bluuebunny/crossref_metadata_2025 huggingface dataset:
CASP10 results compared to those of previous CASP experiments
Authors: Kryshtafovych Andriy , Fidelis Krzysztof , Moult John
Published: October 2013

We compare results of the community efforts in modeling protein structures in the tenth CASP experiment, with those in earlier CASPs particularly in CASP5, a decade ago. There is a substantial improvement in template based model accuracy as reflected in more successful modeling of regions of structure not easily derived from a single experimental structure template, most likely reflecting intensive work within the modeling community in developing methods that make use of multiple templates, as well as the increased number of experimental structures available. Deriving structural information not obvious from a template is the most demanding as well as one of the most useful tasks that modeling can perform. Thus this is gratifying progress. By contrast, overall backbone accuracy of models appears little changed in the last decade. This puzzling result is explained by two factors—increased database size in some ways makes it harder to choose the best available templates, and the increased intrinsic difficulty of CASP targets as experimental work has progressed to larger and more unusual structures. There is no detectable recent improvement in template‐free modeling, but again, this may reflect the changing nature of CASP targets. Proteins 2014; 82(Suppl 2):164–174. © 2013 Wiley Periodicals, Inc.
Deriving consistent approximate models of the global atmosphere using Hamilton's principle
Authors: Staniforth Andrew
Published: October 2013

A quartet of dynamically consistent approximate models of the global atmosphere in non‐spherical coordinates has recently been developed, according to whether approximations of shallow and/or quasi‐hydrostatic nature are made. A model is considered to be dynamically consistent if it formally preserves conservation principles for axial angular momentum, energy and potential vorticity. The development of these approximate models involved detailed examination of conservation budgets to determine which terms to omit, modify, or retain in the equations for the three components of momentum, according to the type of approximation made.

An alternative, complementary, derivation of this quartet of approximate models is developed herein using Hamilton's principle. With this approach, a single term in the Lagrangian is identified, which can then be optionally modified to apply the quasi‐hydrostatic approximation via an on–off switch. As in the previous work, application of the shallow‐atmosphere approximation is achieved by choosing an orthogonal curvilinear coordinate system having an appropriate shallow metric. Application of Hamilton's principle and Noether's theorem then intrinsically preserves the conservation principles for axial angular momentum, energy and potential vorticity. This obviates the need to examine conservation budgets to determine which terms to omit, modify, or retain in the equations for the three components of momentum; everything just falls into place via the application of variational calculus. The resulting unified equation set is then identical to that previously obtained by trial and error examination of conservation budgets.
Influence of a stabilized cap layer on the photodegradation of coextruded high density polyethylene/wood‐flour composites
Authors: Jin Shan , Stark Nicole M. , Matuana Laurent M.
Published: October 2013

The effect of light stabilizer's addition method into wood‐plastic composites (WPCs), i.e., surface versus bulk, on their photostability was evaluated. Blends of ultraviolet absorbers (benzotriazole or hydroxyphenyltriazine) with a hindered amine light stabilizer were used as the stabilizing additives. Both unstabilized and photostabilized uncapped (control) samples, as well as coextruded WPCs counterparts, were exposed to up to 3000 h of accelerated artificial weathering. The light transmittance, surface morphology, and color of the samples before and after weathering were analyzed by UV‐vis spectroscopy, SEM, and Chroma Meter. The experimental results indicated that the method of adding the light stabilizer had a significant effect on the WPC photostability. While bulk addition reduced the degree of fading in uncapped composite, it did not suppress it completely. On the other hand, coextruded WPCs with photostabilized cap layers showed no visible signs of fading, thus clearly indicating that the stabilized cap layers blocked most of the UV radiation, and thereby prevent of UV light to reach the surface of the inner layer of coextruded composites. Cost‐analysis considerations indicated that 50 times more light stabilizer was needed when it was incorporated into the bulk of the composites rather than in the cap layer of coextruded samples. Clearly, these results suggest that adding light stabilizers at the surface of WPCs not only protects them against UV degradation, but also is a most efficient and cost‐effective method of photostabilization than bulk addition. J. VINYL ADDIT. TECHNOL., 19:239–249, 2013. © 2013 Society of Plastics Engineers
Reaction with SO3 in Ionic Liquids: The Example of K2(S2O7)­(H2SO4)
Authors: Weiz Alexander , Bruns Jörn , Wickleder Mathias S.
Published: October 2013

The ionic liquid 1‐butyl‐3‐methylimidazolium hydrogensulfate, [bmim]HSO4, turned out to be resistant even to strong oxidizers like SO3. Thus, it should be a suitable solvent for the preparation of polysulfates at low temperatures. As a proof of principle we here present the synthesis and crystal structure of K2(S2O7)(H2SO4), which has been obtained from the reaction of K2SO4 and SO3 in [bmim]HSO4. In the crystal structure of K2(S2O7)(H2SO4) (orthorhombic, Pbca, Z = 8, a = 810.64(2) pm, b = 1047.90(2) pm, c = 2328.86(6) pm, V = 1978.30(8) Å3) two crystallographically unique potassium cations are coordinated by a different number of monodentate and bidentate‐chelating disulfate anions as well as by sulfuric acid molecules. The crystal structure consists of alternating layers of [K2(S2O7)] slabs and H2SO4 molecules. Hydrogen bonds between hydrogen atoms of sulfuric acid molecules and oxygen atoms of the neighboring disulfate anions are observed.
Vestibular functioning and migraine: pilot study comparing those with and without vertigo
Authors: Baker B J , Curtis A , Trueblood P , Vangsnes E
Published: October 2013

Background:

The current study compared a migrainous vertigo group with a migraine without vertigo group. It was hypothesised that those with migrainous vertigo would have more abnormal test results during a non-migrainous period than those who suffer from migraine without vertigo.

