Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of the Gravitational Lens Magnifying a Type Ia Supernova

Magnified Flare-Up The rise and fall of the luminosity of a supernova detected in 2010 was typical for its class, but its apparent brightness was 30 times greater than similar events. Quimby et al. (p. 396) compared spectra from the time of peak brightness and after the supernova faded, from which they concluded that something was interfering with our line of sight to the supernova. A previously unknown foreground galaxy turned out to be acting as a lens, bending and magnifying the light from the supernova. Potentially, spacetime warping like this could allow direct testing of cosmic expansion. An unusually bright supernova faded away to reveal a foreground galaxy responsible for bending and amplifying its light. Objects of known brightness, like type Ia supernovae (SNIa), can be used to measure distances. If a massive object warps spacetime to form multiple images of a background SNIa, a direct test of cosmic expansion is also possible. However, these lensing events must first be distinguished from other rare phenomena. Recently, a supernova was found to shine much brighter than normal for its distance, which resulted in a debate: Was it a new type of superluminous supernova or a normal SNIa magnified by a hidden gravitational lens? Here, we report that a spectrum obtained after the supernova faded away shows the presence of a foreground galaxy—the first found to strongly magnify a SNIa. We discuss how more lensed SNIa can be found than previously predicted.
Evolutionary algorithm with parallel evaluation strategy using constrained penalty-based boundary intersection

Most of real-world optimization problems correspond to constrained multi-objective optimization problems (CMOPs). Multi-objective evolutionary algorithms (MOEAs) are useful to find out diverse Pareto-optimal solutions in CMOPs, and has been applied in various engineering fields. In order to expand the range of application of MOEAs further, we propose an improved evolutionary algorithm with parallel evaluation strategy (EAPES). In EAPES, feasible solutions and infeasible solution are separately stored in different populations, and infeasible solutions are evaluated in an unusual manner where not only feasible solutions but also useful infeasible solutions are used as parents to reproduce the populations for the next generation. Infeasible solutions are ranked based on a scalarizing function determined by objective function values and a total constraint violation value. This paper investigates the performance of the proposed EAPES to search for Pareto-optimal solutions compared to NSGA-II and the previous EAPES. The proposed EAPES with a well-tuned parameter is most capable to explore Pareto-optimal solutions with good diversity, spread, and convergence to the true Pareto front. The proposed EAPES assigns bad rank to the infeasible solutions that exist away from the true Pareto front, and does not store such solutions. Thus the proposed EAPES exhibits a higher searching capability than the previous EAPES by evaluating infeasible solutions in an appropriate balance between objective functions and total constraint violation. In addition, the results suggest that the proposed EAPES may exhibit high solution search performance even in more difficult CMOPs, which have more objective functions and/or more constraints.
In Situ TEM Observation of a Microcrucible Mechanism of Nanowire Growth

Nanowire Growth Observed In the hypothetical microcrucible growth mechanism for nanowires, a molten catalytic particle located in a pore on a substrate continually feeds the outward growth of the wire. To observe such a mechanism requires the ability to examine nanowire growth in situ. Boston et al. (p. 623) studied various stages of Y2BaCuO5 nanowire growth using transmission electron microscopy and were able to observe a microcrucible growth mechanism directly. Nanowire growth from a microcrucible catalyst particle at the bottom of the wire is observed in situ. The growth of metal oxide nanowires can proceed via a number of mechanisms such as screw dislocation, vapor-liquid-solid process, or seeded growth. Transmission electron microscopy (TEM) can resolve nanowires but invariably lacks the facility for direct observation of how nanowires form. We used a transmission electron microscope equipped with an in situ heating stage to follow the growth of quaternary metal oxide nanowires. Video-rate imaging revealed barium carbonate nanoparticles diffusing through a porous matrix containing copper and yttrium oxides to subsequently act as catalytic sites for the outgrowth of Y2BaCuO5 nanowires on reaching the surface. The results suggest that sites on the rough surface of the porous matrix act as microcrucibles and thus provide insights into the mechanisms that drive metal oxide nanowire growth at high temperatures.
Energy at life's origin

