SOM). The SOM chip is fabricated using an InGaP/GaAs heterojunction bipolar transistor (HBT) foundry process and operates at 2.5 GHz. The chip provides voltage controlled oscillator (VCO) operation, up- and down-conversion mixing, and injection locking functionalities. The voltage down-conversion gain and the power up-conversion gain of up to 15 and 11.5 dB, respectively, are measured for the circuit. There is a compromise between obtaining a high conversion gain, and the oscillator power (-0.3 dBm for a 5-V supply) and phase noise (-84 dBc/Hz at 100 kHz). However, phase noise improvement of 32dB is observed by injection of a -30-dBm stable reference.
Bioethical considerations for algal biotechnology

In this manuscript we discuss different aspects and applications of algal biotechnology and how they are seen through the prism of bioethics. We review how algae have been considered to solve problems on Earth and to ease human suffering. We also take a look at the current state of the production of algal biomass and we offer our suggestions and considerations based on the fact that the biomass is an expensive product and yet its quality is very good.
ACTIVE DEVICE FABRICATION USING FIBER ENCAPSULATION ADDITIVE MANUFACTURING

Fiber Encapsulation Additive Manufacturing (FEAM) is a novel solid freeform fabrication process in which a fiber and a matrix are co-deposited simultaneously within a single printer along straight and curved 2-D and 3-D paths. Using a FEAM approach in which the fiber is a metal wire and the matrix is a thermoplastic polymer, simple electromechanical devices such as voice coils, inductive sensors, and membrane switches have been successfully produced. This paper will present an overview of the FEAM process, describe several fabricated devices, and discuss recent developments in controllably stopping and starting the wire, and in creating electrical junctions between individual wires, which together enable much more complex devices to be made. Introduction and Motivation In recent years a number of researchers have investigated the additive manufacturing (AM) of multi-material, multi-functional structures and active devices. These efforts, which attempt to go well beyond the purely structural and aesthetic dimensions of single-material AM, seek to achieve a higher level of functionality and performance, or significant reductions in size, weight, and cost, for a variety of electromechanical and electronic systems. Such benefits, combined with AM’s intrinsic ability to rapidly produce complex, customized geometries, promise a future in which previously-impossible designs of great sophistication can readily be produced, a future in which AM is truly enabling. An area of interest for the present work, and for which multi-material AM holds great promise, is soft robotics. Soft robotics has emerged as a research topic of considerable interest [Majidi 2013, Lu and Kim, 2013], in part driven by the desire to create “co-robots” that work safely in close proximity to humans. Moreover, robots with soft bodies and limbs might grasp and manipulate delicate and irregular objects—such as picking fruit off of a tree without damage. They might also move in new and complex ways, and transform their shapes: capabilities that open novel application areas, such as search and rescue operations. The tentacle of an octopus, if it could be emulated artificially, is an example of a device useful in a soft robot that would enable complex
A Within-Subject Comparison of Propofol and Methohexital Anesthesia for Electroconvulsive Therapy

Objectives The optimal anesthetic for electroconvulsive therapy (ECT) is a frequently studied but unresolved issue. Methohexital and propofol are 2 widely used anesthetic agents for ECT. The purpose of this study was to determine which of the 2 agents was associated with superior clinical outcomes. Methods Records from all patients who had undergone separate ECT courses with methohexital and propofol between 1992 and 2008 (n = 48) were reviewed for a retrospective within-subject comparison of outcome measures. The clinical outcomes we examined were number of treatments required in a course of ECT, changes in the Montgomery-Åsberg Depression Rating Scale and Mini Mental Status Examination, and length of stay in the hospital after initiation of ECT. Additionally, we compared treatment delivery between methohexital and propofol treatment courses, measuring rate of restimulation for brief seizures, seizure duration, percentage of treatments that were bilateral, and average charge administered. Results Data from 1314 treatments over 155 ECT courses were reviewed. Improvement in depressive symptoms, based on the Montgomery-Åsberg Depression Rating Scale, was not affected by choice of anesthetic agent. However, when right unilateral electrode placement was used, patients receiving propofol required significantly more treatments than those receiving methohexital. Propofol was also associated with a significantly higher requirement for bilateral ECT and higher stimulus dosing. Seizure duration was significantly shorter in the propofol condition, with more patients requiring restimulation for brief seizures. Length of stay in the hospital and cognitive outcomes were not significantly different between propofol and methohexital treatments. Conclusions We recommend methohexital as the induction agent of choice for ECT, especially with right unilateral placement.