bluuebunny/crossref_metadata_2025 huggingface dataset:
Disposable surface plasmon resonance aptasensor with membrane-based sample handling design for quantitative interferon-gamma detection
Authors: Chuang Tsung-Liang , Chang Chia-Chen , Chu-Su Yu , Wei Shih-Chung , Zhao Xi-hong , Hsueh Po-Ren , Lin Chii-Wann
Published: June 2014

A membrane based microfluidic device integrated with a surface plasmon resonance sensor was used for interferon-gamma detection, with the availability of quantitative analysis.
Simple fabrication of flexible electrodes with high metal-oxide content: electrospun reduced tungsten oxide/carbon nanofibers for lithium ion battery applications
Authors: Lee Jaehyuk , Jo Changshin , Park Bangrock , Hwang Woonbong , Lee Hyung Ik , Yoon Songhun , Lee Jinwoo
Published: June 2014

A reduced tungsten oxide-carbon flexible electrode is fabricated by electrospinning, showing high electrochemical performances as a lithium-ion battery anode.
Wafer-scale nanoconical frustum array crystalline silicon solar cells: promising candidates for ultrathin device applications
Authors: Cho Yunae , Gwon Minji , Park Hyeong-Ho , Kim Joondong , Kim Dong-Wook
Published: June 2014

A high photocurrent of 36.96 mA cm−2was achieved for wafer-scaled crystalline Si solar cells with hexagonal nanoconical frustum arrays at the surface. Optical simulations showed that the expected photocurrent of 10 μm thick nanostructured cells could slightly exceed the Lambertian limit.
Nanospace-confined formation of flattened Sn sheets in pre-seeded graphenes for lithium ion batteries
Authors: Li Zhengjie , Lv Wei , Zhang Chen , Qin Jiwen , Wei Wei , Shao Jiao-Jing , Wang Da-Wei , Li Baohua , Kang Feiyu , Yang Quan-Hong
Published: June 2014

Flattened Sn sheets with high electrochemical performance are prepared by pre-seeding and templating techniques in the interlayer nanospace of a graphene membrane.
WS2 nanosheet as a new photosensitizer carrier for combined photodynamic and photothermal therapy of cancer cells
Authors: Yong Yuan , Zhou Liangjun , Gu Zhanjun , Yan Liang , Tian Gan , Zheng Xiaopeng , Liu Xiaodong , Zhang Xiao , Shi Junxin , Cong Wenshu , Yin Wenyan , Zhao Yuliang
Published: June 2014

We have developed a facile strategy to fabricate WS2 nanosheets in a large scale that could not only efficiently load photosensitizers but also regulate their singlet-oxygen generation by NIR irradiation.
Immunomodulatory properties of carbon nanotubes are able to compensate immune function dysregulation caused by microgravity conditions
Authors: Crescio Claudia , Orecchioni Marco , Ménard-Moyon Cécilia , Sgarrella Francesco , Pippia Proto , Manetti Roberto , Bianco Alberto , Delogu Lucia Gemma
Published: June 2014

Short oxidized multi-walled carbon nanotubes functionalized by 1,3-dipolar cycloaddition are able to fight spaceflight immune system dysregulations.
Enantioselective one-pot synthesis of dihydroquinolones via BINOL-derived Lewis acid catalysis
Authors: Knipe Peter C. , Smith Martin D.
Published: June 2014

A high-yielding and diastereoselective route to biologically significant 2-aryl- and 2-alkyl-3-amido dihydroquinolones has been developed in up to 90 : 10 e.r. by employing a novel Lewis acidic BINOL-derived copper(ii) catalyst.
Synthesis of biobased succinimide from glutamic acid via silver-catalyzed decarboxylation
Authors: Deng Jin , Zhang Qiu-Ge , Pan Tao , Xu Qing , Guo Qing-Xiang , Fu Yao
Published: June 2014

Glutamic acid was transformed into succinimide in a two step procedure involving a dehydration in water to pyroglutamic acid followed by an oxidative decarboxylation using a silver catalyst.
Prospective pedagogy for teaching chemical bonding for smart and sustainable learning
Authors: Dhindsa Harkirat S. , Treagust David F.
Published: June 2014

As an important subject in the curriculum, many students find chemistry concepts difficult to learn and understand. Chemical bonding especially is important in understanding the compositions of chemical compounds and related concepts and research has shown that students struggle with this concept. In this theoretical paper based on analysis of relevant science education research, textbooks, and our classroom observations and teaching experiences, the authors argue that the difficulty in learning chemical bonding concepts is associated with the sequence (ionic, covalent and polar covalent bonding) in which students are taught because this sequence receives little support from constructivist theories of learning. Consequently, the paper proposes a sequence to teach chemical bonding (covalent, polar covalent and ionic bonding) for effective and sustainable learning. In this sequence, the concepts are developed with minimum reorganisation of previously learned information, using a format which is claimed to be easy for students to learn. For teaching these concepts, the use of electronegativity and the overlap of atomic orbitals for all types of bonding have also been stressed. The proposed sequence and emphasis on electronegativity and atomic orbital overlap meets the criteria for teaching and learning of concepts based on the psychology of learning including the theory of constructivism necessitating the construction of new knowledge using related prior knowledge. It also provides a better linkage between the bonding concepts learned at secondary and tertiary levels. Considering these proposed advantages for teaching, this sequence is recommended for further research into effective and sustainable teaching.
NIR electrochemiluminescence from Au25− nanoclusters facilitated by highly oxidizing and reducing co-reactant radicals
Authors: Hesari Mahdi , Workentin Mark S. , Ding Zhifeng
Published: June 2014