Analysis of the bioenergetics of primitive organisms suggests that life began at hydrothermal vents Energy-releasing chemical reactions are at the core of the living process of all organisms. These bioenergetic reactions have myriad substrates and products, but their main by-product today is adenosine triphosphate (ATP), life's primary currency of metabolic energy. Bioenergetic reactions have been running in a sequence of uninterrupted continuity since the first prokaryotes arose on Earth more than 3.5 billion years ago, long before there was oxygen to breathe (1). Under what conditions did these bioenergetic processes first evolve?
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs. Elephant bird mitochondrial sequences suggest that flightless bird ancestors were able to fly and dispersed through flight Ruffling ancient ratite feathers Biologists have often pointed to the breakup of the supercontinent Gondwana to explain how related species ended up on far-flung continents, but as new research shows, that explanation doesn't fly with ratite birds. Ratite birds are a lineage of large, mostly flightless birds including the African ostrich, the Australian emu, the South American rhea, the diminutive New Zealand kiwi, and the extinct Madagascar elephant bird. Mitchell et al. examined the phylogeny of these birds, adding ancient mitochondrial DNA sequences from the extinct elephant bird. It seems that ratites originated from flighted ancestors who evolved large sizes and loss of flight only after flying to their new homes. Science, this issue p. 898.
Bradycardia During Dexmedetomidine and Therapeutic Hypothermia

Dexmedetomidine is a centrally acting α2-adrenergic agonist which is currently Food and Drug Administration— approved for the short-term (less than 24 hours) sedation of adults during mechanical ventilation. Given its beneficial physiologic effects and limited adverse effect profile, there is growing interest regarding its potential applications in the Pediatric intensive care unit patient including sedation during mechanical ventilation, procedural sedation, the treatment of withdrawal, and prevention of emergence agitation. Although generally safe and effective, occasional hemodynamic effects including bradycardia and hypotension have been reported. Clinical experience has demonstrated that bradycardia may be more common when dexmedetomidine is administered with other medications that have negative chronotropic effects. We report 2 pediatric patients with traumatic brain injury who had good long-term neurologic outcomes, but developed clinically significant bradycardia when therapeutic hypothermia was added to a sedation regimen that included dexmedetomidine and remifentanil. The role of dexmedetomidine as a neuroprotective agent is explored as well as a review presented of previous reports of bradycardia related to dexmedetomidine.
Cancer Suppression by the Chromosome Custodians, BRCA1 and BRCA2

Germline mutations in BRCA1 and BRCA2 predispose to common human malignancies, most notably tumors of the breast and ovaries. The proteins encoded by these genes have been implicated in a plethora of biochemical interactions and biological functions, confounding attempts to coherently explain how their inactivation promotes carcinogenesis. Here, I argue that tumor suppression by BRCA1 and BRCA2 originates from their fundamental role in controlling the assembly and activity of macromolecular complexes that monitor chromosome duplication, maintenance, and segregation across the cell cycle. A tumor-suppressive role for the BRCA proteins as “chromosome custodians” helps to explain the clinical features of cancer susceptibility after their inactivation, provides foundations for the rational therapy of BRCA-deficient cancers, and offers general insights into the mechanisms opposing early steps in human carcinogenesis.
The Development of New, Primary, Noninvasive Carcinoma of the Breast 29 Years after Bilateral Radical Mastectomy

Abstract: We present the case of a patient with a new, primary noninvasive breast carcinoma arising in residual breast tissue 29 years after radical mastectomy. The patient, a 75‐year‐old black woman with no family history of breast or ovarian cancer, had undergone left radical mastectomy in 1956 (age 35) and right radical mastectomy in 1965 (age 44). Examination revealed a 3‐mm nodule in the right anterior axillary line. On excision, the lesion was a 1.5‐mm intracystic papillary ductal carcinoma in situ arising in a background of atypical ductal hyperplasia (representing residual breast tissue). The patient has not agreed to testing for BRCA1 or BRCA2 mutations. The theoretical risk of new primary breast cancers arising in residual breast tissue has been suggested as a reason why prophylactic mastectomy may not be completely effective. This case suggests that even after what appeared to be aggressive radical mastectomy, enough breast tissue remained so that the patient was at risk for recurrent breast cancer.
The Axis of Tolerance

