Miracle-dz/UniFAR-FTUs huggingface dataset:
Properties of FNR proteins substituted at each of the five cysteine residues

FNR is a transcriptional regulator controlling the expression of a number of Escherichia coli genes in response to anoxia. It is structurally‐related to CRP (the cyclic AMP receptor protein) except for the presence of a cysteine‐rich N‐terminal extension, which may form part of an iron‐binding, redox‐sensing domain in FNR. Site‐directed substitution has previously shown that four of the cysteine residues (C20, C23, C29 and C122) are essential for FNR function, whereas the fifth (C16) is not. The FNR protein exists in two forms separable by non‐reducing SOS‐PAGE, and in studies with altered FNR proteins containing single substitutions at each of the five cysteine residues it was concluded that the faster‐migrating form (FNR(27)), possesses an intramolecular disulphide bond linking C122 to one of the cysteines near the N‐terminus. FNR(27)) was more abundant in aerobic cells but the physiological significance of this was not established. Footprint studies indicated that FNR proteins lacking essential cysteine residues are impaired in their ability to protect FNR sites in the ndh promoter. The non‐essential cysteine residue (C16) was identified as the source of the most reactive sulphydryl group and all of the inactive proteins exhibited different sulphydryl reactivities. The iron content of the C122A‐substituted protein was much reduced but those of the other proteins were less affected. Electrospray mass spectrometry confirmed the accuracy of the gene‐derived amino acid composition of FNR with a mutant protein and it showed that a fraction of the wild‐type protein may carry a 78 Da substituent which could not be removed with dithio‐threitol or β‐mercaptoethanol.
Ras‐Signaling Pathways: Positive and Negative Regulation of Tau Expression in PC12 Cells

Abstract: Tau is a microtubule‐associated protein whose promoter is activated during the first phase of nerve growth factor‐induced PC12 cell differentiation, whereas levels of its mRNA are accumulating throughout differentiation. In this study, we have followed the signal transduction cascades regulating tau induction. Using dominant negative Ras‐expressing PC12 cells, we show that ras regulates tau expression during the first phase of PC12 cell differentiation. The ERK and JNK cascades, which are downstream of Ras; have opposing effects on tau promoter activity: ERK induces tau promoter activity, JNK inhibits it. Tau promoter activity in PC12 cells is correlated with a short‐term activation of ERK, which declines after a few hours and is followed by an activation of the inhibitory JNK cascade 76 h later. These observations suggest that the induction and inhibition of tau promoter are mediated by alternate ERK and JNK activities, which may underlie a mechanism to turn on and off genes during PC12 cell differentiation.
Novel Subtype of Type IIs Restriction Enzymes

The type IIs restriction enzyme BfiI recognizes the non-palindromic nucleotide sequence 5′-ACTGGG-3′ and cleaves complementary DNA strands 5/4 nucleotides downstream of the recognition sequence. The genes coding for the BfiI restriction-modification (R-M) system were cloned/sequenced and biochemical characterization of BfiI restriction enzyme was performed. The BfiI R-M system contained three proteins: two N4-methylcytosine methyltransferases and a restriction enzyme. Sequencing of bisulfite-treated methylated DNA indicated that each methyltransferase modifies cytosines on opposite strands of the recognition sequence. The N-terminal part of the BfiI restriction enzyme amino acid sequence revealed intriguing similarities to an EDTA-resistant nuclease of Salmonella typhimurium. Biochemical analyses demonstrated that BfiI, like the nuclease of S. typhimurium, cleaves DNA in the absence of Mg2+ ions and hydrolyzes an artificial substrate bis(p-nitrophenyl) phosphate. However, unlike the nonspecific S. typhimurium nuclease, BfiI restriction enzyme cleaves DNA specifically. We propose that the DNA-binding specificity of BfiI stems from the C-terminal part of the protein. The catalytic N-terminal subdomain ofBfiI radically differs from that of type II restriction enzymes and is presumably similar to the EDTA-resistant nonspecific nuclease of S. typhimurium; therefore, BfiI did not require metal ions for catalysis. We suggest that BfiI represents a novel subclass of type IIs restriction enzymes that differs from the archetypal FokI endonuclease by the fold of its cleavage domain, the domain location, and reaction mechanism.
Decreased external skeletal robustness due to reduced physical activity?

