nils-herrmann/clean_scirepeval huggingface dataset:
Mechanism of ribosomal subunit association: oligodeoxynucleotides as probes.

From the kethoxal treatment data [Herr, W.; Chapman, N.M.; Noller, H.F. (1979) ] some regions of ribosomal RNAs are thought to be responsible for the association of 30S and 50S ribosomes of E. coli to form 70S ribosomes. In order to test this possibility about a dozen oligodeoxynucleotides complementary to the suspected regions of rRNAs were synthesised. Their association with ribosomes and naked rRNAs was tested by the gel filtration technique. In order to check the effects on the ribosomal subunit association or rRNA association either intact 30S and 50S ribosomes or naked 16S and 23S rRNAs were preincubated with the individual oligodeoxynucleotide and its effect was checked by density gradient centrifugation followed by UV absorbance monitoring. Some oligodeoxynucleotides interfered with either subunit association or 16S RNA and 23S RNA association, some with both. These data clearly indicate that RNA-RNA interaction plays the major role in ribosomal subunit association.

Field of study: Biology, Chemistry, Physics
Optical control of vortices in dense media of gas-filled optical fibers

The problem of the formation of optical vortices in a medium composed of three-level atoms is analyzed with allowance for local-field effects in off-resonance Raman regimes of Λ-scheme interaction. The possibility of optical control of the vortex dynamics without disturbing their stability is demonstrated in the optically dense medium of a hollow fiber filled with 87Rb vapor.

Field of study: Physics
Top-k query processing for replicated data in mobile peer to peer networks

In mobile ad hoc peer to peer (M-P2P) networks, since nodes are highly resource constrained, it is effective to retrieve data items using a top-k query, in which data items are ordered by the score of a particular attribute and the query-issuing node acquires data items with the k highest scores. However, when network partitioning occurs, the query-issuing node cannot connect to some nodes having data items included in the top-k query result, and thus, the accuracy of the query result decreases. To solve this problem, data replication is a promising approach. However, if each node sends back its own data items (replicas) responding to a query without considering replicas held by others, same data items are sent back to the query-issuing node more than once through long paths, which results in increase of traffic. In this paper, we propose a top-k query processing method considering data replication in M-P2P networks. This method suppresses duplicate transmissions of same data items through long paths. Moreover, an intermediate node stops transmitting a query message on-demand.

Field of study: Computer science, Engineering
DNA oligonucleotide-assisted genetic manipulation increases transformation and homologous recombination efficiencies: Evidence from gene targeting of Dictyostelium discoideum.

Artificial gene alteration by homologous recombination in living cells, termed gene targeting, presents fundamental and considerable knowledge of in vivo gene function. In principle, this method can possibly be applied to any type of genes and transformable cells. However, its success is limited due to a low frequency of homologous recombination between endogenous targeted gene and exogenous transgene. Here, we describe a general gene-targeting method in which co-transformation of DNA oligonucleotides (oligomers) could significantly increase the homologous recombination frequency and transformation efficiency. The oligomers were simply designed such that they were identical to both the ends of the homologous flanking regions of the targeting construct. Using this strategy, both targeted alleles of diploid cells were simultaneously replaced in a single transformation procedure. Thus, the simplicity and versatility of this method applicable to any type of cell may increase the application of gene targeting.

Field of study: Biology, Engineering
Government as manager, citizen as consumer: the case of Criminal Justice Act 1991

Over the last fifteen years, wider and wider areas of public administration in the United Kingdom have become infused with a discourse hitherto associated rather with the commercial world. The concern with efficiency, always an important one, has come increasingly to be approached on the assumption that the imposition of a market-type model can deliver improvements in the quality of public  Through full-scale privatisation, but also, more recently, via strategies of partial 'contracting out' and 'market testing,' Government has adopted what might be characterised as a 'managerial approach': one in which an idealised image of the private sector is constantly held up as a model, to be compared favourably with the archaic and inefficient public sector. This has been true both in terms of Government's own strategies and in terms of the frameworks which it has imposed upon a wide range of bodies providing public goods and services.