Methods:

Both groups, comprising 10 participants each, were tested using: the gaze stabilisation test, dynamic visual acuity test, sensory organisation test, head shake sensory organisation test and functional gait assessment.

Results:

Eighteen females and 2 males aged 18–53 years participated. There were no significant differences between the two groups for the dynamic visual acuity test, sensory organisation test or head shake sensory organisation test. However, mean dynamic visual acuity loss was greater in both groups than in a normal population, and the head shake sensory organisation (sway) test was well below the normal mean. The functional gait assessment showed a significant difference (p = 0.0025) between the two groups.

Conclusion:

Both groups showed abnormalities in vestibular functioning compared with norms, suggesting that both had some degree of vestibular dysfunction. However, vestibular dysfunction was greater in the migrainous vertigo group than in the migraine without vertigo group, as evidenced by differences in functional gait assessment.
Clinical outcome and vertical transmission variability among canine Neospora caninum isolates in a pregnant mouse model of infection
Authors: DELLARUPE ANDREA , REGIDOR-CERRILLO JAVIER , JIMÉNEZ-RUIZ ELENA , SCHARES GEREON , UNZAGA JUAN MANUEL , VENTURINI MARÍA CECILIA , ORTEGA-MORA LUIS M.
Published: October 2013

We compared the clinical outcome and vertical transmission of six canine Neospora caninum isolates using a pregnant BALB/c model. Four of the isolates were obtained from oocysts of naturally infected dogs (Nc-Ger2, Nc-Ger3, Nc-Ger6 and Nc-6Arg) and two were from diseased dogs with neurological signs (Nc-Bahia and Nc-Liv). The dams were inoculated with 2×106 tachyzoites of each isolate at day 7 of pregnancy. Morbidity, mortality and the antibody responses were evaluated in both the dams and the offspring, as was parasite transmission to the progeny. The mortality rates varied from 100% in Nc-Bahia and Nc-Liv-infected pups to 19% or less for those infected with the isolates from oocysts. The vertical transmission rates varied from 9 to 53% for N. caninum from oocysts, compared with 100% for the Nc-Liv and Nc-Bahia isolates. All dams showed specific IgG responses against tachyzoite and rNc-GRA7 antigens, confirming Neospora infection. The highest IgG levels were detected in mice inoculated with the Nc-Liv and Nc-Bahia isolates. These results demonstrate marked differences in virulence between the N. caninum isolates obtained from oocysts and neurologically affected dogs. This variability could help us to explain the differences in the outcome of the infection in definitive and intermediate hosts.
A Balanced Time Perspective in Adulthood: Well-being and Developmental Effects
Authors: Webster Jeffrey Dean , Ma Xiaodong
Published: October 2013

Cet article présente une étude qui reproduit directement l’Échelle de perspective temporelle éqilibrée (EPTE), récemment développée, et comprenait des adultes d’âge moyen et plus âgés. Parmi les participants figuraient 90 jeunes, 69 d’âge moyen, et 69 adulte âgés qui ont complété le BPTS comme une mesure de la vie sur la base de la Perspective de temps equilibrée. Une analyse factorielle a répliqué les résultats initiaux avec sous-échelles distinctes pour l’orientation au passé et à l’avenir, avec l’obtention d’une structure simple (alpha = .94 e .95, respectivenment). Une perspective de temps equilibrée prédit des scores plus élevés sur les deux mesures du bien-être, reproduisant les constations originales de J. D. Webster (2011). Comme prévu, une analyse du chi-carré a indiqué que le pourcentage de jeunes adultes avaient tendance à se trouver dans l’orientation axée sur l’avenir, et que les adultes plus âgés avaient tendance à se trouver dans l’orientation axée sur le passé. Les implications d’une perspective temporelle équilibrée sur la santé mentale au cours de la vie sont discutées.
Illegal fishing and catch potentials among small-scale fishers: application of an endogenous Switching regression model
Authors: Akpalu Wisdom , Normanyo Ametefee K.
Published: October 2013

Capture fish stocks are facing an increasing threat of extinction, partly due to the use of illegal fishing methods. In developing coastal countries – where fishing activities are the mainstay of the population along the coast – livelihoods are being directly threatened. Although a number of studies exist on fishing regulations and those who violate them, little has been done on the relationship between intrinsic catch potentials/fishing skills and illegal fishing behavior. Using data on violations of light attraction regulation among small-scale fishers in Ghana, our results show that the risk of punishment, the amount of fishing experience, the skipper's age, and religious norms all influence the decision to violate fishing regulations. Most importantly, we found that violators and non-violators have different fishing skills. Consequently, policies targeting illegal fishing must focus on equalizing efficiency and/or fishing skills among the fishermen as well as on traditional variables that influence violation decisions.
An analysis of genetic differentiation and geographical variation of spinach germplasm using SSR markers
Authors: Kuwahara Kouhei , Suzuki Reimi , Ito Yusuke , Mikami Tetsuo , Onodera Yasuyuki
Published: October 2013

