Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi‐gene phylogenetic analysis reveals that shochu‐fermenting Saccharomyces cerevisiae strains form a distinct sub‐clade of the Japanese sake cluster

Shochu is a traditional Japanese distilled spirit. The formation of the distinguishing flavour of shochu produced in individual distilleries is attributed to putative indigenous yeast strains. In this study, we performed the first (to our knowledge) phylogenetic classification of shochu strains based on nucleotide gene sequences. We performed phylogenetic classification of 21 putative indigenous shochu yeast strains isolated from 11 distilleries. All of these strains were shown or confirmed to be Saccharomyces cerevisiae, sharing species identification with 34 known S. cerevisiae strains (including commonly used shochu, sake, ale, whisky, bakery, bioethanol and laboratory yeast strains and clinical isolate) that were tested in parallel. Our analysis used five genes that reflect genome‐level phylogeny for the strain‐level classification. In a first step, we demonstrated that partial regions of the ZAP1, THI7, PXL1, YRR1 and GLG1 genes were sufficient to reproduce previous sub‐species classifications. In a second step, these five analysed regions from each of 25 strains (four commonly used shochu strains and the 21 putative indigenous shochu strains) were concatenated and used to generate a phylogenetic tree. Further analysis revealed that the putative indigenous shochu yeast strains form a monophyletic group that includes both the shochu yeasts and a subset of the sake group strains; this cluster is a sister group to other sake yeast strains, together comprising a sake‐shochu group. Differences among shochu strains were small, suggesting that it may be possible to correlate subtle phenotypic differences among shochu flavours with specific differences in genome sequences. Copyright © 2017 John Wiley & Sons, Ltd.
The yeasts of the genus Spathaspora: potential candidates for second‐generation biofuel production

Yeasts of the Spathaspora clade have the ability to convert d‐xylose to ethanol and/or xylitol. This is an important trait, as these yeasts may be used to produce bioethanol from lignocellulosic biomass or as a source of new d‐xylose metabolism genes for recombinant industrial strains of Saccharomyces cerevisiae. The core group of the genus Spathaspora has 22 species, both formally described and not yet described. Other species, such as Sp. allomyrinae, Candida alai, C. insectamans, C. lyxosophila, C. sake, Sp. boniae and C. subhashii are weakly associated with this clade, based on LSU rRNA gene D1/D2 sequence analyses. Spathaspora passalidarum, Sp. arborariae, Sp. gorwiae and Sp. hagerdaliae produce mostly ethanol from d‐xylose, whereas the remaining species within the Spathaspora clade already tested for this property may be considered xylitol producers. Among the d‐xylose‐fermenting Spathaspora species, Sp. passalidarum is the best ethanol producer, displaying high ethanol yields and productivities when cultured in media supplemented with this pentose under oxygen‐limited or anaerobic conditions. The species also exhibits rapid d‐xylose consumption and the ability to ferment glucose, xylose and cellobiose simultaneously. These characteristics suggest that Sp. passalidarum is a potential candidate for domestication and use in the fermentation of lignocellulosic materials. Copyright © 2017 John Wiley & Sons, Ltd.
Individualized Medicine for Epilepsy -Based on Genetic Information-

Current antiepileptic drug (AED) therapy requires trial and error in determining the most effective AED and dosage for a patient, and almost one-fourth of patients are resistant to AED therapy. The introduction of individualized medicine for epilepsy based on genetic information is a new avenue to improve current AED therapy. However, several crucial issues remain to be resolved before the development of individualized medicine for epilepsy can proceed further. The epilepsy genes responsible for common phenotypes have not yet been identified, and ongoing pharmacogenetic studies continue to search for an explanation of why 25 to 30% of patients do not respond to AEDs. There is no convincing clinical evidence indicating the impact of P-glycoprotein on prediction of clinical response. This article provides a critical review of the status and perspectives for the development of individualized medicine for epilepsy based on genetic polymorphisms/mutations in relation to core elements such as pharmacodynamic pathway, pharmacokinetic pathway, prediction of idiosyncratic reaction to AED, and mechanisms of action of AEDs.
Gene–gene and gene–environment interactions in complex traits in yeast