Childhood obesity is a global problem, e.g., due to physical inactivity. External skeletal robustness (Frame‐Index) has decreased in German schoolchildren. An association between Frame‐Index and physical activity was assumed. Further often body mass index (BMI) is analyzed without reference to bone structure. Therefore, we analyze relationships between Frame‐Index, BMI, % body fat, and physical activity.
Commitment or Disaffection? Framing the Forms, Meanings, and Predictors of Youth Civic Engagement in Italy

HIV prevention efforts have expanded beyond individual-level interventions to address structural determinants of risk. Coalitions have been an important vehicle for addressing similar intractable and deeply rooted health-related issues. A root cause analysis process may aid coalitions in identifying fundamental, structural-level contributors to risk and in identifying appropriate solutions. For this article, strategic plans for 13 coalitions were analyzed both before and after a root cause analysis approach was applied to determine the coalitions' strategic plans potential impact and comprehensiveness. After root cause analysis, strategic plans trended toward targeting policies and practices rather than on single agency programmatic changes. Plans expanded to target multiple sectors and several changes within sectors to penetrate deeply into a sector or system. Findings suggest that root cause analysis may be a viable tool to assist coalitions in identifying structural determinants and possible solutions for HIV risk.
Transformations for Resilient Rural Futures: The Case of Kaikōura, Aotearoa-New Zealand

On 14 November 2016, a magnitude (Mw) 7.8 earthquake struck the small coastal settlement of Kaikōura, Aotearoa-New Zealand. With an economy based on tourism, agriculture, and fishing, Kaikōura was immediately faced with significant logistical, economic, and social challenges caused by damage to critical infrastructure and lifelines, essential to its main industries. Massive landslips cut off road and rail access, stranding hundreds of tourists, and halting the collection, processing and distribution of agricultural products. At the coast, the seabed rose two metres, limiting harbour-access to high tide, with implications for whale watching tours and commercial fisheries. Throughout the region there was significant damage to homes, businesses, and farmland, leaving owners and residents facing an uncertain future. This paper uses qualitative case study analysis to explore post-quake transformations in a rural context. The aim is to gain insight into the distinctive dynamics of disaster response mechanisms, focusing on two initiatives that have emerged in direct response to the disaster. The first examines the ways in which agriculture, food harvesting, production and distribution are being reimagined with the potential to enhance regional food security. The second examines the rescaling of power in decision-making processes following the disaster, specifically examining the ways in which rural actors are leveraging networks to meet their needs and the consequences of that repositioning on rural (and national) governance arrangements. In these and other ways, the local economy is being revitalised, and regional resilience enhanced through diversification, capitalising not on the disaster but the region’s natural, social, and cultural capital. Drawing on insights and experience of local stakeholders, policyand decision-makers, and community representatives we highlight the diverse ways in which these endeavours are an attempt to create something new, revealing also the barriers which needed to be overcome to reshape local livelihoods. Results reveal that the process of transformation as part of rural recovery must be grounded in the lived reality of local residents and their understanding of place, incorporating and building on regional social, environmental, and economic characteristics. In this, the need to respond rapidly to realise opportunities must be balanced with the community-centric approach, with greater recognition given to the contested nature of the decisions to be made. Insights from the case examples can inform preparedness and recovery planning elsewhere, and provide a rich, real-time example of the ways in which disasters can create opportunities for reimagining resilient futures.
An effective methodology for mixed scan and reset design based on test generation and structure of sequential circuits