To assess the genetic diversity of spinach germplasm, 250 individuals of 50 accessions collected from geographically diverse regions (West Asia, East Asia, Japan, Europe and the USA) were analysed using simple sequence repeat (SSR) markers. A total of 39 polymorphic alleles were identified, with an average of 6.5 alleles per locus for six loci. The overall gene diversity (0.62) in the entire set of individuals suggests that the germplasm has high genetic variability. The West Asian accessions showed the highest gene diversity, with a value of 0.57, followed by the East Asian accessions. These results help confirm the notion that spinach originated from West Asia. Hierarchical analysis of molecular variance revealed significant genetic differentiation among the geographical regions, which accounts for 26% of the total variation detected. Furthermore, pairwise Φstvalues indicate low genetic differentiation between the East Asian and Japanese germplasm accessions, both of which showed high genetic differentiation from the European accessions. The differentiation between the East Asian and European gene pools may be attributed to the founder effect associated with crop dissemination, as well as to the selection and genetic drift that occurred during the breeding process.
Priming of T follicular helper cells by dendritic cells
Authors: Ballesteros‐Tato André , Randall Troy D
Published: October 2013

T follicular helper cells (Tfh) are required to generate long‐lived antibody responses, which confer long‐term protection to pathogens following vaccination or infection. Despite significant advances in the field, however, little is known about the early steps that drive Tfh cell differentiation. In this review, we will discuss the mechanisms by which dendritic cells promote the initial commitment of activated CD4+ T cells to the Tfh cell differentiation pathway.
Optimization of physical data tables by simulated annealing
Authors: Corey Ellen M. , Young David A.
Published: October 2013

A simulated annealing program, HMCTAB, has been developed to optimize equation of state data tables for use in large physics simulation codes. A cost function dependent on table error and table size is defined and is used to accept or reject randomly chosen table grid configurations. An annealing schedule reduces the ‘‘temperature’’ parameter and drives the grid configuration toward the optimum. The result is a much smaller table with acceptable error.
PC-based data acquisition system for the Gulmarg gamma-ray telescope
Authors: Sawhney K. J. S. , Kaul I. K. , Koul R. , Bhat C. L. , Rawat H. S. , Kaul S. K.
Published: October 2013

The Gulmarg gamma-ray telescope used for the study of very-high-energy cosmic gamma-ray sources has been recently coupled to an IBM PC/XT personal computer to enhance its data acquisition and storage capabilities. The principle underlying the interface circuitry is outlined and the data acquisition and storage software developed is described.
Gaussian random number generators on a CYBER-205
Authors: Black S. C. , Kennedy A. D.
Published: October 2013

Normally distributed pseudorandom numbers are needed for many applications. Simple procedures for producing such a distribution can be found in many standard mathematical libraries. When many numbers are needed, however, the relatively slow speed of these methods can be a serious drawback. This is especially true on a vector computer, where the standard libraries contain scalar routines. The vectorization of several Gaussian random number generators on a CDC CYBER-205 is discussed. Four methods for producing a normal distribution are reviewed in detail. The first two considered are simple algorithms often referred to by the same name, the polar method. The latter two are more complex procedures which speed up the generating process by dividing the normal distribution into various parts. These are the rectangle–wedge–tail and ziggurat methods. Implementation on a CYBER-205 of the rectangle–wedge–tail, ziggurat, and one of the polar methods is discussed in detail. In evaluating their performance, it is found that the rectangle–wedge–tail and ziggurat methods offer significant improvements in execution speed over the polar method. Of these two, the ziggurat method is appreciably faster and requires fewer auxiliary constants. If only a few random numbers are needed, however, the polar method is probably the best choice. It may be coded in a few lines, and the sacrifice in speed is found to be only about a factor of 3.
Simulation of the dynamics of ion-bombarded surfaces on a desktop computer
Authors: Smith R. , Harrison D. E.
Published: October 2013

It is shown that desktop computers are excellent tools for carrying out the detailed calculations necessary in molecular dynamics simulations. The high-quality graphical capabilities of these machines allow detailed visual presentations of dynamically evolving collision cascades which can help provide new insights into the mechanisms by which atoms are ejected.
Simulated response of multilayer x-ray reflectors to damaging fluxes
Authors: Gray K. J. , Peterson B. G. , Knight L. V. , Thorne J. M.
Published: October 2013

A computer code ROMULS has been developed which computes the x-ray reflectivity versus angle versus time response of multilayer x-ray reflectors exposed to damaging, monochromatic, x-ray fluxes for short pulse applications. The code employs exponential x-ray absorption, hydrodynamic and thermodynamic modeling of structural and individual layer damage, and recursive calculation of the multilayer reflectivity. Comparison of simulations and experiments indicates that the code underestimates the useful life of multilayers by about a factor of 2. Simulations require approximately 1 min of MicroVAX II CPU time per multilayer layer pair per nanosecond of simulated time.
Computer-aided design and analysis of electronic circuits for instrumentation and control
Authors: Castaño Victor M. , Bribiesca Adolfo
Published: October 2013