By means of spooling spectroscopy, we demonstrate our discovery on near-infrared electrochemiluminescence of Au25− nanoclusters at 950 and 900 nm, which can be attributed to the Au25−*, Au250* and Au25+* excited species being controllable chemically and electrochemically.
A comprehensive constitutive law for waxy crude oil: a thixotropic yield stress fluid
Authors: Dimitriou Christopher J. , McKinley Gareth H.
Published: June 2014

A constitutive model is developed that predicts the rheological response of waxy crude oil to a number of different flows.
Facile preparation of yttrium and aluminum co-doped ZnO via a sol–gel route for photocatalytic hydrogen production
Authors: Huo Jingpei , Fang Liting , Lei Yaling , Zeng Gongchang , Zeng Heping
Published: June 2014

Yttrium and aluminum co-doped ZnO were successfully synthesized by the sol–gel method. The obtained products showed high photocatalytic activity for hydrogen production (5.71 mmol h−1 g−1), and exhibited excellent stability and recyclability.
Intrinsically conducting polymer nanowires for biosensing
Authors: Travas-Sejdic J. , Aydemir N. , Kannan B. , Williams D. E. , Malmström J.
Published: June 2014

The fabrication of conductive polymer nanowires and their sensing of nucleic acids, proteins and pathogens is reviewed in this feature article.
Real‐time text tracking in natural scenes
Authors: Merino‐Gracia Carlos , Mirmehdi Majid
Published: June 2014

The authors present a system that automatically detects, recognises and tracks text in natural scenes in real‐time. The focus of the author's method is on large text found in outdoor environments, such as shop signs, street names, billboards and so on. Built on top of their previously developed techniques for scene text detection and orientation estimation, the main contribution of this work is to present a complete end‐to‐end scene text reading system based on text tracking. They propose to use a set of unscented Kalman filters to maintain each text region's identity and to continuously track the homography transformation of the text into a fronto‐parallel view, thereby being resilient to erratic camera motion and wide baseline changes in orientation. The system is designed for continuous, unsupervised operation in a handheld or wearable system over long periods of time. It is completely automatic and features quick failure recovery and interactive text reading. It is also highly parallelised to maximise usage of available processing power and achieve real‐time operation. They demonstrate the performance of the system on sequences recorded in outdoor scenarios.
Cooperative object tracking using dual‐pan–tilt–zoom cameras based on planar ground assumption
Authors: Cui Zhigao , Li Aihua , Feng Guoyan , Jiang Ke
Published: June 2014

Pan–tilt–zoom (PTZ) cameras play an important role in visual surveillance system. Dual‐PTZ camera system is the simplest and most typical one. The superiority of this system lies in that it can obtain both large‐view information and high‐resolution local‐view information of the tracked object at the same time. One method to achieve such task is to use master–slave configuration. One camera (master) tracks moving objects at low resolution and provides the positional information to another camera (slave). Then the slave camera can point towards the object at high resolution and track it dynamically. In this paper, we propose a novel framework exploiting planar ground assumption to achieve cooperative tracking. The approach differs from conventional methods in that we exploit planar geometric constraint to solve the camera collaboration problem. Compared with the existing approach, the proposed framework can be used in the case of wide baseline, and allows the depth change of the tracked object. The proposed method can also adapt to the dynamic change of the surveillance scene. Besides, we also describe a self‐calibration method of homography matrix which is induced by the ground plane between two cameras. We demonstrate the effectiveness of the proposed method by testing it with a tracking system for surveillance applications.
Analysis of sub‐synchronous resonance in doubly‐fed induction generator‐based wind farms interfaced with gate – controlled series capacitor
Authors: Mohammadpour Hossein Ali , Ghaderi Amin , Santi Enrico
Published: June 2014