In this paper, a flip-flop selection methodology, which utilizes reachable states of flip-flops, required states for hard-to-detect faults, which are obtained from test generation, and the structural connection relationship of flip-flops, to achieve a nearly optimal mixed partial-scan/reset design, is proposed. The methodology first generates and simulates test patterns for the circuit-under-test to obtain information of reachable states and states needed for excitation and propagation of hard-to-detect faults. It then searches the connection relationship among flip-flops and arranges flip-flops in an appropriate order for mixed partial scan and reset selection. Experimental results show that the method achieves higher testability than reported methods with a lesser number of scan/reset flip-flops.
The Murine Cl-/HCO3- Exchanger Ae3 (Slc4a3) is Not Required for Acid-Base Balance but is Involved in Magnesium Handling by the Kidney

Background: The Slc4 family of bicarbonate transporters consists of several members, many of which are highly expressed in the kidney and play an important role in acid-base homeostasis. Among them are Ae1 (Slc4a1) and Ae2 (Slc4a2). Another member, Ae3 (Slc4a3), is suggested to be expressed in the kidney, however, its localization and impact on renal function is still unknown. Ae3 has also been implicated in the central control of breathing. Aims: Here, we analyzed the expression of Ae3 transcripts in isolated nephron segments and investigated systemic and renal acid-base homeostasis and renal electrolyte handling in the absence of Ae3, using a knock out mouse model. Methods: qPCR was used to localize Ae3 transcripts in the murine nephron, metabolic studies and whole body plethysmography to assess the role of Ae3 in renal functions. Results: Two Ae3 transcripts, the brain variant bAe3 and the cardiac variant cAe3, are expressed at low levels in the murine kidney. Although differentially distributed, they localize mostly to the distal nephron and renal collecting duct system. At baseline and after an acid challenge, mice deficient for Ae3 did not show major disturbances in renal acid-base excretion. Respiratory responses in whole body plethysmography to acid loading and CO2 and O2 challenges were normal. No major differences in renal electrolyte handling were discovered except for small changes in magnesium, potassium and sodium excretion after 7 days of acid loading. We therefore challenged mice with diets with high and low magnesium diets and found no differences in renal magnesium excretion but elevated expression of the Trpm6 magnesium channel in Ae3 KO mice. In conclusion, Ae3 is expressed in murine kidney at very low levels. Conclusions: Ae3 plays no role in systemic acid-base homeostasis but may modify renal magnesium handling inducing a higher expression of Trpm6.
Pitfalls With Radiopharmaceuticals

Introduction:There is a considerable body of evidence describing that the pharmacokinetics and pharmacodynamics of radiopharmaceuticals may be changed by a variety of drugs, disease states and in some cases, surgical procedures. Objective:To systematically search the medical literature and review the published evidence on adverse reactions to radiopharmaceuticals. Method:MEDLINE, EMBASE, International Pharmaceutical Abstracts and Science Citation Index were searched for studies reporting adverse reactions to radiopharmaceuticals. Controlled trials, cohort studies, case-control studies and case series published in major Western languages were considered for the review. Each study included in the present review was described in a narrative way, and major components of each study were reported (ie, research design, patient characteristics, types of drugs and radiopharmaceuticals, dosing information and adverse reactions). Results:The majority of adverse reactions to radiopharmaceuticals described in the literature required little or no treatment, and their negative effects were generally mild and self-limited. Large longitudinal greater than 5-year studies reported prevalence rates of adverse reactions due to radiopharmaceuticals ranging from 0 to 25 cases per 100,000 administrations. Case studies on the use of technetium reported mild adverse reactions; however, some led to potentially harmful complications. Similarly, studies involving fluorodeoxyglucose reported more severe adverse reactions. Conclusion:The literature on radiopharmaceuticals adverse effects is scarce, and just a few studies were conducted to investigate the association between radiopharmaceuticals and adverse reactions. Despite relatively mild and self-limited symptoms, the current widespread use of radiopharmaceuticals requires constant monitoring for adverse reactions.
Plasmids for C‐terminal tagging in Saccharomyces cerevisiae that contain improved GFP proteins, Envy and Ivy