A computer program for obtaining symbolic transfer functions of complex electronic circuits is described. The program accepts both numerical and symbolic elements as input and it is capable of performing some analysis of the calculated transfer function (Bode and Nyquist plots, for example). The mathematical algorithm underlying the program is briefly discussed as well.
Special purpose image display devices and techniques at the National Radio Astronomy Observatory
Authors: Rots Arnold H.
Published: October 2013

The NRAO has developed an image storage unit/control panel that greatly enhances the functionality and user-friendliness of its image display computers. Described here are the hardware design and capabilities of this system. In addition, a selection is presented from an image display software ‘‘bag of tricks’’: various image display techniques that have been found to be extremely useful in the analysis of radio astronomical imaging data and may be of interest to those in other fields of the physical sciences.
Block truncation image compression with bit-map compensation
Authors: Siedband Melvin P. , Zhang Huilian , Gray James
Published: October 2013

A modification to the block truncation coding technique is described in which images are improved by using the bit map to increase contrast gradients. In the image, amplitude values are functions of the ‘‘1’s’’ and ‘‘0’s’’ in the bit map and a weighting factor is determined by spatially convolving each pixel of the bit map. The effect is a general improvement in the appearance and a reduction of the ‘‘blockiness’’ of the image.
A note on computer experiments with chaotic shattering of level sets
Authors: Pickover Clifford A.
Published: October 2013

Computational and graphical results on a root-finding method for a 7th-deg Chebyshev polynomial in the complex plane C are presented. Level sets for sup{‖Hnζ0‖@B:n=1,2,...} reveal a visually striking and intricate class of patterns indicating behavior ranging from stable points to chaos. ‘‘Chaotic shattering’’ of the level sets is illustrated as the relaxation coefficient increases.
Investigation of sorting algorithms on a variety of computers
Authors: Bishop Marvin , Perel Jordan D. , Swan Victoria
Published: October 2013

Four sorting algorithms—bubble, insertion, heap, and quick—are studied on an IBM 3090/600, a VAX 11/780, and the NYU Ultracomputer. It is verified that for N items the bubble and insertion sorts are of order N2 whereas the heap and quick sorts are of order N ln N. It is shown that the choice of algorithm is more important than the choice of machine. Moreover, the influence of paging on algorithm performance is examined.
Continuous antialiased 2-D and 3-D transformations in discrete space
Authors: Snider A. , Mackie T. R.
Published: October 2013

This paper presents a vectorizable set of transformations for antialiased translation, shearing, and rescaling of two- or three-dimensional discrete data. Also described is a fast, acceptably accurate, flexible algorithm for performing antialiased zoom and rotation of discrete data that uses a sequence of these simpler operations. Although it was designed for applications in radiotherapy physics, it has applications in other areas of physics and other fields utilizing image processing.
Three-dimensional Fourier convolution with an array processor
Authors: Wells N. H. , Burrus C. S. , Desobry G. E. , Boyer A. L.
Published: October 2013

This paper describes techniques for reducing CPU time, memory, and I/O time required to perform a three-dimensional convolution on real data, and the use of an array processor. These techniques capitalize on the Hermitian nature of the Fourier transform of mathematically real input data, take advantage of convolution kernels having mirror symmetry in three dimensions, and eliminate trivial transformations. The result is convolution over a three-dimensional 64×64×64 array containing 250 K real elements that requires only 28 s to execute. Memory space of a medium-sized array processor is sufficiently large for the procedures to be carried out on entire real, single-precision arrays at one time without transferring data between the array processor and disk storage.
Using ADA tasks to simulate operating equipment
Authors: DeAcetis Louis A. , Schmidt Oron , Krishen Kumar
Published: October 2013

A method of simulating equipment using ADA tasks is discussed. Individual units of equipment are coded as concurrently running tasks that monitor and respond to input signals. This technique has been used in a simulation of the space-to-ground Communications and Tracking subsystem of Space Station Freedom.
Spreadsheets for computing charged-particle trajectories in 3-D electrostatic fields
Authors: Leclerc G. , Sanche L.
Published: October 2013

Use of a spreadsheet program to solve the Laplace equation and calculate charged-particle trajectories in geometrically complex electrostatic fields is described. The technique is applied to the development of a new electron-scattering apparatus.
Effect of vitamin D3 and strontium on performance, nutrient retention, and bone mineral composition in broiler chickens
Authors: Browning L. C. , Cowieson A. J.
Published: October 2013