This paper first presents a step‐by‐step tutorial on modal analysis of a doubly‐fed induction generator (DFIG)‐based series compensated wind farm. The model of the system includes a wind turbine aerodynamics, a sixth‐order order induction generator, a second‐order two‐mass shaft system, a fourth‐order order series compensated transmission line, an eighth‐order rotor‐side converter (RSC) and grid‐side converter (GSC) controllers, and a first‐order DC‐link model. Then, using modal analysis and time‐domain simulations, it is shown that a fixed‐series compensated DFIG is highly unstable due to the sub‐synchronous resonance (SSR) mode. In order to damp the SSR mode, the wind farm is interfaced with the gate‐controlled series capacitor (GCSC) ‐ which is a new series flexible AC transmission system (FACTS) device. A SSR damping controller (SSRDC) is designed for the GCSC using residue‐based analysis and root locus diagrams, and an effective input control signal (ICS) to the SSRDC is identified in order to simultaneously increase damping of both the SSR and super‐synchronous (SupSR) modes. The IEEE first benchmark model on SSR is adapted with an integrated DFIG‐based wind farm to perform studies. Matlab/Simulink is used as a tool for designing process, and PSCAD/EMTDC is used for time‐domain simulations.
Passive wireless local area network radar network using compressive sensing technique
Authors: Weiß Matthias
Published: June 2014

Distributed networks constructed from heterogeneous or homogeneous sensors, which are also called multiple‐input–multiple‐output systems, offer several advantages compared to single sensor systems. In particular for a distributed homogeneous sensor network targets are illuminated from various aspect angles and reflections are received at different locations simultaneously. Hence, these networks outperform single‐input–single‐output systems easily by several aspects. This spatial diversity improves target detection and parameter estimation dramatically. Therefore these radar networks attract more and more scientists worldwide. This study shows the potential of compressive sensing technique applied to a distributed homogeneous sensor network comprised of several wireless local area network routers as transmitters and dedicated receivers. The CS group sparsity approach is employed to reduce the required data rate, which has to be transferred to a central processing unit for data fusion, without decreasing the performance of the sensor network.
Online partial discharge signal conditioning for φ–q–n representation under noisy condition in cable systems
Authors: Shahsavarian Tohid , Shahrtash Seyyed Mohammad
Published: June 2014

Almost all on‐site measured partial discharge (PD) signals in cable networks suffer from the contributions of reflected PD pulses and noise which both decrease precision of measurement. This study explores an online digital signal conditioning procedure for PD signals being measured under noisy conditions in cable networks, that is, proposing a novel procedure for online preparing clean φ–q–n representation of PD signals with neither directly applying de‐noising methods and nor requiring voltage waveform (for calculation of φ). In order to demonstrate the accuracy of the results, they are compared with noise‐free conditions, where successes of the proposed method have been proved.
Approach for improved positioning of an atomic force microscope piezoelectric tube scanner
Authors: Rana Md Sohel , Pota Hemanshu R. , Petersen Ian R.
Published: June 2014

There is a need, in the wide ranging scientific community, to perform fast scans using an atomic force microscope (AFM) with nanoscale accuracy. The performance of an AFM at high scanning speeds is limited because of some serious limitations of its scanning unit; that is, the piezoelectric tube scanner (PTS). To increase the imaging speed of an AFM, a multi‐input–multi‐output (MIMO) model predictive control scheme is applied in the axes of the PTS to reduce its vibration and cross‐coupling effect. The design of this controller is based on an identified MIMO model of the AFM PTS. Moreover, a damping compensator is designed and included in the feedback loop with the plant to suppress the vibration of the PTS at the resonant frequency. Consequently, the proposed controller achieves a higher closed‐loop bandwidth, significant damping of the resonant mode of the AFM PTS and results in compensation of the above effects. To evaluate the performance improvement using the proposed control scheme, an experimental comparison of its results with those of the AFM in‐built proportional–integral controller is performed. This comparison shows the effectiveness of the proposed controller.
Recent Advances Using Guanidinate Ligands for Chemical Vapour Deposition (CVD) and Atomic Layer Deposition (ALD) Applications
Authors: Kurek Agnieszka , Gordon Peter G. , Karle Sarah , Devi Anjana , Barry Seán T.
Published: June 2014

Volatile metal complexes are important for chemical vapour deposition (CVD) and atomic layer deposition (ALD) to deliver metal components to growing thin films. Compounds that are thermally stable enough to volatilize but that can also react with a specific substrate are uncommon and remain unknown for many metal centres. Guanidinate ligands, as discussed in this review, have proven their utility for CVD and ALD precursors for a broad range of metal centres. Guanidinate complexes have been used to deposit metal oxides, metal nitrides and pure metal films by tuning process parameters. Our review highlights use of guanidinate ligands for CVD and ALD of thin films over the past five years, design trends for precursors, promising precursor candidates and discusses the future outlook of these ligands.
Frontiers and perspectives on research strategies in grassland technology
Authors: Schellberg J. , Verbruggen E.
Published: June 2014

Grassland scientists and farmers are increasingly faced with emerging new technologies and information systems that have been primarily developed in engineering sciences, in particular, precision agriculture, remote sensing, geographic information and biotechnology. Judgment upon whether the implementation of any of these technologies may be beneficial in economic and ecological respects is challenging, especially to those who have to make on-farm decisions. New technologies have been applied on grassland only partially and with some delay compared with arable land. However, as we will show here, there is scope for successful implementation of new technologies in various climatic regions and for a wide range of applications. The paper presents the most important recent developments of new technologies in agriculture that have scope for application in grasslands. It defines the relevant terms and processes, provides examples of successful implementation, and discusses future directions and research needs.
Development of a thermal-time model for combinational dormancy release of hairy vetch (Vicia villosa ssp. villosa)
Authors: Renzi Juan P. , Chantre Guillermo R. , Cantamutto Miguel A.
Published: June 2014