Field of study: Law
Catherine Davies, Claire Brewster and Hilary Owen, South American Independence: Gender, Politics, Text (Liverpool: Liverpool University Press, 2006), pp. xi+321, £50.00, hb.

dominated by creoles. This was attempted through the introduction of intendentes, whose subdelegados assumed responsibility for urban finance and a wide range of public works. At the same time, the power of cabildos over their cities’ hinterlands was reduced. In attempting to provide order and symmetry to the towns, the authorities began to separate public from private space, constructing new public buildings, regulating markets and public spaces, cleaning the streets, and organising police forces (alcaldes de barrios) based on designated districts. While the major cities grew, Lucena Giraldo shows that growth was greatest in areas of substantial European and African slave immigration, such as Caracas, Buenos Aires and Havana, and in fortified frontier towns ; while most major cities saw an increased military presence. Finally, in the Conclusion, he describes how conflicts with the British in Venezuela and Argentina, followed by the wars of independence were catastrophic for urban development in many parts of region. This is well-conceived book. It is one of the few to consider the whole colonial period in some detail. Another of its strengths is its wide coverage of cities at different levels in the urban hierarchy and in different regions, whereas many texts concentrate on the major capital cities. Nevertheless, this is a book that approaches the topic very much from the perspective of how Spain’s power was reflected in the physical plan and structure of the city. Those seeking an economic or social history of cities, and especially the role of non-Spanish groups, will have to look elsewhere. That said, the book is based on a very wide-range of published sources and constitutes a sound introduction to the nature of urbanism in colonial Spanish America. The topic lends itself to the use of illustrations and it is disappointing that none are included. Nevertheless, it is written in a lively manner and is a welcome addition to the literature on the Spanish colonial city in the Spanish language.

Field of study: Political science
The Proterozoic macrofossil Tawuia as a coenocytic eukaryote and a possible macroalga

Proterozoic carbonaceous macrofossils are key to understand the evolution of early eukaryotes and how they acquired macroscopic sizes. However, phylogenetic interpretation of these macrofossils is challenging because most of them are morphologically simple and lack phylogenetically diagnostic features. Among Proterozoic carbonaceous macrofossils, the tomaculate fossil Tawuia is relatively rich in characters and is common in Proterozoic successions. However, its phylogenetic interpretation is uncertain and Tawuia has been variously interpreted as a bacterium or an alga (photosynthetic eukaryote), in part because certain aspects of its morphologies have not been consistently documented, hampering their functional interpretations. Here we report exceptionally preserved Tawuia specimens from the Tonian Liulaobei and Shiwangzhuang formations in North China. These fossils show that Tawuia is a tomaculate organism, sometimes with an axial stripe, terminal discoidal structures, and transverse constrictions, features that were previously documented but variously interpreted. We infer that Tawuia was a coenocytic organism with recalcitrant cell walls, asexual reproduction through asymmetric constrictions, and possible abscission structures. These features indicate that Tawuia is probably a coenocytic eukaryote, and possibly a macroalga, although more evidence is needed to confirm these interpretations, particularly the photosynthetic nature of Tawuia. A literature review reveals that the key features described here occur not only in many Tonian Tawuia specimens, but also in some possible Mesoproterozoic Tawuia fossils as much as ca. 1.6 Ga old. The new data and interpretations of Tawuia presented here provide important constraints on the origin and early evolution of coenocytic eukaryotes, primary plastids, and macroalgae, particularly if the Mesoproterozoic Tawuia fossils are confirmed as macroalgae.

