Miracle-dz/UniFAR-FTUs huggingface dataset:
Laboratory-evolved Vanillyl-alcohol Oxidase Produces Natural Vanillin*

The flavoenzyme vanillyl-alcohol oxidase was subjected to random mutagenesis to generate mutants with enhanced reactivity to creosol (2-methoxy-4-methylphenol). The vanillyl-alcohol oxidase-mediated conversion of creosol proceeds via a two-step process in which the initially formed vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) is oxidized to the widely used flavor compound vanillin (4-hydroxy-3-methoxybenzaldehyde). The first step of this reaction is extremely slow due to the formation of a covalent FAD N-5-creosol adduct. After a single round of error-prone PCR, seven mutants were generated with increased reactivity to creosol. The single-point mutants I238T, F454Y, E502G, and T505S showed an up to 40-fold increase in catalytic efficiency (kcat/Km) with creosol compared with the wild-type enzyme. This enhanced reactivity was due to a lower stability of the covalent flavin-substrate adduct, thereby promoting vanillin formation. The catalytic efficiencies of the mutants were also enhanced for other ortho-substituted 4-methylphenols, but not for p-cresol (4-methylphenol). The replaced amino acid residues are not located within a distance of direct interaction with the substrate, and the determined three-dimensional structures of the mutant enzymes are highly similar to that of the wild-type enzyme. These results clearly show the importance of remote residues, not readily predicted by rational design, for the substrate specificity of enzymes.
A multi-hop mobility management protocol for heterogeneous wireless networks: OTHER ARTICLE

Purpose – Mobility management for single‐hop cellular networks has received much research attention in the last few years. One of the research challenges for 4G wireless systems is the design of mobility management techniques that integrate cellular and ad‐hoc networks. Currently, there are no structured mobility management schemes for these heterogeneous multi‐hop networks. This paper aims to address these issues.Design/methodology/approach – This paper describes techniques for tracking a mobile node (MN) in an integrated architecture with minimum overhead. This paper proposes group rerouting concept.Findings – The paper implements and evaluates the proposed protocol by using the network simulator (NS‐2). The proposed protocol increases performance compared to broadcasting schemes.Research limitations/implications – This scheme considers devices with two interfaces only.Practical implications – The paper proposes a scheme to extend the coverage of cellular base stations by using ad‐hoc devices.Originalit.
Measuring Effective Democracy: The Human Empowerment Approach

The core idea inspiring democracy is to empower people. To measure democracy in ways that capture its empowering nature one must focus on popular rights and take into account rule of law as a state quality that makes these rights effective. Based on this premise, we portray an index of "effective democracy" and test its qualities against six alternative indicators of democracy for some 150 states. We find the index of effective democracy to best represent the empowering nature of democracy because it most clearly captures democracy’s embedding in empowering conditions in the wider society. Specifically, effective democracy is shown to be most firmly embedded in (a) empowering socioeconomic conditions that make people capable of practicing democracy and (b) in empowering sociocultural conditions that make them willing to do so. In light of these findings, people empowerment appears to be a unity of empowering societal conditions and empowering regime characteristics, the latter of which are best depicted by the index of effective democracy.
3-D velocity estimation for two planes in vivo

3-D velocity vectors can provide additional flow information applicable for diagnosing cardiovascular diseases e.g. by estimating the out-of-plane velocity component. A 3-D version of the Transverse Oscillation (TO) method has previously been used to obtain this information in a carotid flow phantom with constant flow. This paper presents the first in vivo measurements of the 3-D velocity vector, which were obtained over 3 cardiac cycles in the common carotid artery of a 32-year-old healthy male volunteer. Data were acquired using a Vermon 3.5 MHz 32×32 element 2-D phased array transducer and stored on the experimental scanner SARUS. The full 3-D velocity profile can be created and examined at peak-systole and end-diastole without ECG gating in two planes. Maximum out-of-plane velocities for the three peak-systoles and end-diastoles were 68.5-5.1 cm/s and 26.3-3.3 cm/s, respectively. In the longitudinal plane, average maximum peak velocity in flow direction was 65.2-14.0 cm/s at peak-systole and 33.6-4.3 cm/s at end-diastole. A commercial BK Medical ProFocus UltraView scanner using a spectral estimator gave 79.3 cm/s and 14.6 cm/s for the same volunteer. This demonstrates that real-time 3-D vector velocity imaging without ECG gating yields quantitative in vivo estimations on flow direction and magnitude.
Temperature-Sensitive Mutants and Revertants in the Coronavirus Nonstructural Protein 5 Protease (3CLpro) Define Residues Involved in Long-Distance Communication and Regulation of Protease Activity