The therapeutic use of vitamin D3 and strontium has been successful for the treatment of osteoporosis in humans; however, the value of similar strategies in poultry is not clear. Male Ross broiler chicks (n = 216) were used in a 28-day broiler trial to assess effects of vitamin D3 and strontium supplementation on performance, nutrient retention, bone composition, and bone mass. Treatments included an industry-standard control diet and five additional diets where vitamin D3 was added at 5000, 20 000, or 35 000 IU/kg and strontium was added at 0 or 1200 mg/kg in a 3 × 2 factorial design. Broiler chickens supplemented with strontium and additional vitamin D3 did not increase bodyweight; however, there was a significant improvement in feed efficiency at medium levels of vitamin D3, and although not statistically significant, there was also an improvement in feed conversion ratio with strontium supplementation at normal vitamin D3 concentrations. Strontium supplementation at normal levels of vitamin D3 significantly (P < 0.01) increased calcium, phosphorus, sodium, potassium, and magnesium retention. A high concentration of vitamin D3 produced a significant improvement in apparent metabolisable energy, protein, and dry matter utilisation in the broiler chicken. Paradoxically, however, there was a detrimental effect of high vitamin D3 on bodyweight and feed efficiency, which was partially ameliorated by strontium supplementation. Strontium addition did not change bone mass but did change bone composition. High levels of vitamin D3 significantly (P < 0.01) reduced bone ash content and increased strontium content of bone. In conclusion, both vitamin D3 and strontium have the potential to positively influence the performance, mineral retention, and bone characteristics of broiler chicks. However, as with calcium and phosphorus, vitamin D3 and strontium interact and so more research is required with strontium on the optimum dose rate and its relationship with vitamin D3, calcium, phosphorus, and IGF-1 in broiler nutrition.
Charge-dependent secretion of an intrinsically disordered protein via the autotransporter pathway
Authors: Kang’ethe Wanyoike , Bernstein Harris D.
Published: October 2013

Significance

Bacterial autotransporter proteins contain a large segment that is transported from the periplasm (the space between the inner and outer membranes) to the extracellular milieu. Because the periplasm lacks ATP, the energy required for the transport reaction is thought to be derived from the folding of this segment following its secretion. Contrary to the prevailing view, we found that a heterologous polypeptide that cannot fold was secreted efficiently when it was fused to an autotransporter. Reducing the negative charge of this polypeptide, however, strongly impaired secretion. Our results identify net charge as a potentially important factor that drives autotransporter secretion.
Molecular mechanism underlying ethanol activation of G-protein–gated inwardly rectifying potassium channels
Authors: Bodhinathan Karthik , Slesinger Paul A.
Published: October 2013

Significance

G-protein–gated inward-rectifying K
+
(GIRK) channels control neuronal excitability in the brain’s reward circuit. Ethanol, a widely available drug of abuse, directly binds to a hydrophobic pocket in the GIRK channel and activates it. The molecular mechanism underlying ethanol activation of GIRK channel remained unknown. Here, we used specialized biophysical tools and discovered that ethanol associates directly with the GIRK channel, leading to enhanced interaction with a membrane phospholipid phosphatidylinositol 4,5-bisphosphate and activation of the channel. Most importantly, the alcohol-binding pocket in GIRK channels can be occupied by non-alcohol-like chemical groups that activate the channel. This study will enable the design of therapeutics to selectively block alcohol’s access to GIRK channel.
Landscape of somatic mutations and clonal evolution in mantle cell lymphoma
Authors: Beà Sílvia , Valdés-Mas Rafael , Navarro Alba , Salaverria Itziar , Martín-Garcia David , Jares Pedro , Giné Eva , Pinyol Magda , Royo Cristina , Nadeu Ferran , Conde Laura , Juan Manel , Clot Guillem , Vizán Pedro , Di Croce Luciano , Puente Diana A. , López-Guerra Mónica , Moros Alexandra , Roue Gael , Aymerich Marta , Villamor Neus , Colomo Lluís , Martínez Antonio , Valera Alexandra , Martín-Subero José I. , Amador Virginia , Hernández Luis , Rozman Maria , Enjuanes Anna , Forcada Pilar , Muntañola Ana , Hartmann Elena M. , Calasanz María J. , Rosenwald Andreas , Ott German , Hernández-Rivas Jesús M. , Klapper Wolfram , Siebert Reiner , Wiestner Adrian , Wilson Wyndham H. , Colomer Dolors , López-Guillermo Armando , López-Otín Carlos , Puente Xose S. , Campo Elías
Published: October 2013

Significance

This is a comprehensive whole-genome/whole-exome analysis of mantle cell lymphoma (MCL). We sequenced 29 MCL cases and validated the findings by target sequencing of 172 additional tumors. We identified recurrent mutations in genes regulating chromatin modification and genes such as
NOTCH2
that have a major impact on clinical outcome. Additionally, we demonstrated the subclonal heterogeneity of the tumors already at diagnosis and the modulation of the mutational architecture in the progression of the disease. The identification of new molecular mechanisms may open perspectives for the management of MCL patients.
Golgi-associated RhoBTB3 targets Cyclin E for ubiquitylation and promotes cell cycle progression
Authors: Lu Albert , Pfeffer Suzanne R.
Published: October 2013