Field of study: Environmental science, Geography
Selecting Sagittarius:identification and chemical characterization of the Sagittarius stream

Wrapping around the Milky Way, the Sagittarius stream is the dominant substructure in the halo. Our statistical selection method has allowed us to identify 106 highly likely members of the Sagittarius stream. Spectroscopic analysis of metallicity and kinematics of all members provides us with a new mapping of the Sagittarius stream. We find correspondence between the velocity distribution of stream stars and those computed for a triaxial model of the Milky Way dark matter halo. The Sagittarius trailing arm exhibits a metallicity gradient, ranging from −0.59 to −0.97 dex over 142°. This is consistent with the scenario of tidal disruption from a progenitor dwarf galaxy that possessed an internal metallicity gradient. We note high metallicity dispersion in the leading arm, causing a lack of detectable gradient and possibly indicating orbital phase mixing. We additionally report on a potential detection of the Sextans dwarf spheroidal in our data.

Field of study: Physics
Avoidance of structural pitfalls in spinal meningioma resection.

Creating a surgical avenue through which to resect an intraspinal meningioma requires dissection of the musculoligamentous structures of the spine. Variable vertebral components must be removed to create a corridor to the intraspinal compartment. The cardinal principles of intraspinal tumor resection are to minimize the intraoperative risk of deformation and traumatic injury of the spinal cord. Therefore, the appropriate planning for access to and removal of the osseous elements is critical. Of equal importance is the consideration of the biomechanics of the spine. In cases of potential spinal instability instrumentation-assisted fusion should be performed at the time of tumor resection. The authors discuss the techniques for creating access to these tumors and propose a simple classification scheme to assist with this decision-making process.

Field of study: Medicine
Visions of the Emerald City: Modernity, Tradition, and the Formation of Porfirian Mexico (review)

This work makes an important and engaging contribution to our understanding of peripheral modernity in late-nineteenth and early-twentieth century Mexico, and especially the role of provincial cities like Oaxaca "in mediating the experience of modernity" (p. 6). As Overmyer-Velazquez carefully explains, modernity is a cultural construct that emerges out of the discursive interplay between things represented as "modern" and things represented as "traditional." Straightforward as this explanation might seem (a testimony to the author's cogent exposition of a complex and often convoluted body of theory), modernity's emergence is never simple. In Oaxaca, for example, "elites and commoners alike constructed modernity physically in the streets, plazas, neighborhoods, and buildings of the Emerald City . . . and discursively through notions of class, race, gender, sexuality, and religion as displayed in things like civic regulations, newspapers, and public rituals" (p. 2). This potent combination of multiple authorship and contentious social issues meant that although modernity might have promised Oaxacans "order and progress," it produced instead all manner of "anxieties."

Field of study: History
Efficacy of the MEK Inhibitor Cobimetinib and its Potential Application to Colorectal Cancer Cells

Mutations in the Ras/Raf/MEK/ERK pathway are detected in 50% of colorectal cancer cases and play a crucial role in cancer development and progression. Cobimetinib is a MEK inhibitor approved for the treatment of advanced melanoma and inhibits the cell viability of other types of cancer cells.  HCT116 colorectal cancer cells were treated with cobimetinib, and MTT assay, colony formation assay, and flow cytometry were used to evaluate cell viability, cell cycle, and apoptosis, respectively. The expression of genes associated with the cell cycle and apoptosis were evaluated by quantitative real-time PCR and western blotting. To explore use of cobimetinib in colorectal cancer treatment and further understand its mechanisms, RNA-seq technology was used to identify differentially expressed genes (DEGs) between cobimetinib-treated and untreated HCT116 cells. Furthermore, we compared these DEGs with Gene Expression Omnibus data from colorectal cancer tissues and normal colonic epithelial tissues.  We found that cobimetinib not only inhibited cell proliferation but also induced G1 phase arrest and apoptosis in HCT116 colorectal cancer cells, suggesting that cobimetinib may useful in colorectal cancer therapy. After cobimetinib treatment, 3,495 DEGs were obtained, including 2,089 upregulated genes and 1,406 downregulated genes, and most of these DEGs were enriched in the cell cycle, DNA replication, and DNA damage repair pathways. Our results revealed that some genes with high expression in colorectal cancer tissues were downregulated by cobimetinib in HCT116 cells, including CCND1, E2F1, CDC25C, CCNE2, MYC, and PCNA. These genes have vital roles in DNA replication and the cell cycle. Furthermore, genes with low expression in colorectal cancer tissues were upregulated by cobimetinib, including PRKCA, PI3K, RTK, and PKC. Based on our results, the PKC and PI3K pathways were activated after cobimetinib treatment, and inhibition of these two pathways can increase the cytotoxicity of cobimetinib in HCT116 cells. Notably, cobimetinib appeared to enhance the efficacy of 5-fluorouracil (5-FU) by decreasing TYMS expression, high expression of which is responsible for 5-FU resistance in colorectal cancer.  Our results suggest the potential use of cobimetinib in colorectal cancer therapy.