Green fluorescent protein (GFP) has become an invaluable tool in biological research. Many GFP variants have been created that differ in brightness, photostability, and folding robustness. We have created two hybrid GFP variants, Envy and Ivy, which we placed in a vector for the C‐terminal tagging of yeast proteins by PCR‐mediated recombination. The Envy GFP variant combines mutations found in the robustly folding SuperfolderGFP and GFPγ, while the Ivy GFP variant is a hybrid of GFPγ and the yellow‐green GFP variant, Clover. We compared Envy and Ivy to EGFP, SuperfolderGFP and GFPγ and found that Envy is brighter than the other GFP variants at both 30°C and 37°C, while Ivy is the most photostable. Envy and Ivy are recognized by a commonly used anti‐GFP antibody, and both variants can be immunoprecipitated using the GFP TRAP Camelidae antibody nanotrap technology. Because Envy is brighter than the other GFP variants and is as photostable as GFPγ, we suggest that Envy should be the preferred GFP variant, while Ivy may be used in cases where photostability is of the utmost importance. The GenBank Accession No. for Envy is KM891731, for Ivy is KM891732 and for the yeast optimized GFPγ described in this paper is KM891733. Copyright © 2015 John Wiley & Sons, Ltd.
Predictability of return and volatility in Bitcoin markets

Graduate School Master of Science in Finance Predictability of return and volatility in the Bitcoin market By Lina Karlsson and Martin Eimer We study how abnormal liquidity affects the predictive power of returns and volatility in Bitcoin markets. The presence of abnormal liquidity can be explained by price manipulation which is the result from previous studies that found manipulators present in the market. We find that abnormal liquidity has no predictive power for returns but that abnormal liquidity has some predictive power of volatility. We cannot conclude a presence of price manipulators but according to our results regarding volatility there are elements that show irregularities in the markets. Our results further highlight the mechanisms of the market and how traders deal with fees. The results for volatility indicates that the amount of abnormal liquidity have an effect on future volatility which tells us something about how the market is functioning. This study highlights the importance of further exploration of the effects abnormal liquidity has on
The Behaviour of Banking Stocks During the Financial Crisis and Recessions. Evidence from Changes‐In‐Changes Panel Data Estimations

This paper examines the impact of the financial crisis and economic recessions on bank shares compared to the overall stock market index for 18 OECD countries from 1993 to 2015. The empirical methodology utilizes the changes-in-changes approach. We compare and contrast the returns of the bank ing stock price index (treatment group) in each country with their general stock price index (control group), which experiences smaller changes. Our results suggest that bank returns on average perform significantly worse than that of the general stock pr ice index during recessions. In addition we also find significantly greater volatility in bank share returns.
Purinergic signaling mediated by P2X7 receptors controls myelination in sciatic nerves

Adenosine‐5′‐triphosphate, the physiological ligand of P2X receptors, is an important factor in peripheral nerve development. P2X7 receptor is expressed in Schwann cells (SCs), but the specific effects of P2X7 purinergic signaling on peripheral nerve development, myelination, and function are largely unknown. In this study, sciatic nerves from P2X7 knockout mice were analyzed for altered expression of myelin‐associated proteins and for alterations in nerve morphology. Immunohistochemical analyses revealed that, in the wild‐type peripheral nerves, the P2X7 receptor was localized mainly in myelinating SCs, with only a few immunopositive nonmyelinating SCs. Complete absence of P2X7 receptor protein was confirmed in the sciatic nerves of the knockout mice by Western blot and immunohistochemistry. Western blot analysis revealed that expression levels of the myelin proteins protein zero and myelin‐associated glycoprotein are reduced in P2X7 knockout nerves. In accordance with the molecular results, transmission electron microscopy analyses revealed that P2X7 knockout nerves possess significantly more unmyelinated axons, contained in a higher number of Remak bundles. The myelinating/nonmyelinating SC ratio was also decreased in knockout mice, and we found a significantly increased number of irregular fibers compared with control nerves. Nevertheless, the myelin thickness in the knockout was unaltered, suggesting a stronger role for P2X7 in determining SC maturation than in myelin formation. In conclusion, we present morphological and molecular evidence of the importance of P2X7 signaling in peripheral nerve maturation and in determining SC commitment to a myelinating phenotype. © 2014 Wiley Periodicals, Inc.
Integration of RF functionalities in microwave waveguide components through 3D metal printing