Cyclin E regulates the cell cycle transition from G1 to S phase and is degraded before entry into G2 phase. Here we show that RhoBTB3, a Golgi-associated, Rho-related ATPase, regulates the S/G2 transition of the cell cycle by targeting Cyclin E for ubiquitylation. Depletion of RhoBTB3 arrested cells in S phase, triggered Golgi fragmentation, and elevated Cyclin E levels. On the Golgi, RhoBTB3 bound Cyclin E as part of a Cullin3 (CUL3)-dependent RING–E3 ubiquitin ligase complex comprised of RhoBTB3, CUL3, and RBX1. Golgi association of this complex was required for its ability to catalyze Cyclin E ubiquitylation and allow normal cell cycle progression. These experiments reveal a novel role for a Ras superfamily member in catalyzing Cyclin E turnover during S phase, as well as an unexpected, essential role for the Golgi as a ubiquitylation platform for cell cycle control.
SIRPα polymorphisms, but not the prion protein, control phagocytosis of apoptotic cells
Authors: Nuvolone Mario , Kana Veronika , Hutter Gregor , Sakata Daiji , Mortin-Toth Steven M. , Russo Giancarlo , Danska Jayne S. , Aguzzi Adriano
Published: October 2013

Prnp−/− mice lack the prion protein PrPC and are resistant to prion infections, but variable phenotypes have been reported in Prnp−/− mice and the physiological function of PrPC remains poorly understood. Here we examined a cell-autonomous phenotype, inhibition of macrophage phagocytosis of apoptotic cells, previously reported in Prnp−/− mice. Using formal genetic, genomic, and immunological analyses, we found that the regulation of phagocytosis previously ascribed to PrPC is instead controlled by a linked locus encoding the signal regulatory protein α (Sirpa). These findings indicate that control of phagocytosis was previously misattributed to the prion protein and illustrate the requirement for stringent approaches to eliminate confounding effects of flanking genes in studies modeling human disease in gene-targeted mice. The plethora of seemingly unrelated functions attributed to PrPC suggests that additional phenotypes reported in Prnp−/− mice may actually relate to Sirpa or other genetic confounders.
Experiments of the Richtmyer–Meshkov instability
Authors: Prestridge Katherine , Orlicz Gregory , Balasubramanian Sridhar , Balakumar B. J.
Published: October 2013

The Richtmyer–Meshkov instability is caused by a shock interacting with a density-stratified interface. The mixing of the fluids is driven by vorticity created by the interaction of the density and pressure gradients. Because the flow is shock driven, the ensuing mixing occurs rapidly, making experimental measurements difficult. Over the past 10 years, there have been significant improvements in the experimental techniques used in shock-driven mixing flows. Many of these improvements have been driven by modelling and simulation efforts, and others have been driven by technology. High-resolution measurements of turbulence quantities are needed to advance our understanding of shock-driven flows, and this paper reviews the current state of experimental diagnostics, as well as paths forward in studying shock-driven mixing and turbulence.
After the financial crisis: a cost efficiency analysis of banks from Saudi Arabia
Authors: Hanif Akhtar Mohammad
Published: October 2013

Purpose

– This paper aims to estimate the cost efficiency scores of banks in KSA before and during financial crisis by using a data envelopment analysis (DEA) approach.

Design/methodology/approach

– The study uses the intermediation approach of banking services where banks are considered as manufacturing units. The research methodology consists of cost efficiency DEA and a second stage Tobit regression model.

Findings

– The results reveal that banks in KSA are least affected by the crisis as the efficiency scores remain the same during all the periods. However, the average levels of inefficiency remain higher suggesting that KSA banks are lagging behind in exploiting the resources fully. The major source of cost inefficiency stems from allocative inefficiency rather than the technical one. Results of the Tobit regression also disclose that the impact of financial crisis across bank efficiency remains weak and inconclusive.

Research limitations/implications

– The study bears some useful managerial implications for various stakeholders. Although banks do not seem to be affected by the crisis, yet they need to improve their efficiency since the levels are far below the frontier. For successful existence and growth of banking, it remains vital that these banks control their costs regardless of the fact are operating in a concentrated market.

Practical implications

– The paper suggests that the banks in KSA need to bring down their operating expenses to reach the efficiency frontier. The average level of inefficiency (82 per cent) reflects a greater amount of input waste which needs to be controlled by these banks.

Originality/value

– The study is novel in a way that it evaluates the cost efficiency performance of KSA banks before and during the financial crisis, followed by a second stage regression on the determinants of cost efficiency. It provides valuable insights to both the bank managers and public policy makers who can look for the optimal levels of efficiency and competitiveness of Saudi banking sector.
Islamic rates of return and conventional interest rates in the Malaysian deposit market
Authors: Ito Takayasu
Published: October 2013

Purpose

– This paper aims to analyze Islamic rates of return, conventional interest rates in the Malaysian deposit markets, and Kuala Lumpur Interbank Offered Rate (KLIBOR) rates in the short-term money market from the view point of co-movement and transmission.

Design/methodology/approach

– The non-stationary time series models such as cointegration and Granger causality tests are applied to analyze the daily data.

Findings

– Islamic rates of return and conventional interest rates co-move in the Malaysian deposit market. The Islamic rates of return propel conventional interest rates in the three-, six-, and 12-month maturities. Islamic rates of return and conventional interest rates form a short-term money market with KLIBOR rates.

Research limitations/implications

– The author analyzes econometrically the sample period from May 16, 2005 to January 12, 2012. This paper concentrates on the period after the development of Islamic banking in Malaysia.