Field of study: Biology, Chemistry
Heuristic algorithm for finding boundary cycles in location-free low density wireless sensor networks

Wireless sensor networks (WSNs) comprise a large number of sensor nodes, which are spread out within a region to be monitored and communicate using wireless links. In some WSN applications, recognizing boundary nodes is important for topology discovery, geographic routing, tracking and guiding. In this paper, we study the problem of identifying the boundary nodes of a WSN. In a WSN, close-by nodes can establish direct communications with their neighbors and have the ability to estimate distances to nearby nodes, but not necessarily the true distances. Our objective is to find the boundary nodes by using only the connectivity relation and neighbor distance information without any other knowledge of node locations. Moreover, our main aim is to design a distributed algorithm that works even when the average degree is low. We propose a heuristic algorithm to find the boundary nodes which are connected in a boundary cycle of a location-free, low density (average degree 5-6), randomly deployed WSN. We develop the key ideas of our boundary detection algorithm in the centralized scenario and extend these ideas to the distributed scenario. The distributed implementation is more realistic for real WSNs, especially for sparse networks when all local information cannot be collected very well due to sparse connectivity. In addition, the distributed implementation can tolerate faults by recomputing the boundary locally when a boundary node is faulty. Simulations in ns-2 show that the distributed implementation outperforms the centralized one with higher quality of boundaries.

Field of study: Computer science
The Role of Signal Transducer and Activator of Transcription 3 (Stat3) in Stretch Injury to Bladder Smooth Muscle Cells

Excessive stretch of the bladder can lead to wall thickening including the growth of bladder smooth muscle cells (BSMC) and bladder dysfunction. We uncovered a factor previously unexamined for its role in bladder stretch injury: signal transducer and activator of transcription 3 (STAT3). STAT3 was assessed for its role in mitogen- and stretch-induced BSMC proliferation.  In vivo stretch model: Eight mice underwent bladder hyper-distention (40 cm H2O for 5 min). Controls were catheterized only (n = 3). Bladders were harvested and total protein extracts were screened for activated signaling proteins using a bank of phospho-specific antibodies (Kinexus, AB, Canada). Screen results demonstrated novel induction of STAT3, which was assessed further for its requirement in supporting growth factor (GF) and stretch-induced bSMC proliferation. In vitro proliferation and stretch model: Bladder smooth muscle cell were grown on stretch and culture plates. Smooth muscle cell proliferation was induced by growth factors such as EGF, PDGF, 10% serum and mechanical stretch. To half of the plates STAT3 inhibitor was added and bladder smooth muscle proliferation was assessed using 3H-Thymidine incorporation and visual cell counting.  In vivo stretch model: In vivo bladder stretch confirmed activation of MAPK pathway, as well as a previously unrecognized STAT3. In vitro proliferation and stretch model: Using an upstream STAT3 specific inhibitor, (AG-490) the proliferative responses to mitogenic and mechanical stimuli was blunted. Cell counting confirmed 3H-thymidine incorporation results.  STAT3 signaling is activated by in vivo bladder stretch, a condition associated with FP. In vitro, STAT3 inhibition blocks mitogenic and stretch-induced bSMC proliferation.