ABSTRACT Positive-strand RNA virus genomes are translated into polyproteins that are processed by viral proteases to yield functional intermediate and mature proteins. Coronaviruses (CoVs) carry genes that encode an nsp5 protease (also known as 3CLpro or Mpro) responsible for 11 maturation cleavages. The nsp5 structure contains two chymotrypsin-like domains (D1 and D2) and a unique domain (D3), and forms functional dimers. However, little is known of interactions or communication across the structure of the protease during nsp5 activity. Using reverse genetic mutagenesis of the CoV murine hepatitis virus (MHV) nsp5, we identified a new temperature-sensitive (ts) mutation in D2 of nsp5 (Ser133Ala) and confirmed a ts residue in D3 (Phe219Leu). Both D2-tsS133A and D3-tsF219L were impaired for viral replication and nsp5-mediated polyprotein processing at the nonpermissive temperature. Passage of tsS133A and tsF219L at the nonpermissive temperature resulted in emergence of multiple second-site suppressor mutations, singly and in combinations. Among the second-site mutations, a D2 His134Tyr change suppressed the ts phenotype of D2-tsS133A and D3-tsF219L, as well as the previously reported D2-tsV148A. Analysis of multiple CoV nsp5 structures, and alignment of nonredundant nsp5 primary sequences, demonstrated that ts and suppressor residues are not conserved across CoVs and are physically distant (>10 Å) from each other, from catalytic and substrate-binding residues, and from the nsp5 dimer interface. These findings demonstrate that long-distance communication pathways between multiple residues and domains of nsp5 play a significant role in nsp5 activity and viral replication, suggesting possible novel targets for non-active site inhibitors of nsp5.
Prognosis of depression in old age compared to middle age: a systematic review of comparative studies.

OBJECTIVE Depression in old age has a poor long-term prognosis; equal evidence shows that the same is true of depression in middle age. The authors sought to identify research that has compared the prognosis of depression in late life with depression in midlife under similar conditions. METHOD The authors separated studies that examined age at presentation/recruitment from studies of age at first episode of depression, studies that examined remission/response from those that examined relapse/recurrence, and those that examined mortality/risk of dementia. RESULTS Evidence suggests that response and remission rates to pharmacotherapy and ECT are not sufficiently different in old-age depression and middle-age depression to be clinically significant. Older patients at study entry appear to have a higher risk of further episodes, which informs the debate about the duration of continuation treatment for depression in older people. However, older patients and patients with late-onset depression are at increased risk of medical comorbidity. Medical comorbidity is a risk factor for inferior treatment response and poor antidepressant tolerability. Elderly patients with early-onset depression are more likely to have had a higher number of previous episodes, which also adversely influences prognosis compared to elderly depressed patients with late onset of illness. CONCLUSIONS With control for confounding variables, remission rates of depression in patients in late life are little different from those in midlife, but relapse rates appear higher. Findings underline the importance of assessing factors related to patient age and not just to age itself in evaluations of risk factors for poor prognosis.
Avoidable interruptions during drug administration in an intensive rehabilitation ward: improvement project.