Practical implications

– Islamic and conventional deposit markets are competitive in Malaysia; in particular, the competition in the one-month deposit market is very keen. Islamic rates of return have more impact on the formation of short-term interest rates than conventional interest rates.

Originality/value

– This paper makes three contributions to the related literatures. First, it uses daily data in the maturities of one month, three months, six months and 12 months for its analyses. Second, it uses the Granger causality method of Toda and Yamamoto to avoid the issue of the non-stationarity of the data. The results of the Granger causality tests in this paper are different from related literatures. Third, this paper focuses on the relationship of KLIBOR rates and Islamic rates of return, and of KLIBOR rates and conventional interest rates.
Males' trust and mistrust of females in Muslim matrimonial sites
Authors: Al-Saggaf Yeslam
Published: October 2013

Purpose

– The aim of this study is to examine interpersonal trust in Muslim matrimonial sites (MMS) from a male perspective. Specifically how users perceive interpersonal trust in MMS; what are the signs of lack of trust in MMS (if any); and what strategies do users adopt to handle the lack of trust in MMS.

Design/methodology/approach

– This empirical qualitative study used ethnographic techniques to collect data. In addition to briefly observing five MMS, the study conducted semi-structured interviews with ten participants, who were all males, between the ages of 25-35, and residing in different locations, including the USA, the UK, the UAE, Australia and Bahrain. While the interviews focused on participants' experience in MMS, the analysis of these interviews focused on the issue of trust in these sites.

Findings

– The analysis has revealed that participants associated trust with “risk taking”, “reliance” on one's abilities, “self-confidence” and honesty with the first three being the major themes that transpired from the analysis of data. The analysis has also revealed three signs of lack of trust in MMS. Users expressed concern over a large number of members' profiles being fake; they appeared suspicious about these sites and approached them with caution and felt intimidated by the unrealistic expectations members placed on them. However, it was found users adopted several strategies to handle the lack of trust in MMS including using their communication skills to study others carefully, doing “police work” to uncover any inconsistencies in their statements, “interrogating” them using a pre-developed list of questions and involving their family members in their negotiations.

Originality/value

– Despite MMS immense popularity within the Islamic world, with the exception of a few articles, there are not many articles available in the academic literature on them. This article seeks to address this imbalance.
Open source assessment of academic library patron satisfaction
Authors: Angell Katelyn
Published: October 2013

Purpose

– While academic libraries have often purchased proprietary software to assess patron satisfaction, the open source movement has generated high-quality software available free of charge. These tools are useful alternatives in an era marked by tremendous budget cuts familiar to many academic libraries. The purpose of this paper is to demonstrate the ability of open source software to effectively and affordably measure the quality of service at academic libraries.

Design/methodology/approach

– The author's experience with using the open source tool LimeSurvey to administer a library survey over a three-year period serves as a case study for other institutions. A literature review contextualizes the history of patron satisfaction surveys within academic libraries and questions the lack of an open source presence. Popular proprietary survey software is reported as a viable but expensive option, leading to a detailed case study of Sarah Lawrence College's successful addition of open source software to its assessment procedures.

Findings

– LimeSurvey is a flexible, customizable, and cost-effective tool for a small college library investing in querying its patrons for constructive feedback as a means of improving user experience.

Originality/value

– This paper will be of value to any library on a fixed budget looking to assess patron satisfaction with resources and services. Very little literature currently exists on this topic, but as the open source movement continues to flourish this software can play an integral role in allowing libraries to cut costs but not indispensable patron feedback.
Detection of Anthrax and Other Pathogens Using a Unique Liquid Array Technology
Authors: Schweighardt Andrew J. , Battaglia Amanda , Wallace Margaret M.
Published: October 2013

A bead‐based liquid hybridization assay, Luminex® 100™, was used to identify four pathogenic bacteria, Bacillus anthracis, Clostridium botulinum, Francisella tularensis subsp. tularensis, and Yersinia pestis, and several close relatives. Hybridization between PCR‐amplified target sequences and probe sequences (located within the 23S ribosomal RNA gene rrl and the genes related to the toxicity of each bacterium) was detected in single‐probe or multiple‐probe assays, depending on the organism. The lower limits of detection (LLDs) for the probes ranged from 0.1 to 10 ng. Sensitivity was improved using lambda exonuclease to digest the noncomplementary target strand. All contributors in 33 binary, ternary, and quaternary mixtures in which all components were present in a 1:1 ratio were identified with an 80% success rate. Twenty‐eight binary mixtures in which the two components were combined in various ratios were further studied. All target sequences were detected, even when the minor component was overshadowed by a tenfold excess of the major component.
A Test of a Recently Devised Method of Estimating Skeletal Age at Death using Features of the Adult Acetabulum
Authors: Mays Simon
Published: October 2013