One of the fundamental questions in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that, in most cases, the effect of a genetic locus on the phenotype is context‐dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects. This does not reflect an absence of the contribution of genetic interactions to phenotypic variation, but instead is a consequence of the technical limitations in mapping gene–gene interactions (GGI) and gene–environment interactions (GEI). Yeast, with its detailed molecular understanding, diverse population genomics and ease of genetic manipulation, is a unique and powerful resource to study the contributions of GGI and GEI in the regulation of phenotypic variation. Here we review studies in yeast that have identified GGI and GEI that regulate phenotypic variation, and discuss the contribution of these findings in explaining missing heritability of complex traits, and how observations from these GGI and GEI studies enhance our understanding of the mechanisms underlying genetic robustness and adaptability that shape the architecture of the genotype–phenotype map.
A self-calibrated 2–1–1 cascaded continuous-time ΔΣ modulator

A 2–1–1 cascaded continuous-time ΔΣ modulator (DSM) is self-calibrated with LMS-based adaptation. Its noise cancellation filter (NCF) is derived using a parameter-based continuous-time (CT) to discrete-time (DT) transform. These techniques reduce the quantization noise leakage due to the mismatch between analog modulator and digital NCF. A 0.18-µm CMOS prototype operating at 360MHz with a 1-Vpp full-scale demonstrates a leakage noise spectral density below 10nV/√Hz over a 30-MHz bandwidth after the capacitors in the Gm-C loop filters are self-trimmed with a 1.1% step. This level of noise leakage is well below the noise floor of most CT DSM designs.
Layout-dependent proximity effects in deep nanoscale CMOS

As CMOS scaling extends into the nanoscale regime, designers need to be aware that device behavior depends not only on traditional geometric parameters such as channel length and width, but also on layout implementation details of the device and its surrounding neighborhood. The advent of stress engineering, in which intentional mechanical stress is applied to improve device performance, also adds new geometric dependencies. This paper reviews the major process technology features that cause layout-dependent proximity effects and how to account for these effects in circuit and layout design.
Preclinical evaluation of a novel drug-eluting balloon in an animal model of in-stent stenosis

Despite advances in contemporary stent technology, in-stent restenosis (ISR) remains the major limitation following revascularization procedures. We developed a porcine model of ISR to specifically investigate the preclinical outcomes of a novel drug-eluting balloon (DEB) in this particular setting. Fifteen pigs received bare metal stents in each of the major coronary arteries for 28 days to induce neointimal growth. Following repeat angiography, animals were allocated to fourdifferent treatment groups. The control group consisted of a bare angioplasty catheter, while the Pantera Lux™ (3.0 µg/mm2 paclitaxel) (30 s inflation) was compared to two consecutive deployments of the Pantera Lux™ (60 s inflation each) and the commercial SeQuent® Please balloon (60 s inflation). Twenty-eight days following balloon deployment, the animals underwent repeat angiography and were subsequently sacrificed for histopathologic assessment. There was a trend in reduction of percent diameter stenosis in the DEB group versus control (13.9% vs. 20.4%), while longer inflation duration or consecutive DEB deployment had no additional growth-limiting effect. Neointimal thickness was reduced from 0.38 ± 0.13 to 0.30 ± 0.09 mm in the control versus DEB group. All DEB groups showed delayed vascular healing characterized by dose-dependent increases in fibrin deposition and neointimal cell vacuity. Investigation of DEB in a porcine model of ISR is feasible and more accurately represents human disease conditions. The magnitude of neointima suppression is lower than that observed in non-diseased animal models and is accompanied by delayed vascular healing.
Synthesis and detection of a seaborgium carbonyl complex