AIMS To record the frequency of interruptions and their causes, to identify 'avoidable' interruptions and to build an improvement project to reduce 'avoidable' interruptions. BACKGROUND In Italy each year 30,000-35,000 deaths per year are attributed to health-care system errors, of which 19% are caused by medication errors. The factors that contribute to drug management error also include interruptions and carelessness during treatment administration. METHODS A descriptive study design was used to record the frequency of interruptions and their causes and to identify 'avoidable' interruptions in an intensive rehabilitation ward in Northern Italy. A data collection grid was used to record the data over a 6-month period. RESULTS A total of 3000 work hours were observed. During the study period 1170 interruptions were observed. The study identified 14 causes of interruption. CONCLUSIONS The study shows that of the 14 cases of interruptions at least nine can be defined as 'avoidable'. An improvement project has been proposed to reduce unnecessary interruptions and distractions to avoid making errors. IMPLICATIONS FOR NURSING MANAGEMENT An additional useful step to reduce the incidence of treatment errors would be to implement the use of a single patient medication sheet for the recording of drug prescription, preparation and administration and also the incident reporting.
What Drives China's Current Account?

The paper offers an empirical taxonomy of the factors driving China's current account. A simple present-value model with non-tradeable goods explains more than 70 percent of current account variability over the period 1982–2007, including the persistent surpluses since 2001. It also correctly predicts the decline of China's current account since 2008. Expected increases in the prices of non-tradeables (e.g. housing and medical care) and expected declines in net output (GDP less investment and government spending) are the main channels of external adjustment. Much of China's current account surplus seems driven by shocks that have global effects by persistently depressing the world real interest rate. This is consistent with recent theoretical models that suggest that factors related to China's domestic financial development are key in understanding global imbalances.
Patrones genómicos de divergencia en el complejo Anthothoe del hemosferio sur Implicancias para la delimitación de especies en las anémonas de mar (orden actiniaria)

Sea anemones (order Actiniaria) constitute a relatively well defined group within the phylum Cnidaria and are characterized as soft-bodied, generally solitary polyps that inhabit marine environments worldwide. During the last two centuries, morphology-based taxonomy permitted the proliferation of species descriptions given the conspicuous phenotypic variability of these seemingly simple animals. The molecular revolution and the debate over the species concept led in recent decades to re-evaluate the species hypothesis within many taxa, including Actiniaria. The problem in this group, however, is accentuated by the inadequacy of most taxonomic descriptions, high levels of morphological convergences, and the lack of knowledge about the structure and evolution of the diagnostic features presently used for taxa determination. Furthermore, signs of morphological variability at micro-scale has been accumulating for many of the characteristics frequently required to distinguish anemone species. Spatial distribution has been emerging instead as a more reliable variable to explain cryptic
Aerodynamic effects of corrugation in flapping insect wings in hovering flight

SUMMARY We have examined the aerodynamic effects of corrugation in model insect wings that closely mimic the wing movements of hovering insects. Computational fluid dynamics were used with Reynolds numbers ranging from 35 to 3400, stroke amplitudes from 70 to 180 deg and mid-stroke angles of incidence from 15 to 60 deg. Various corrugated wing models were tested (care was taken to ensure that the corrugation introduced zero camber). The main results are as follows. At typical mid-stroke angles of incidence of hovering insects (35–50 deg), the time courses of the lift, drag, pitching moment and aerodynamic power coefficients of the corrugated wings are very close to those of the flat-plate wing, and compared with the flat-plate wing, the corrugation changes (decreases) the mean lift by less than 5% and has almost no effect on the mean drag, the location of the center of pressure and the aerodynamic power required. A possible reason for the small aerodynamic effects of wing corrugation is that the wing operates at a large angle of incidence and the flow is separated: the large angle of incidence dominates the corrugation in determining the flow around the wing, and for separated flow, the flow is much less sensitive to wing shape variation. The present results show that for hovering insects, using a flat-plate wing to model the corrugated wing is a good approximation.
Abolition of endocrine dimorphism in hyperthyroid males? An argument for the positive feedback effect of hyperoestrogenaemia on LH secretion