Estimation of age at death from adult skeletal remains is highly problematic, due in great part to interpopulation variability in skeletal age changes. Thorough testing of aging methods is therefore of key importance. A method recently devised by Calce (Am J Phys Anthropol 148 (2012): 11–23) for placing adult skeletons into three broad age at death classes (17–39, 40–64, 65+ years) on the basis of acetabular morphology is tested on a collection of 18–19th century AD skeletons (N = 185) of documented age at death from London. Results showed that 45% were correctly assigned to age class using this method. This compares with 81% reported by Calce on 20th century North American material. This indicates significant interpopulation differences in the relationship between the Calce acetabular variables and age, even between populations of European ancestry. Until the sources of this variation are better understood, caution should be used before applying this method to estimate age in unknown skeletons.
Use of Craniofacial Superimposition in Historic Investigation
Authors: Bailey James A. , Brogdon G. B. , Nichols Brandon
Published: October 2013

A skeleton discovered in Grand Forks, North Dakota was purported to belong to Clelland “Clell” Miller, a James‐Younger gang member, who was killed during the Northfield Bank robbery on September 7, 1876. A 3‐D image from a computer tomography (CT) scan of the skull was obtained, and a craniofacial superimposition was conducted to determine if the skull could belong to Miller. The superimposition method used in this case was to overlay the CT image of the skull onto Miller's postmortem photograph. In addition to the craniofacial superimposition, the images were juxtaposed to compare similarities or differences in facial morphology between the skull and photograph. Superimposition methods can be used to exclude identifications; however, they should not be used as a conclusive method for identification. In this case, there were sufficient similarities between the skull and Miller's photograph; therefore, the skull could not be eliminated as possibly being that of Miller.
The Discrimination of Colored Acrylic, Cotton, and Wool Textile Fibers Using Micro‐Raman Spectroscopy. Part 1: In situ Detection and Characterization of Dyes
Authors: Buzzini Patrick , Massonnet Genevieve
Published: October 2013

Raman spectroscopy has been applied to characterize fiber dyes and determine the discriminating ability of the method. Black, blue, and red acrylic, cotton, and wool samples were analyzed. Four excitation sources were used to obtain complementary responses in the case of fluorescent samples. Fibers that did not provide informative spectra using a given laser were usually detected using another wavelength. For any colored acrylic, the 633‐nm laser did not provide Raman information. The 514‐nm laser provided the highest discrimination for blue and black cotton, but half of the blue cottons produced noninformative spectra. The 830‐nm laser exhibited the highest discrimination for red cotton. Both visible lasers provided the highest discrimination for black and blue wool, and NIR lasers produced remarkable separation for red and black wool. This study shows that the discriminating ability of Raman spectroscopy depends on the fiber type, color, and the laser wavelength.
Neonatal IGF‐1/IGFBP‐1 axis and retinopathy of prematurity are associated with increased blood pressure in preterm children
Authors: Kistner Anna , Sigurdsson Jon , Niklasson Aimon , Löfqvist Chatarina , Hall Kerstin , Hellström Ann
Published: October 2013

Aim

Preterm children are at risk of developing increased blood pressure (BP). We evaluated possible associations between BP, early insulin‐like growth factor‐1 (IGF‐1) and IGF‐binding protein‐1 (IGFBP‐1) levels and retinopathy of prematurity (ROP) in preterm children.

Methods

The study included 32 infants: median gestational age 28.1 weeks (range 24.6–31.3) and birthweight standard deviation scores (SDS) (±SD) 1.0 ± 2.7. IGF‐1 and IGFBP‐1 at postnatal weeks 32.6–34.6 and ROP stages were established after birth. BP was measured at the age of 4 years. The ratio (IGF‐1)2/IGFBP‐1 was created to investigate the influence of both IGF‐1 and IGFBP‐1 to later BP.

Results

Diastolic BP correlated with IGFBP‐1, inversely correlated with IGF‐1 and IGF‐12/IGFBP‐1 (r = −0.71, p < 0.0001) and positively correlated with catch‐up growth velocity from lowest weight SDS to age 36.5 weeks (r = 0.48, p < 0.01), independent of gestational age. Children with moderate‐to‐severe ROP as neonates had higher mean arterial BP [78 (±95%CI 74–83) vs 71 (±95%CI 68–75) mm Hg, p < 0.05] adjusted for gestational age and birthweight SDS compared to children diagnosed with no to mild ROP.

Conclusion

Low neonatal IGF‐12/IGFBP‐1 and severe ROP were associated with higher BP in 4‐year‐old children born very preterm and may thus predict future cardiovascular morbidity.
Mitochondrial dysfunction in amyotrophic lateral sclerosis – a valid pharmacological target?
Authors: Muyderman H , Chen T
Published: October 2013

Amyotrophic lateral sclerosis (ALS) is an adult‐onset neurodegenerative disease characterized by the selective death of upper and lower motor neurons which ultimately leads to paralysis and ultimately death. Pathological changes in ALS are closely associated with pronounced and progressive changes in mitochondrial morphology, bioenergetics and calcium homeostasis. Converging evidence suggests that impaired mitochondrial function could be pivotal in the rapid neurodegeneration of this condition. In this review, we provide an update of recent advances in understanding mitochondrial biology in the pathogenesis of ALS and highlight the therapeutic value of pharmacologically targeting mitochondrial biology to slow disease progression.

Linked Articles

This article is part of a themed issue on Mitochondrial Pharmacology: Energy, Injury & Beyond. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2014.171.issue‐8