Seed dormancy could be a factor related to natural reseeding of hairy vetch (Vicia villosa ssp. villosa Roth.), a winter annual species cultivated for seed, pasture, hay, green manure and cover crop. The presence of combinational dormancy (physical dormancy + physiological dormancy, PY + PD) in hairy vetch was explored by a model using laboratory and field measures. At the stage of natural dispersal, dry seeds of hairy vetch were stored under laboratory conditions at 5, 10, 20 and 30°C (±2°C) or buried at 5 cm depth in an experimental field. Germination at 5, 8, 10, 15, 20 and 25°C was assessed at regular intervals up to 295 days after harvest. Following the hypothesis of the existence of a combinational dormancy mechanism, model development was based on the estimation of: (i) the fraction of non-PY seed as a function of after-ripening thermal-time accumulation, and (ii) seed population thermal parameters associated with a given level of PD. The developed model adequately described the after-ripening thermal-time requirements for PY + PD release of V. villosa. Based on model predictions, under a semi-arid thermal regime, >45% of vetch seeds shed during the summer season would be able to germinate during early autumn. Thus, the seed-bank size threshold at the end of the first growing season should be >65 seeds m–2 in order to reach a minimum stand of 30 plants m–2 necessary for a productive pasture.
Durum wheat quality in high-input irrigation systems in south-eastern Australia
Authors: Sissons Mike , Ovenden Ben , Adorada Dante , Milgate Andrew
Published: June 2014

To extend the production base of durum wheat in Australia, field trials were conducted on seven registered durum varieties across four seasons and six sites in locations where irrigation was supplied during crop growth. The purpose was to determine if the quality of the grain produced met the requirements for good milling and pasta-making quality and to understand the genotype, environment and their interaction in affecting yield and technological quality of the grain and derived pasta. High grain yields and grain protein were obtained, producing large grain weights, low screenings and low percentage of hard vitreous kernels. Yellow colour of semolina and pasta was reduced marginally but dough and other pasta technological characteristics were similar to typical dryland durum production, with some exceptions. Varieties were identified with potential for production under irrigation.
Soil microbe Bacillus subtilis (GB03) induces biomass accumulation and salt tolerance with lower sodium accumulation in wheat
Authors: Zhang Jin-Lin , Aziz Mina , Qiao Yan , Han Qing-Qiang , Li Jing , Wang Yin-Quan , Shen Xin , Wang Suo-Min , Paré Paul W.
Published: June 2014

Bacillus subtilis strain GB03 has been shown to confer salt tolerance in Arabidopsis thaliana. In this study, the potential for GB03 to promote biomass accumulation and increase salt tolerance was investigated in wheat (Triticum aestivum). Soil-grown wheat seedlings were assayed for dry-weight increase. Endogenous Na+ and K+ contents were determined in plants with or without soil inoculation with GB03 along with 0, 25 or 100 mm NaCl solution added to the soil. We demonstrated that the introduction of GB03 in the soil triggered wheat biomass accumulation. Furthermore, GB03 improved salt tolerance as measured by increased tissue mass, lower Na+ accumulation and improved K+/Na+ ratio when GB03-inoculated plants were grown under elevated salt conditions. This study provides insight for the application of selected bacteria to monocot crops to combat saline toxicity.
Agronomic evaluation and phenotypic plasticity of Camelina sativa growing in Lombardia, Italy
Authors: Masella Piernicola , Martinelli Tommaso , Galasso Incoronata
Published: June 2014

The agronomic performance of Camelina sativa (L.) Crantz (camelina or false flax) sown in autumn and spring over two consecutive years was tested in northern Italy. Seven C. sativa genotypes were tested and compared with rapeseed (Brassica napus L.). The main phenological stages and biometric traits were recorded, along with seed yield. In general, camelina showed a seed yield similar to that of rapeseed cultivated in the same locality and in the last decade in Italy. On average, the grain yields of camelina and rapeseed grown in the same location and conditions were ~1340 and 1625 kg ha–1, respectively. The agronomic performance of camelina varied, with climatic events having a greater effect than sowing season or genotypes. Among the investigated genotypes, however, C. sativa accession CAM 40 was the most adaptable to unfavourable environmental conditions and CAM 172 to favourable conditions. With regard to the two sowing seasons, autumn planting allowed for better performance than spring planting during the second cultivation year. The phenotypic plasticity of camelina was estimated for the first time in the present work. Branching capability was the most plastic trait under favourable yielding conditions. Among the tested genotypes, CAM 40 showed limited yield plasticity and CAM 172 demonstrated high plasticity for the same trait, offering a greater potential for future genetic improvement.
Trends in planktonic copepod diversity in reservoirs and lotic stretches in a large river basin in South America
Authors: Perbiche-Neves Gilmar , Boxshall Geoffrey A. , Nogueira Marcos G. , da Rocha Carlos E. F.
Published: June 2014