Communication between different immune cells of the intestinal mucosa acts as a rheostat that maintains tolerance to gut microbes. [Also see Research Article by Mortha et al.] The gut poses a unique challenge to the organism. The host must tolerate beneficial commensal bacteria, yet allow for rapid protective responses to invading pathogens. Failure to maintain this balance may cause intestinal disorders such as chronic inflammatory bowel disease. Fortunately, a dynamic, yet robust, state of chronic, low-grade inflammation maintains this balance (“primed homeostasis”). Thus, the host actively engages the gut microbiota, controlling its composition by secreting antimicrobial peptides and immunoglobulins. Conversely, commensals shape the gut-associated immune system by controlling the prevalence of distinct T cell populations (1). On page 1477 of this issue, Mortha et al. (2) show how communication between specific myeloid and lymphoid cells controls immune homeostasis under exposure to the gut microflora. Such cellular details of this steady state may guide the development of rational therapies for intestinal inflammatory conditions.
Epstein-Barr Virus Turns 50

Fifty years after the discovery of Epstein-Barr virus and its association with cancer, a vaccine or therapy for the virus remains elusive. This month marks the 50th anniversary of the discovery of Epstein-Barr virus (EBV) as the first human tumor virus. In March 1964, a team led by Anthony Epstein identified herpesvirus-like particles in cultured tumor cells derived from African Burkitt's lymphoma tissue (1). At that time, the idea that a virus caused human cancer was met with some skepticism because the theory that cancer was infectious had been dismissed in the previous century. Stalwart investigators continued to track EBV until the viral culprit was declared a class I carcinogen by the International Agency for Research on Cancer and the World Health Organization in the late 1990s. Despite the consensus that EBV is a bona fide tumor virus, the mechanisms of cancer causation by EBV remain an area of active investigation and controversy 50 years since its initial discovery.
Caspase-mediated cleavage of phospholipid flippase for apoptotic phosphatidylserine exposure

How cells haul down their “eat me” flags Dead and dying cells expose a membrane lipid called phosphatidylserine (PS) on their cell surface as a sort of “eat me” signal. Segawa et al. identified the membrane enzyme responsible for flipping any PS that inadvertently makes it way from the inner to the outer leaflet of the plasma membrane lipid bilayer. Without the enzyme, macrophages gobbled up healthy cells. Science, this issue p. 1164 An enzyme maintains the asymmetrical distribution of a surface phospholipid during programmed cell death. Phospholipids are asymmetrically distributed in the plasma membrane. This asymmetrical distribution is disrupted during apoptosis, exposing phosphatidylserine (PtdSer) on the cell surface. Using a haploid genetic screen in human cells, we found that ATP11C (adenosine triphosphatase type 11C) and CDC50A (cell division cycle protein 50A) are required for aminophospholipid translocation from the outer to the inner plasma membrane leaflet; that is, they display flippase activity. ATP11C contained caspase recognition sites, and mutations at these sites generated caspase-resistant ATP11C without affecting its flippase activity. Cells expressing caspase-resistant ATP11C did not expose PtdSer during apoptosis and were not engulfed by macrophages, which suggests that inactivation of the flippase activity is required for apoptotic PtdSer exposure. CDC50A-deficient cells displayed PtdSer on their surface and were engulfed by macrophages, indicating that PtdSer is sufficient as an “eat me” signal.
Transactions in Distributed Event-Based Middleware

Distributed event-based middleware (DEBM) provides a basis for the interoperation of autonomous components in large-scale systems. Transactions ensure the atomic and reliable execution of operations that involve interconnected clients. Integrating transactions and DEBM is a challenging software design problem with important applications. This paper presents the Hermes transaction service (HTS), a service that supports event-driven applications with transactional requirements. HTS uses transaction-context propagation via event notifications, where the contexts of publishers and subscribers are interrelated within a mixed transaction. Clients may opt to be compensatable or non-compensatable. Optional anonymity of transaction participants is supported through hash-based set memberships
Identification of common traits in improved xylose‐growing Saccharomyces cerevisiae for inverse metabolic engineering

Four recombinant Saccharomyces cerevisiae strains with enhanced xylose growth (TMB3400, C1, C5 and BH42) were compared with two control strains (TMB3399, TMB3001) through genome‐wide transcription analysis in order to identify novel targets for inverse metabolic engineering. A subset of 13 genes with changed expression levels in all improved strains was selected for further analysis. Thirteen validation strains and two reference strains were constructed to investigate the effect of overexpressing or deleting these genes in xylose‐utilizing S. cerevisiae. Improved aerobic growth rates on xylose were observed in five cases. The strains overexpressing SOL3 and TAL1 grew 19% and 24% faster than their reference strain, and the strains carrying deletions of YLR042C, MNI1 or RPA49 grew 173%, 62% and 90% faster than their reference strain. Copyright © 2008 John Wiley & Sons, Ltd.
Optogenetic Regeneration