Our aim was (i) to investigate the hypothalamo–hypophyseal–gonadal axis in hyperthyroid Indian males, (ii) to rule out the modulatory role of adrenal steroids on it and (iii) to determine if the simultaneous rise in oestradiol and luteinising hormone (LH) in hyperthyroid males is due to a positive feedback action of oestradiol on pituitary LH release. Age‐ and BMI‐matched men were divided into two groups, I, euthyroid subjects (n = 17) and II, hyperthyroid patients (n = 12) on the basis of their thyroid hormone levels. Serum levels of thyroid‐stimulating hormone, triiodothyronine, thyroxine, LH, follicle‐stimulating hormone (FSH), prolactin, E2, T, P4, sex hormone binding globulin and dehydroepiandrosterone sulphate (DHEAS) were assayed. Mean levels of T and E2 were approximately two times higher in group II in comparison with group I. DHEAS levels were similar in both groups ruling out any adrenal involvement. Mean serum LH level was 2.6 folds higher in group II in comparison with group I. Mean serum levels of FSH were higher in group II, it was marginally nonsignificant. On the basis of these and previous observations, we hypothesise that endocrinological dimorphism in human male and female is not rigid; a sustained rise in serum oestradiol probably induces a positive feedback action on pituitary leading to elevated gonadotrophin levels.
Porphyromonas gingivalis Genes Involved in fimA Regulation

ABSTRACT Porphyromonas gingivalis is an important component of the complex plaque biofilm that is a direct precursor of periodontal disease. The major fimbriae are required for attachment to oral surfaces and are an important virulence factor. Fimbrillin (FimA) expression in P. gingivalis is inhibited by surface molecule of Streptococcus cristatus, an early colonizer of dental plaque. In this study, differential display PCR was used to identify P. gingivalis genes that are regulated in response to S. cristatus. Of several differentially expressed genes, pg2131 and pg2167 were upregulated by S. cristatus signaling molecules. A null mutant of pg2167 did not transcriptionally regulate fimA following exposure to S. cristatus. In fact, fimA transcription was enhanced in the pg2167 mutant, suggesting that pg2167 may act to repress fimA expression. In contrast, a mutation in pg2131 did not affect transcription of fimA in the presence of S. cristatus. However, production of fimbrillin was significantly diminished in the pg2131 mutant, implicating involvement in posttranscriptional regulation in fimbriation. These data suggest that P. gingivalis fimbriation is controlled by more than one regulation mechanism, involving both transcriptional and posttranscriptional processes.
Roles of H+-ATPase and proton motive force in ATP-dependent protein translocation in vitro

Membrane vesicles from an Escherichia coli mutant with a deletion of the uncBC operon required ATP to translocate proteins, thus ruling out an essential role of F1F0-H+-ATPase in ATP-dependent protein translocation. Moreover, proteins could be translocated in the absence of proton motive force. At suboptimal ATP concentrations, D-lactate stimulated protein translocation, indicating that proton motive force, although insufficient to support translocation, could facilitate the process.
Swarm intelligence for groundwater management optimization

This paper presents some simulation–optimization models for groundwater resources management. These models couple two of the most successful global optimization techniques inspired by swarm intelligence, namely particle swarm optimization (PSO) and ant colony optimization (ACO), with one of the most commonly used groundwater flow simulation code, MODFLOW. The coupled simulation–optimization models are formulated and applied to three different groundwater management problems: (i) maximization of total pumping problem, (ii) minimization of total pumping to contain contaminated water within a capture zone and (iii) minimization of the pumping cost to satisfy the given demand for multiple management periods. The results of PSO- and ACO-based models are compared with those produced by other methods previously presented in the literature for the three case studies considered. It is found that PSO and ACO are promising methods for solving groundwater management problems, as is their ability to find optimal or near-optimal solutions.
A technique for quantitative three-dimensional analysis of microvascular structure.