Copepod assemblages were analysed across La Plata River basin, the second largest in South America. High values of species richness and Shannon–Wiener diversity were found in the lower Paraná River, the main and largest river of the basin, and in eutrophic reservoirs located in the upper basin. The species richness was negatively correlated with turbidity, probably because of the negative impact on filtration rates in calanoids. There was a trend of decreasing richness correlated with high water flow in reservoirs with short water-retention time (<40 days) and simple morphometric shape, and also in deeper oligo-mesotrophic reservoirs with very long water-retention time and dendritic shape (variables that occurred in combination in the present study). The number of copepod species (46) found in our study is only about half of the gamma diversity estimated using Jack1 non-parametric analysis for the basin (86 species). There are groups of copepod species typical of reservoirs and rivers, and others that can occur in both of these habitat types. Reservoir and lentic species are favoured by a deeper water column, higher temperatures and higher transparency, whereas the opposite is the case of typical riverine species. There is also a group of species that occur in both sets of conditions.
Facilitating upstream passage of small-bodied fishes: linking the thermal dependence of swimming ability to culvert design
Authors: Rodgers Essie M. , Cramp Rebecca L. , Gordos Matthew , Weier Anna , Fairfall Sarah , Riches Marcus , Franklin Craig E.
Published: June 2014

Fish passage through road culverts is poorly understood, particularly for small-bodied fishes, despite this information being integral to the restoration of waterway connectivity. We assessed the prolonged swimming performance of a small-bodied fish, empire gudgeon (Hypseleotris compressa; 3.2–7.7 cm total length, TL), and juvenile Australian bass (Percalates novemaculeata; 3.5–7.8 cm TL). Swimming trials were conducted in a hydraulic flume across a range of fixed and increasing velocities in response to acute and long-term thermal treatments. A new statistical approach (Tobit analysis) was used to relate the thermal dependence of swimming endurance to hydraulic characteristics of culverts, providing estimates of maximum water velocity allowing upstream fish passage. Reductions in water temperature of 10°C, similar to those caused by cold-water releases from dams, significantly impaired critical swimming speeds of both species. Traversable water-velocity models identified H. compressa as a weak swimmer, requiring very low water velocities (≤0.10 m s–1 or 2.86 body lengths (BL) s–1) for unrestricted passage, whereas P. novemaculeata was predicted to traverse water velocities of ≤0.39 m s–1 or 12.12 BL s–1. Culvert designs can be improved by limiting water velocities to accommodate weak-swimming fishes and by accounting for the thermal sensitivity of swimming performance.
Effects of river inputs on nutrient and organic-carbon conditions and net ecosystem metabolism in the Kaoping (Taiwan) coastal sea
Authors: Hung J.-J. , Ho C.-M. , Shiah F.-K.
Published: June 2014

This study aims to understand the variability of net ecosystem metabolism in a tropical sea. The contrasting pattern of metabolic state between wet and dry seasons was caused by the pronounced difference of river exports in the Kaoping coastal sea. The depth-integrated gross primary production (IGPP) through the euphotic zone ranged from 2451 to 16 230 mg C m–2 day–1 in summer, and from 844 to 5549 mg C m–2 day–1 in winter, and was apparently regulated by oceanic temperature, nutrients and organic carbon. The depth-integrated dark community respiration (IDCR), attributed largely to bacterial respiration (BR, ~69%), ranged from 861 to 12 418 mg C m–2 day–1 in summer, and from 997 to 5781 mg C m–2 day–1 in winter. GPP and DCR correlated inversely with salinity but positively with nutrients, Chlorophyll a, dissolved organic carbon (DOC) and particulate organic carbon (POC). The autotrophic state (IGPP : IDCR > 1) prevailed in most stations in summer, whereas the heterotrophic state (IGPP : IDCR < 1) occurred in all but Station B1 in winter. Bacterial production (BP) and bacterial respiration (BR) also correlated inversely with salinity but positively with nutrients and DOC. Bacterial carbon demand (BCD) was 0.15 GPP in summer and 0.64 GPP in winter, supporting the autotrophic and heterotrophic conditions in summer and winter, respectively. The metabolic state is apparently determined by seasonal variation of temperature and river exports.
GSK3-like kinases positively modulate abscisic acid signaling through phosphorylating subgroup III SnRK2s in
Arabidopsis
Authors: Cai Zhenying , Liu Jingjing , Wang Haijiao , Yang Cangjing , Chen Yuxiao , Li Yongchi , Pan Shanjin , Dong Rui , Tang Guiliang , Barajas-Lopez Juan de Dios , Fujii Hiroaki , Wang Xuelu
Published: June 2014