This work reports on the integration of RF functionalities in microwave waveguide components through the selective laser melting process. A specific integrated component has been developed for the relevant application domain of satellite communications. The component operates in the Ku-K bands and integrates a H-plane bend, a 90-deg twist and ninth-order pass-band filter. The AlSi10Mg prototype manufactured through selective laser melting exhibits excellent RF performances (return loss > 20 dB, insertion loss < 0.23 dB, and rejection > 60 dB), while significantly minimizing mass, envelope and mechanical complexity.
Roles of Human Parainfluenza Virus Type 3 Bases 13 to 78 in Replication and Transcription: Identification of an Additional Replication Promoter Element and Evidence for Internal Transcription Initiation

ABSTRACT The genomic promoter of human parainfluenza virus type 3 (HPIV3) contains multiple cis-elements controlling transcription and replication. Previous work showed that regions 1 to 12 and 79 to 96 were critical in promoting replication of an HPIV3 minireplicon, while the intergenic sequence and N gene start signal (IS/Ngs, bases 49 to 61) were important for transcription. Because these data were collected primarily using point mutations, not every base from position 1 to 96 was analyzed, and some important control elements may have been missed. To clarify the role of bases 13 to 78 in transcription and replication, a series of mutations were made which collectively scanned this entire region. Mutation of bases 13 to 28 resulted in markedly decreased HPIV3 minireplicon replication, indicating these bases constitute an additional cis-element involved in the synthesis of the HPIV3 antigenomic RNA. The position dependence of the IS/Ngs was also examined. Analysis of mutants in which the IS/Ngs was shifted 5′ or 3′ showed that this segment could be moved without significantly disrupting transcription initiation. Additional mutants which contained two successive IS/Ngs segments were created to test whether the polymerase accessed the gene start signal by proceeding along the template 3′ to 5′ or by binding internally at the gene start signal. Based on analysis of the double gene start mutants, we propose a model of internal transcription initiation in which the polymerase enters the template at approximately the location of the natural N gene start but then scans the template bidirectionally to find a gene start signal and initiate transcription.
Phenotypic Susceptibilities to Tenofovir in a Large Panel of Clinically Derived Human Immunodeficiency Virus Type 1 Isolates

ABSTRACT Tenofovir is a nucleotide analogue human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) inhibitor, and its oral prodrug, tenofovir disoproxil fumarate, has recently been approved for the treatment of HIV-1 infection in the United States. The objective of this study was to characterize the in vitro susceptibility profiles of a large panel of clinically derived HIV-1 isolates for tenofovir. The distribution of tenofovir susceptibilities in over 1,000 antiretroviral-naive, HIV-1-infected individuals worldwide was determined using the Virco Antivirogram assay. In addition, phenotypic susceptibilities to tenofovir and other RT inhibitors were determined in a panel of nearly 5,000 recombinant HIV-1 clinical isolates from predominantly treatment-experienced patients analyzed as a part of routine drug resistance testing. Greater than 97.5% of isolates from treatment-naive patients had tenofovir susceptibilities <3-fold above those of the wild-type controls by the Antivirogram. The clinically derived panel of 5,000 samples exhibited a broad range of antiretroviral drug susceptibilities, including 69, 43, and 16% having >10-fold-decreased susceptibilities to at least one, two, and three antiretroviral drug classes, respectively. Greater than 88% of these 5,000 clinical isolates were within the threefold susceptibility range for tenofovir, and >99% exhibited <10-fold-reduced susceptibilities to tenofovir. Decreased susceptibility to tenofovir was not directly associated with resistance to other RT inhibitors; r2 values of log-log linear regression plots of susceptibility to tenofovir versus susceptibility to other RT inhibitors were <0.4. The results suggest that the majority of treatment-naive and treatment-experienced individuals harbor HIV that remains within the normal range of tenofovir susceptibilities and may be susceptible to tenofovir disoproxil fumarate therapy.