Research into angiogenesis and vascular microarchitecture has contributed to progress in a wide variety of biomedical fields, but increased understanding is limited, in part, by the available assays and imaging modalities. Techniques that allow quantitation of vascular microarchitecture are needed. A comprehensive method is presented that uses 6-microm-thick serial sections of frozen tissue samples, immunostaining for CD31, brightfield microscopy, automated alignment of two-dimensional serial sections, and volume rendering to produce high-resolution, three-dimensional, quantifiable images of microvascular structure. Application of the technique is shown by characterizing vascularization into a fibrin gel implanted against the skeletal muscle of rats and explanted after 7 days. Comparing measurements from automated and manually aligned MRI and fibrin samples verified quantitation. Automation removes concerns of observer bias or variation inherent in manual alignment and increases the speed of analysis. Analysis of the fibrin gel reveals a dense (4.3 +/- 1.1% endothelial cell density) network of tortuous (1.37 +/- 0.05 tortuosity) capillaries that replaces the gel as it degrades. There is a high level of void space (22.8 +/- 3.6%) in the gel, and average capillary length in the fibrovascular tissue was 93.0 +/- 7.4 microm. Data obtained from these automatically aligned images agreed with those obtained using manual analysis (no statistical difference), and the results are consistent with data from traditional methods.
SPC 72 : a spindle pole component required for spindle orientation in the yeast Saccharomyces cerevisiae

The monoclonal antibody 78H6 recognises an 85 kDa component of the yeast spindle pole body. Here we identify and characterise this component as Spc72p, the product of YAL047C. The sequence of SPC72 contains potential coiledcoil domains; its overexpression induced formation of large polymers that were strictly localised at the outer plaque and at the bridge of the spindle pole body. Immunoelectron microscopy confirmed that Spc72p was a component of these polymers. SPC72 was found to be non-essential for cell growth, but its deletion resulted in abnormal spindle positioning, aberrant nuclear migration and defective mating capability. Precisely, deletion of SPC72 resulted in a decreased number of astral microtubules: early in the cell cycle only few were detectable, and these were unattached to the spindle pole body in small-budded cells. Later in the cell cycle few, if any, remained, and they were unable to align the spindle properly. We conclude that Spc72p is not absolutely required for nucleation per se, but is needed for normal abundance and stability of astral microtubules.
Common and rare side‐effects of low‐dose thalidomide in multiple myeloma: focus on the dose‐minimizing peripheral neuropathy

Objectives: Thalidomide has demonstrated a remarkable efficacy in the treatment of multiple myeloma but its use may cause several toxicities. We have investigated the common and rare side‐effects, especially analysing peripheral neuropathy, in order to optimise the thalidomide dose for minimizing this harmful side‐effect.
Joint design of relay precoding and artificial noise with presence of an eavesdropper

Wireless devices have experienced great development in the past decade. During this period, secrecy studies have drawn heated attention. Traditionally, there mainly exist two methods to optimize secrecy transmissions, precoding scheme and artificial-noise-aided scheme. In this paper, we propose a joint design of precoding and artificial noise in a relay-aided network with the channel state information (CSI) already known. Besides, based on wiretapping knowledge known or not, defined by whether we have known which user is wiretapped, we proposed two different schemes. Simulation results are given to verify the effectiveness of our proposed schemes.
Iodine based optical frequency reference with 10−15 stability

We present different setups for frequency stabilization of Nd:YAG lasers to absorption lines in molecular iodine featuring frequency stabilities of 3 · 10−15 at averaging times between 100 s and 1000 s. First results of a semi-monolithic setup, developed aiming at a space qualifiable iodine frequency reference, are shown.
The arsD gene encodes a second trans‐acting regulatory protein of the plasmid‐encoded arsenical resistance operon

The plasmid‐encoded arsenical resistance (ars) operon produces resistance to trivalent and pentavalent salts of arsenic and antimony. The first gene in the operon, arsR, was previously shown to encode a repressor protein. A newly identified gene, arsD, is shown here to encode a regulatory protein, the ArsD protein. The gene was identified by construction of an in‐frame fusion between the C‐terminally truncated arsD gene and the coding region for the mature form of β‐lactamase (blaM). The native arsD gene product was overexpressed and radioactively labelled as a 13kDa polypeptide. A frameshift mutation within the arsD gene resulted in elevated levels of expression of downstream ars genes. Co‐expression of a wild‐type arsD gene in trans with the operon containing the mutated arsD gene reduced expression of the downstream genes to wild‐type levels. The presence of the arsD gene had no effect on the basal level of operon expression set by the arsR gene product, and the repression produced by the arsD gene product was not affected by inducers of the operon. The results indicate that the ArsD protein is an inducer‐independent trans‐acting regulatory protein.