Significance

Abscisic acid (ABA) is a key stress-responsive hormone. Subgroup III Snf1-related kinase 2s (SnRK2s) are crucial positive regulators in ABA signaling pathway, but it is still not clear how SnRK2s are activated. In addition, besides ABA, some abiotic stresses can also activate SnRK2s with unknown mechanisms. Here we provide several lines of evidence to strongly support that brassinosteroid insensitive 2, a glycogen synthase kinase 3 (GSK3)-like kinase, interacts with and phosphorylates SnRK2s on specific novel sites to activate SnRK2s, which provides significant insights into the function of GSK3-like kinases in ABA signaling and transactivation of SnRK2s. Moreover, many GSK3-like kinases are regulated at transcriptional and/or posttranslational levels by many abiotic stresses, implying the presence of direct regulation of ABA signaling by other abiotic stresses.
Node labels and features: Stable and unstable dialects and variation in acquisition
Authors: Roeper Thomas , Green Lisa
Published: June 2014

We argue that the smallest shifts in grammar should give us the most precise insight into grammatical mechanisms. The often tiny differences captured by dialects become a natural focus for linguistic theory, precisely because of their variability and instability in the history of language and in the grammatical commitments of individual speakers. The notion of stability refers to where dialects differ, where registers add or drop features, where historical change moves, what proves difficult in the steps in acquisition, and where second language learners easily stumble. In a word, we argue that nodes are stable and features are unstable. In particular, node labels, which reflect head features in a feature bundle, are stable, while non-head features are unstable and subject to variation. We show that specific nodes in African American English, such as Negative Focus (CP) in negative inversion constructions, are stable (Don’t nobody play baseball.). Also, particle positions (he threw (up) the ball (up)) and various features, like those associated with tense inflection (if it is under a V node not a T node) or presuppositionality (if it is under a CP node), are inherently unstable. Many other predictions for dialect, acquisition, and diachronic patterns follow as well.
Copying vs. structure sharing a semantic argument
Authors: Sauerland Uli
Published: June 2014

The term Focus Dependency describes an important phenomenon at the syntax-semantics interface: Elided material can exhibit bound-variable-like behavior when its antecedent is a focussed phrase in the same sentence. In the past, focus dependency has been analyzed as actual binding or by means of copying. This paper presents a new account of focus dependency that relies on the syntactic idea of structure-sharing. Structure-sharing allows sub-phrases to be syntactically linked to more than one position of a phrase marker. The proposal better explains focus dependency than existing accounts considering data from sentence-boundedness, insensitivity to c-command, extraction from the focus-dependent material, and the formal link to the antecedent. It also achieves a theoretical unification with other phenomena where structure sharing has been made use of, specifically movement.
Towards a restrictive theory of (remnant) movement!
Authors: Abels Klaus
Published: June 2014

A restrictive theory of syntax needs both a restrictive theory of structures and a restrictive theory of operations.Much recent effort has gone into narrowing the class of allowable structures and a lot has been learned. This paper proposes that operations are linearly ordered on an essentially constituent by constituent basis. A universal constraint on the ordering of operations in language is proposed whose function is to fix the order in which operations apply. This constraint is deployed using a generalized prohibition against improper movement. The proposal captures some but not all effects of what has traditionally been called the freezing principle. It is argued that empirically exactly the right cut is made. It is further argued that the proposal rules out an entire class of remnant movement derivations, including the analysis of cross-serial dependencies in Nilsen (2003) and the analysis of order-preservation in Koopman and Szabolcsi (2000).
Agreement with coordinated subjects: A comparative perspective
Authors: van Koppen Marjo
Published: June 2014

I discuss the variation concerning agreement with coordinated subjects in Dutch dialects. I show that a verb or a complementizer in several variants of Dutch agrees with the first conjunct of a coordinated subject and in other variants with the coordinated subject as a whole. I argue that this variation can be accounted for by the interaction between the syntactic derivation and the post-syntactic morphological component.More specifically, I argue that syntax establishes an agreement relation with both the coordinated subject as a whole and the first conjunct of the coordinated subject. Subsequently, during the post-syntactic morphological derivation, one of these agreement relations will be overtly expressed on the Probe. The decision as to which one of the two relations is spelled out depends on the affix inventory of the language or dialect. More specifically, the subset principle is extended in such a way that, confronted with the situation in which a Probe is related to two Goals, an affix is inserted for the relation which results in the most specific agreement morphology. The analysis is extended to the typologically unrelated languages Irish and Arabic.
The Brythonic Reconciliation
Authors: Jouitteau Mélanie
Published: June 2014

I argue that despite their traditional verb-first vs. verb second partition, Welsh and Breton both instantiate a ban on verb-first and I present an analysis of these two languages as fundamentally verb second. In this view, so-called verb first orders prototypically illustrated byWelsh result from inconspicuous strategies to fill in the preverbal position, whereas traditional verb second prototypically illustrated by Breton results from conspicuous strategies to fill in the preverbal position. I show that both conspicuous and inconspicuous verb second orders are present in bothWelsh and Breton. The difference in word order between Welsh and Breton is reduced to (i) a lexical parameter, that is availability of a free preverbal expletive particle inWelsh, and (ii) a syntactic parameter: Breton allows for the creation of expletives by short movement, a parameter shared with Icelandic and other languages instantiating stylistic fronting.
Evidentials as epistemic modals: Evidence from St'át'imcets
Authors: Matthewson Lisa , Davis Henry , Rullmann Hotze
Published: June 2014