Applying tools from optogenetics with ideas from regenerative medicine may herald a new era of translational optogenetics. [Also see Report by Bryson et al.] The first decade of optogenetics has seen many efforts to improve our understanding of normal and pathological neural circuitry (1). The great impact of these efforts has stemmed from an alliance between systems neuroscientists and protein engineers—the first group identifying neural circuits amenable to causal dissection, the second developing tools that enable unprecedented degrees of control over neural activity. The next decade of optogenetics is likely to see the development of a new alliance that may have similarly important implications–one between optogenetics and translational medicine. On page 94 of this issue, Bryson et al. describe one model for how such an alliance may proceed, applying tools from optogenetics in concert with ideas in regenerative medicine to restore muscle function in a mouse model of peripheral nerve injury (2).
Genomic-scale exchange of mRNA between a parasitic plant and its hosts

Strangleweed shares too much information Because RNA normally functions within an individual cell, we generally think that we keep our RNAs to ourselves. Kim et al. now show that the parasitic dodder plant breaks that rule. When dodder attacks a host plant, it opens up a conduit through which messenger and perhaps other regulatory RNAs are exchanged between parasite and host. Because a single dodder plant can attack multiple hosts, such exchanges may underlie instances of genes transferring between species. Science, this issue p. 808 Strangleweed (Cuscuta pentagona) can exchange large numbers of messenger RNAs with different host plants. Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.
RRD1, a component of the TORC1 signalling pathway, affects anaesthetic response in Saccharomyces cerevisiae

The molecular mechanisms of action of volatile anaesthetics remain unknown despite clinical use for over 150 years. While many effects of these agents have been characterized, clear insight into how these effects relate to the physiological state of anaesthesia has not been established. Volatile anaesthetics arrest cell division in Saccharomyces cerevisiae in a manner that parallels the anaesthetic actions of these drugs in mammals. To gain additional insight into the cellular activities of these drugs, we isolated genes that, when present on multi‐copy plasmids, render S. cerevisiae resistant to the volatile anaesthetic isoflurane. One of these genes, RRD1, encodes a subunit of the Tap42p–Sit4p–Rrd1p phosphatase complex that functions in the target of rapamycin complex 1 (TORC1) signalling pathway. In addition, we show that mutations in two other genes encoding components of the TORC1 pathway, GLN3 and URE2, also affect yeast anaesthetic response. These findings suggest that TORC1‐mediated signalling is involved in cellular response to volatile anaesthetics in S. cerevisiae. Copyright © 2009 John Wiley & Sons, Ltd.
Dosage‐dependent roles of the Cwt1 transcription factor for cell wall architecture, morphogenesis, drug sensitivity and virulence in Candida albicans

The Cwt1 transcription factor is involved in cell wall architecture of the human fungal pathogen Candida albicans. We demonstrate here that deficiency of Cwt1 leads to decreased β1,6‐glucan in the cell wall, while mannoproteins are increased in the cell wall of exponentially growing cells and are released into the medium of stationary phase cells. Hyphal morphogenesis of cwt1 mutants is reduced on the surfaces of some inducing media. Unexpectedly, the CWT1/cwt1 heterozygous strains shows some stronger in vitro phenotypes compared to the homozygous mutant. The heterozygous but not the homozygous strain is also strongly impaired for its virulence in a mouse model of systemic infection. We suggest that an intermediate dosage of Cwt1 affects phenotypes profoundly, while its complete absence may elicit compensatory responses of C. albicans. Copyright © 2009 John Wiley & Sons, Ltd.
Identifying Relevant Users and Groups in the Context of Credit Analysis Based on Data from Twitter

In recent years several online social networks have emerged with very different purposes. This huge popularity is associated with common functionality to provide users with new ways to interact, producing content and commenting on various subjects and interests. This fact makes social networks favorable to research related to the organization and management of large amounts of data, besides constituting an ideal environment for knowledge extraction and application of data mining techniques. In this sense, this study collected data from the social network Twitter, and compared them with data from a financial institution in order to model the network and analyze their similarities. Three thousand users from Twitter were analyzed and 504 matched with the database from company for credit analysis. The results demonstrated that most of those users have more credit restriction than their neighbors, and users with no restrictions normally have also neighborhoods with no credit restriction as well.