A carbonyl compound that tips the scales Life is short for the heaviest elements. They emerge from high-energy nuclear collisions with scant time for detection before they break up into lighter atoms. Even et al. report that even a few seconds is long enough for carbon to bond to the 106th element, seaborgium (see the Perspective by Loveland). The authors used a custom apparatus to direct the freshly made atoms out of the hot collision environment and through a stream of carbon monoxide and helium. They compared the detected products with theoretical modeling results and conclude that hexacarbonyl Sg(CO)6 was the most likely structural formula. Science, this issue p. 1491; see also p. 1451 A special apparatus enables synthesis of a compound with carbon bonds to a short-lived element produced via nuclear reaction. [Also see Perspective by Loveland] Experimental investigations of transactinoide elements provide benchmark results for chemical theory and probe the predictive power of trends in the periodic table. So far, in gas-phase chemical reactions, simple inorganic compounds with the transactinoide in its highest oxidation state have been synthesized. Single-atom production rates, short half-lives, and harsh experimental conditions limited the number of experimentally accessible compounds. We applied a gas-phase carbonylation technique previously tested on short-lived molybdenum (Mo) and tungsten (W) isotopes to the preparation of a carbonyl complex of seaborgium, the 106th element. The volatile seaborgium complex showed the same volatility and reactivity with a silicon dioxide surface as those of the hexacarbonyl complexes of the lighter homologs Mo and W. Comparison of the product’s adsorption enthalpy with theoretical predictions and data for the lighter congeners supported a Sg(CO)6 formulation.
Sharp increase in central Oklahoma seismicity since 2008 induced by massive wastewater injection

Wastewater disposal linked to earthquakes The number of earthquakes is increasing in regions with active unconventional oil and gas wells, where water pumped at high pressure breaks open rock containing natural gas, leaving behind wastewater in need of disposing. Keranen et al. show that the steep rise in earthquakes in Oklahoma, USA, is likely caused by fluid migration from wastewater disposal wells. Twenty percent of the earthquakes in the central United States could be attributed to just four of the wells. Injected fluids in high-volume wells triggered earthquakes over 30 km away. Science, this issue p. 448 The recent surge in central U.S. seismicity is likely attributable to injection of wastewater at a small number of wells. Unconventional oil and gas production provides a rapidly growing energy source; however, high-production states in the United States, such as Oklahoma, face sharply rising numbers of earthquakes. Subsurface pressure data required to unequivocally link earthquakes to wastewater injection are rarely accessible. Here we use seismicity and hydrogeological models to show that fluid migration from high-rate disposal wells in Oklahoma is potentially responsible for the largest swarm. Earthquake hypocenters occur within disposal formations and upper basement, between 2- and 5-kilometer depth. The modeled fluid pressure perturbation propagates throughout the same depth range and tracks earthquakes to distances of 35 kilometers, with a triggering threshold of ~0.07 megapascals. Although thousands of disposal wells operate aseismically, four of the highest-rate wells are capable of inducing 20% of 2008 to 2013 central U.S. seismicity.
On the Complexity of Matrix Group Problems I

We build a theory of black box groups, and apply it to matrix groups over finite fields. Elements of a black box group are encoded by strings of uniform length and group operations are performd by an oracle. Subgroups are given by a list of generators. We prove that for such subgroups, membership and divisor of the order are in NPB. (B is the group box oracle.) Under a plausible mathematical hypothesis on short presentations of finite simple groups, nom membership and exaact order will also be in NPB and thus in NPB ∩ NPB.
Shortest Paths in Euclidean Graphs (Extended Abstract)

We analyze a simple method for finding shortest paths in Euclidean graphs (where vertices are points in a Euclidean space and edge weights are distances between points). For many graph models, the running time of the algorithm to find the shortest path between a specified pair of vertices in a graph with V vertices and E edges is shown to be O(V) as compared with O (V log V + E) required by the classical (Dijkstra) algorithm.
RGD-conjugated iron oxide magnetic nanoparticles for magnetic resonance imaging contrast enhancement and hyperthermia