This paper argues that evidential clitics in St’át’imcets (a.k.a. Lillooet; Northern Interior Salish) must be analyzed as epistemic modals.We apply a range of tests which distinguish the modal analysis from the main alternative contender (an illocutionary operator analysis, as in Faller 2002), and show that the St’át’imcets evidentials obey the predictions of a modal analysis. Our results support the growing body of evidence that the functions of encoding information source and epistemic modality are not necessarily distinct. The St’át’imcets data further provide a novel argument against the claim that evidentiality and epistemic modality are separate categories. Many authors argue that evidentials differ from modals in that the former do not encode speaker certainty (see, e.g., de Haan 1999; Aikhenvald 2004).We argue that modals are also not required to encode speaker certainty; we provide evidence from St’át’imcets that marking quantificational strength is not an intrinsic property of modal elements.
Jung as philosopher: archetypes, the psychoid factor, and the question of the supernatural
Authors: Mills Jon
Published: June 2014

In a previous essay offering an exegesis of Jung's metaphysics, I concluded that his position on the archetypes emphasizes basic constitutional patterns that manifest as imago, thought, affect, fantasy, and behavior inherent in all forms of human psychic life (bios) that are genetically transmitted yet realized on different stratifications of psychical order, including mystical properties emanating from supernatural origins. Mark Saban and Robert Segal provide thoughtful critiques of my work that challenge my basic premises. Saban represents a particular Jungian camp conforming to empirical apologetics, while Segal is more critical of Jung's philosophical ideas. The two main themes that emerge from their criticism are that I fail to show that Jung is a metaphysician, and that the archetypes are not supernatural phenomena. Here I will be concerned with recapitulating Jung's metaphysical postulations about the world and psyche and address more specifically the question of his commitment to supernaturalism.
Jung, a mystical aesthetic, and abstract art
Authors: Dourley John
Published: June 2014

On the question of aesthetics, Jung makes a clear distinction between aestheticism and aesthetics. He dismissed the former as lacking substance and moral commitment, but allows that his psychology can never usurp but can contribute to a depth aesthetic. On close examination, this aesthetic rests on the manifestation of the archetypal in all forms of creativity. As such, it is closely related to the spiritual and religious. Modern expressionist and abstract art was consciously influenced by the apophatic mystical tradition to which Jung himself was drawn. Kandinsky and Arp are significant representatives of this tradition who were influenced by mystical experience – especially that of Jacob Boehme, one of Jung's key intellectual ancestors. The paper works to identify the rudiments of a Jungian aesthetic and show its compatibility with the work and theory of Kandinsky, Arp and the expressionist/abstract project.
Localization of elliptic multiscale problems
Authors: Målqvist Axel , Peterseim Daniel
Published: June 2014

This paper constructs a local generalized finite element basis for elliptic problems with heterogeneous and highly varying coefficients. The basis functions are solutions of local problems on vertex patches. The error of the corresponding generalized finite element method decays exponentially with respect to the number of layers of elements in the patches. Hence, on a uniform mesh of size

H
H

, patches of diameter

H
log
⁡
(
1

/

H
)

H\log (1/H)

are sufficient to preserve a linear rate of convergence in

H
H

without pre-asymptotic or resonance effects. The analysis does not rely on regularity of the solution or scale separation in the coefficient. This result motivates new and justifies old classes of variational multiscale methods.
Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies
Authors: Messih Mario Abdel , Lepore Rosalba , Marcatili Paolo , Tramontano Anna
Published: June 2014

Motivation: Antibodies are able to recognize a wide range of antigens through their complementary determining regions formed by six hypervariable loops. Predicting the 3D structure of these loops is essential for the analysis and reengineering of novel antibodies with enhanced affinity and specificity. The canonical structure model allows high accuracy prediction for five of the loops. The third loop of the heavy chain, H3, is the hardest to predict because of its diversity in structure, length and sequence composition.

Results: We describe a method, based on the Random Forest automatic learning technique, to select structural templates for H3 loops among a dataset of candidates. These can be used to predict the structure of the loop with a higher accuracy than that achieved by any of the presently available methods. The method also has the advantage of being extremely fast and returning a reliable estimate of the model quality.

Availability and implementation: The source code is freely available at http://www.biocomputing.it/H3Loopred/

Contact:  anna.tramontano@uniroma1.it

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Using association rule mining to determine promising secondary phenotyping hypotheses
Authors: Oellrich Anika , Jacobsen Julius , Papatheodorou Irene ,   The Sanger Mouse Genetics Project, Smedley Damian
Published: June 2014

Motivation: Large-scale phenotyping projects such as the Sanger Mouse Genetics project are ongoing efforts to help identify the influences of genes and their modification on phenotypes. Gene–phenotype relations are crucial to the improvement of our understanding of human heritable diseases as well as the development of drugs. However, given that there are ∼20 000 genes in higher vertebrate genomes and the experimental verification of gene–phenotype relations requires a lot of resources, methods are needed that determine good candidates for testing.