Field of study: Medicine
Constructing candidate word lists using acoustically similar word groups

A method for identifying a set of candidate words that matches well with a given utterance is discussed. The method uses precomputed groups of acoustically similar words. Given a vocabulary, for each word a short list of words that are acoustically similar to it is computed. These groups are constructed using training utterances recorded by several speakers and used in an isolated utterance recognition system to construct candidate word lists during recognition. Experiments show that the correct word appears on the short list of candidate words constructed during recognition using this scheme over 98% of the time.

Field of study: Engineering
Recent advances in the chemistry and biological activities of the Pimpinella species of Turkey

Two new natural products incorporating a phenylpropyl subunit ("phenylpropanoids"), [4-(prop-2-enyl)phenyl angelate and 4-(3-methyloxiranyl)phenyl 2-methylbutyrate], one new bisabolene-type sesquiterpenoid [1-methyl-4-(6-methylhepta-1,5-dien-2-yl)-7-oxabicyclo[4.1.0]heptane ("aureane")], and one new trinorsesquiterpene [4-(6-methylbicyclo[4.1.0]hept-2-en-7yl)butan-2-one ("traginone")] have been isolated from the essential oils of Pimpinella species occurring in Turkey, together with nine known phenylpropanoids and other natural products. Six of the known compounds are newly reported for Umbelliferae, whilst one is newly reported for Pimpinella species. Compound structures were determined by 1D and 2D NMR analysis. Isolated compounds were evaluated for antimalarial, antimicrobial, estrogenic, and aphidicidal activities. Pure compounds were also tested for antifungal activity against strawberry anthracnose-causing fungal plant pathogens Colletotrichum acutatum, C. fragariae, and C. gloeosporioides using direct bioautography and microdilution broth assays.

Field of study: Chemistry
Vacancy- and acceptor-H complexes in InP

It has been suggested that iron in InP is compensated by a donor, related to the local vibrational mode and previously assigned to the fully hydrogenated indium vacancy, . Using AIMPRO, an ab initio local density functional cluster code, we find that acts as a single shallow donor. It has a triplet vibrational mode at around this value, consistent with this assignment. We also analyse the other hydrogenated vacancies , and determine their structure, vibrational modes, and charge states. Substitutional group II impurities also act as acceptors in InP, but can be passivated by hydrogen. We investigate the passivation of beryllium by hydrogen and find that the hydrogen sits at a bond-centred site and is bonded to its phosphorus neighbour. Its calculated vibrational modes are in good agreement with experiment.

Field of study: Materials science
Extrapolation of tectonic boundaries across the Labrador shelf: U–Pb geochronology of well samples

Near Saglek Fiord, a northerly trending boundary between the early Archean Saglek block and the middle Archean Hopedale block extends between drill sites which, respectively, sampled Uivak amphibolite gneiss with U–Pb zircon intercept ages of 3742 ± 12 and 2752 ± 42 Ma, and migmatitic Lister gneiss with concordant ages of for restite and , for leucosome. Titanite ages of ca. 2508 Ma are common to both rocks. A nearby metapsammitic gneiss has detrital zircon and monazite ages of 2681 ± 5, 2700 ± 4, ca. 2730, and 2750 ± 2 Ma representing high-grade metamorphism related to the Hopedale–Saglek collision and metamorphic monazite of ca. 2560 Ma age representing metamorphism of the sediment during reactivation of the Saglek–Hopedale suture. Two hundred kilometres southeast, a gneissic granite records a protolith age of 3170 Ma and Late Proterozoic Pb loss. Near the Nain–Makkovik boundary, 1269 ± 4 Ma zircons indicate a significant extension of the Nain Platonic Suite. South of the Makkovik boundary, a foliated g...

Field of study: Environmental science