The purpose of this study was to develop a specific targeting magnetic nanoparticle probe for magnetic resonance imaging and therapy in the form of local hyperthermia. Carboxymethyl dextran–coated ultrasmall superparamagnetic iron oxide nanoparticles with carboxyl groups were coupled to cyclic arginine-glycine-aspartic peptides for integrin αvβ3 targeting. The particle size, magnetic properties, heating effect, and stability of the arginine-glycine-aspartic–ultrasmall superparamagnetic iron oxide were measured. The arginine-glycine-aspartic–ultrasmall superparamagnetic iron oxide demonstrates excellent stability and fast magneto-temperature response. Magnetic resonance imaging signal intensity of Bcap37 cells incubated with arginine-glycine-aspartic–ultrasmall superparamagnetic iron oxide was significantly decreased compared with that incubated with plain ultrasmall superparamagnetic iron oxide. The preferential uptake of arginine-glycine-aspartic–ultrasmall superparamagnetic iron oxide by target cells was further confirmed by Prussian blue staining and confocal laser scanning microscopy.
Encapsulation of simvastatin in PLGA microspheres loaded into hydrogel loaded BCP porous spongy scaffold as a controlled drug delivery system for bone tissue regeneration

The main objective of this study was to fabricate a controlled drug delivery which is simultaneously effective for bone regeneration. We have encapsulated simvastatin, which enhances osteoblastic activity, in the poly (lactic-co-glycolic acid) microspheres. Loading of these microspheres inside the spongy scaffold of biphasic calcium phosphate with the help of Gelatin (Gel) hydrogel controls the delivery of the drug, and ensures a more favorable drug release profile. As a result, some significant benefits have been achieved, such as higher mechanical strength, excellent biocompatibility in in vitro experiments. For determining the characteristics of the composite scaffold, several analysis, such as scanning electron microscope, EDX, X-ray diffraction, FT-IR, and porosity were carried out. The in vitro drug release profile clearly indicates that simvastatin release from the microsphere was more controlled and prolonged after loading in the scaffold. Biocompatibility was certainly higher for the final composite scaffold compared to drug unloaded scaffold, as assessed through MTT assay and Confocal imaging with MC3T3-E1 pre-osteoblast cells. Cell attachment and proliferation were certainly higher in the presence of drug loaded microspheres. Bone remodeling gene and protein expression were observed by real-time polymerase chain reaction and Western blot respectively. Simvastatin loaded scaffold exhibited the best results in every determination which was carried out.
Unique in the shopping mall: On the reidentifiability of credit card metadata

Large-scale data sets of human behavior have the potential to fundamentally transform the way we fight diseases, design cities, or perform research. Metadata, however, contain sensitive information. Understanding the privacy of these data sets is key to their broad use and, ultimately, their impact. We study 3 months of credit card records for 1.1 million people and show that four spatiotemporal points are enough to uniquely reidentify 90% of individuals. We show that knowing the price of a transaction increases the risk of reidentification by 22%, on average. Finally, we show that even data sets that provide coarse information at any or all of the dimensions provide little anonymity and that women are more reidentifiable than men in credit card metadata.
Universal packet routing algorithms

The packet-routing problem is examined in a network-independent context. The goal is to devise a strategy for routing that works well for a wide variety of networks. To achieve this goal, the routing problem is partitioned into two stages: a path-selection stage and a scheduling stage. In the first stage, paths for the packets are found with small maximum distance and small maximum congestion. Once the paths are fixed, both are lower bounds on the time required to deliver the packets. In the second stage, a schedule is found for the movement of each packet along its path so that no two packets traverse the same edge at the same time and the total time and maximum queue size required to route all of the packets to their destinations are minimized. The second stage is more challenging and is the focus of this study. <<ETX>>
Polytopes, permanents and graphs with large factors