Results: In this study, we applied an association rule mining approach to the identification of promising secondary phenotype candidates. The predictions rely on a large gene–phenotype annotation set that is used to find occurrence patterns of phenotypes. Applying an association rule mining approach, we could identify 1967 secondary phenotype hypotheses that cover 244 genes and 136 phenotypes. Using two automated and one manual evaluation strategies, we demonstrate that the secondary phenotype candidates possess biological relevance to the genes they are predicted for. From the results we conclude that the predicted secondary phenotypes constitute good candidates to be experimentally tested and confirmed.

Availability: The secondary phenotype candidates can be browsed through at http://www.sanger.ac.uk/resources/databases/phenodigm/gene/secondaryphenotype/list.

Contact:  ao5@sanger.ac.uk or ds5@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
EPIQ—efficient detection of SNP–SNP epistatic interactions for quantitative traits
Authors: Arkin Ya’ara , Rahmani Elior , Kleber Marcus E. , Laaksonen Reijo , März Winfried , Halperin Eran
Published: June 2014

Motivation: Gene–gene interactions are of potential biological and medical interest, as they can shed light on both the inheritance mechanism of a trait and on the underlying biological mechanisms. Evidence of epistatic interactions has been reported in both humans and other organisms. Unlike single-locus genome-wide association studies (GWAS), which proved efficient in detecting numerous genetic loci related with various traits, interaction-based GWAS have so far produced very few reproducible discoveries. Such studies introduce a great computational and statistical burden by necessitating a large number of hypotheses to be tested including all pairs of single nucleotide polymorphisms (SNPs). Thus, many software tools have been developed for interaction-based case–control studies, some leading to reliable discoveries. For quantitative data, on the other hand, only a handful of tools exist, and the computational burden is still substantial.

Results: We present an efficient algorithm for detecting epistasis in quantitative GWAS, achieving a substantial runtime speedup by avoiding the need to exhaustively test all SNP pairs using metric embedding and random projections. Unlike previous metric embedding methods for case–control studies, we introduce a new embedding, where each SNP is mapped to two Euclidean spaces. We implemented our method in a tool named EPIQ (EPIstasis detection for Quantitative GWAS), and we show by simulations that EPIQ requires hours of processing time where other methods require days and sometimes weeks. Applying our method to a dataset from the Ludwigshafen risk and cardiovascular health study, we discovered a pair of SNPs with a near-significant interaction (P = 2.2 × 10−13), in only 1.5 h on 10 processors.

Availability:  https://github.com/yaarasegre/EPIQ

Contact:  heran@post.tau.ac.il
An efficient parallel algorithm for accelerating computational protein design
Authors: Zhou Yichao , Xu Wei , Donald Bruce R. , Zeng Jianyang
Published: June 2014

Motivation: Structure-based computational protein design (SCPR) is an important topic in protein engineering. Under the assumption of a rigid backbone and a finite set of discrete conformations of side-chains, various methods have been proposed to address this problem. A popular method is to combine the dead-end elimination (DEE) and A* tree search algorithms, which provably finds the global minimum energy conformation (GMEC) solution.

Results: In this article, we improve the efficiency of computing A* heuristic functions for protein design and propose a variant of A* algorithm in which the search process can be performed on a single GPU in a massively parallel fashion. In addition, we make some efforts to address the memory exceeding problem in A* search. As a result, our enhancements can achieve a significant speedup of the A*-based protein design algorithm by four orders of magnitude on large-scale test data through pre-computation and parallelization, while still maintaining an acceptable memory overhead. We also show that our parallel A* search algorithm could be successfully combined with iMinDEE, a state-of-the-art DEE criterion, for rotamer pruning to further improve SCPR with the consideration of continuous side-chain flexibility.

Availability: Our software is available and distributed open-source under the GNU Lesser General License Version 2.1 (GNU, February 1999). The source code can be downloaded from http://www.cs.duke.edu/donaldlab/osprey.php or http://iiis.tsinghua.edu.cn/∼compbio/software.html.

Contact:  zengjy321@tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach
Authors: Kotera Masaaki , Tabei Yasuo , Yamanishi Yoshihiro , Muto Ai , Moriya Yuki , Tokimatsu Toshiaki , Goto Susumu
Published: June 2014

Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale.

Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways.

Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2014/

Contact:  goto@kuicr.kyoto-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
ExSPAnder: a universal repeat resolver for DNA fragment assembly
Authors: Prjibelski Andrey D. , Vasilinetc Irina , Bankevich Anton , Gurevich Alexey , Krivosheeva Tatiana , Nurk Sergey , Pham Son , Korobeynikov Anton , Lapidus Alla , Pevzner Pavel A.
Published: June 2014

Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

Availability and implementation:  http://bioinf.spbau.ru/en/spades

Contact:  ap@bioinf.spbau.ru