Randomized algorithms for approximating the number of perfect matchings in a graph are considered. An algorithm that is a natural simplification of one suggested and analyzed previously is introduced and analyzed. One of the key ideas is to view the analysis from a geometric perspective: it is proved that for any graph G the k-slice of the well-known Edmonds matching polytope has magnification 1. For a bipartite graph G=(U, V, E), mod U mod = mod V mod =n, with d edge-disjoint perfect matchings, it is proved that the ratio of the number of almost perfect matchings to the number of perfect matchings is at most n/sup 3n/d/. For any constant alpha >0 this yields a a fully polynomial randomized algorithm for approximating the number of perfect matchings in bipartite graphs with d>or= alpha n. Moreover, for some constant c>0 it is the fastest known approximation algorithm for bipartite graphs with d>or= clog n. <<ETX>>
A case report of pregnancy tumor and its management using the diode laser

Pyogenic granuloma (PG) is a tumor-like growth in the oral cavity. It is manifested as a painless sessile or pedunculated, erythematous, exophytic and specific papular or nodular with a smooth or lobulated surface, which may have a fibrinous covering. The lesion usually bleeds easily on a slight provocation. PG is considered to be a non-neoplastic in nature. It is a reactive lesion, also classified in pregnancy associated gingival diseases. It occurs due to irritation or physical trauma from calculus or cervical restorations as also some contribution by hormonal factors and usually affects the gingiva, but can be seen in areas of frequent trauma such as lower lip, tongue, oral mucosa, and palate. The growth is typically seen on or after the third month of pregnancy and may grow rapidly to acquire a large size, thus, requiring surgical removal. The diode laser has also been used as an alternative treatment modality. This is a case report of PG in a patient treated with the diode laser.
A double-edged sword for tropical forests

Contrary to expectation, high-yielding tropical crops may cause forest loss in the tropics With a growing global population and increasing per capita consumption, reconciling agricultural production with biodiversity conservation is a major challenge to humanity (1). A frequently promoted solution to stem the tide of agricultural expansion is to increase crop yields, allowing global demand to be met without further tropical forest losses. Recent genome sequencing of key crops such as oil palm, eucalyptus, rubber, soybean, rice, and cocoa could facilitate substantial yield increases (2–4). Could such yield improvements offer a solution to both tropical forest loss and agricultural demand, or could they pose further challenges to tropical conservation?
Guest editorial: Science, technology, innovation and research: the ultimate conundrum?

I was recently working with a group of researchers who are in the field of nursing informatics; it was an international group who have only recently been brought together. The researchers came from a broad range of discipline backgrounds and not all of us were nurses. There were computer scientists, psychologists and informaticians; as a consequence the conversation was broad and interweaved. However, what did emerge was a real tension in the group between the need to provide policy makers and purchasers of health services with the evidence they need now to support real-time decisions and the time it takes for researchers to develop, design, set up and undertake a robust programme of research. This was graphically displayed when we started to talk about the evidence in the field of telehealth. These technologies are currently very fashionable. There are a lot of companies actively seeking to sell their goods into an expanding market place. Everyone would appear to see some aspect of telehealth as a solution to some aspect of health need, but look again at the evidence base for this and we know so little. This, however, has not stopped the UK committing itself to putting 3 million people into interventions in the next few years. As a recent public launch of the campaign notes: ‘‘‘3millionlives’’ is about transforming service delivery for people with long-term conditions, and/or social care needs, by utilising telehealth and telecare within health and social care services, enabling millions of people to receive the significant benefits evidenced in the UK’s Whole System Demonstrator trials; the largest randomised control trial of telecare and telehealth in the world’ (http:// www.3millionlives.co.uk). All this sounds very reassuring but really from a low base it is not difficult to be the largest randomised telecare control trial. We have not really asked how these technologies should be deployed. Which aspects of these technologies add value to patient outcomes and not just cost reduction? Does seeing someone using a visual link as well as speaking to them really make a big enough difference to justify the cost? Do you leave a telehealth system in for 2 weeks, 2 months, a year or a life time? We just do not know, yet their impact on aspects of clinical