bluuebunny/crossref_metadata_2025 huggingface dataset:
Defect study of Cu2ZnSn(SxSe1−x)4 thin film absorbers using photoluminescence and modulated surface photovoltage spectroscopy
Authors: Lin Xianzhong , Ennaoui Ahmed , Levcenko Sergiu , Dittrich Thomas , Kavalakkatt Jaison , Kretzschmar Steffen , Unold Thomas , Lux-Steiner Martha Ch.
Published: January 2015

Defect states in Cu2ZnSn(SxSe1−x)4 thin films with x = 0.28, 0.36, and 1 were studied by combining photoluminescence (PL) and modulated surface photovoltage (SPV) spectroscopy. A single broad band emission in the PL spectra was observed and can be related to quasi-donor-acceptor pair transitions. The analysis of the temperature dependent quenching of the PL band (x = 0.28, 0.36, and 1) and SPV (x = 0.28) signals resulted in activation energies below 150 meV for PL and about 90 and 300 meV for SPV. Possible intrinsic point defects that might be associated with these observed activation energies are discussed.
Hydrogen-mediated long-range magnetic ordering in Pd-rich alloy film
Authors: Lin Wen-Chin , Tsai Cheng-Jui , Huang Han-Yuan , Wang Bo-Yao , Mudinepalli Venkata Ramana , Chiu Hsiang-Chih
Published: January 2015

The effect of hydrogenation on a 14 nm Co14Pd86/Al2O3(0001) thin film was investigated on the basis of the magnetooptical Kerr effect. After exposure to H2 gas, the squareness of the hysteresis loop showed a large transition from approximately 10% to 100% and the saturation Kerr signal was reduced to nearly 30% of the pristine value. The reversibility of the transition was verified and the response time was within 2–3 s. These observations indicate that the hydride formation transformed the short-range coupled and disordered magnetic state of the Co14Pd86 film to a long-range-ordered ferromagnetic state and induced appreciable decrease in the magnetic moment. The enhanced long-range-ordering and the reduction of the magnetic moment were attributed to the change of electronic structure in Co14Pd86 with hydrogen uptake.
Independent dynamic acousto-mechanical and electrostatic control of individual quantum dots in a LiNbO3-GaAs hybrid
Authors: Pustiowski Jens , Müller Kai , Bichler Max , Koblmüller Gregor , Finley Jonathan J. , Wixforth Achim , Krenner Hubert J.
Published: January 2015

We demonstrate tuning of single quantum dot emission lines by the combined action of the dynamic acoustic field of a radio frequency surface acoustic wave and a static electric field. Both tuning parameters are set all-electrically in a LiNbO3-GaAs hybrid device. The surface acoustic wave is excited directly on the strong piezoelectric LiNbO3 onto which a GaAs-based p-i-n photodiode containing a single layer of quantum dots was epitaxially transferred. We demonstrate dynamic spectral tuning with bandwidths exceeding 3 meV of single quantum dot emission lines due to deformation potential coupling. The center energy of the dynamic spectral oscillation can be independently programmed simply by setting the bias voltage applied to the diode.
Assisted extraction of the energy level spacings and lever arms in direct current bias measurements of one-dimensional quantum wires, using an image recognition routine
Authors: Lesage A. A. J. , Smith L. W. , Al-Taie H. , See P. , Griffiths J. P. , Farrer I. , Jones G. A. C. , Ritchie D. A. , Kelly M. J. , Smith C. G.
Published: January 2015

A multiplexer technique is used to individually measure an array of 256 split gates on a single GaAs/AlGaAs heterostructure. This results in the generation of large volumes of data, which requires the development of automated data analysis routines. An algorithm is developed to find the spacing between discrete energy levels, which form due to transverse confinement from the split gate. The lever arm, which relates split gate voltage to energy, is also found from the measured data. This reduces the time spent on the analysis. Comparison with estimates obtained visually shows that the algorithm returns reliable results for subband spacing of split gates measured at 1.4 K. The routine is also used to assess direct current bias spectroscopy measurements at lower temperatures (50 mK). This technique is versatile and can be extended to other types of measurements. For example, it is used to extract the magnetic field at which Zeeman-split 1D subbands cross one another.
Harmonic gyrotrons operating in high-order symmetric modes
Authors: Nusinovich Gregory S. , Kashyn Dmytro G. , Antonsen T. M.
Published: January 2015

It is shown that gyrotrons operating at cyclotron harmonics can be designed for operation in symmetric TE0,p-modes. Such operation in fundamental harmonic gyrotrons is possible only at small radial indices (p≤3) because of the severe mode competition with TE2,p-modes, which are equally coupled to annular beams as the symmetric modes. At cyclotron harmonics, however, this “degeneracy” of coupling is absent, and there is a region in the parameter space where harmonic gyrotrons can steadily operate in symmetric modes. This fact is especially important for sub-THz and THz-range gyrotrons where ohmic losses limit the power achievable in continuous-wave and high duty cycle regimes.
Influence of quantum diffraction and shielding on electron-ion collision in two-component semiclassical plasmas
Authors: Hong Woo-Pyo , Jung Young-Dae
Published: January 2015

The influence of quantum diffraction and shielding on the electron-ion collision process is investigated in two-component semiclassical plasmas. The eikonal method and micropotential taking into account the quantum diffraction and shielding are used to obtain the eikonal scattering phase shift and the eikonal collision cross section as functions of the collision energy, density parameter, Debye length, electron de Broglie wavelength, and the impact parameter. The result shows that the quantum diffraction and shielding effects suppress the eikonal scattering phase shift as well as the differential eikonal collision cross section, especially, in small-impact parameter regions. It is also shown that the quantum shielding effect on the eikonal collision cross section is more important in low-collision energies. In addition, it is found that the eikonal collision cross section increases with an increase in the density parameter. The variations of the eikonal cross section due to the quantum diffraction and shielding effects are also discussed.
Simulation study of HEMT structures with HfO2 cap layer for mitigating inverse piezoelectric effect related device failures
Authors: Nagulapally Deepthi , Joshi Ravi P. , Pradhan Aswini
Published: January 2015

The Inverse Piezoelectric Effect (IPE) is thought to contribute to possible device failure of GaN High Electron Mobility Transistors (HEMTs). Here we focus on a simulation study to probe the possible mitigation of the IPE by reducing the internal electric fields and related elastic energy through the use of high-k materials. Inclusion of a HfO2 “cap layer” above the AlGaN barrier particularly with a partial mesa structure is shown to have potential advantages. Simulations reveal even greater reductions in the internal electric fields by using “field plates” in concert with high-k oxides.
Maximum screening fields of superconducting multilayer structures
Authors: Gurevich Alex
Published: January 2015

It is shown that a multilayer comprised of alternating thin superconducting and insulating layers on a thick substrate can fully screen the applied magnetic field exceeding the superheating fields Hs of both the superconducting layers and the substrate, the maximum Meissner field is achieved at an optimum multilayer thickness. For instance, a dirty layer of thickness ∼0.1 μm at the Nb surface could increase Hs ≃ 240 mT of a clean Nb up to Hs ≃ 290 mT. Optimized multilayers of Nb3Sn, NbN, some of the iron pnictides, or alloyed Nb deposited onto the surface of the Nb resonator cavities could potentially double the rf breakdown field, pushing the peak accelerating electric fields above 100 MV/m while protecting the cavity from dendritic thermomagnetic avalanches caused by local penetration of vortices.
Microwave power coupling in a surface wave excited plasma
Authors: Kar Satyananda , Alberts Lukas , Kousaka Hiroyuki
Published: January 2015

In recent decades, different types of plasma sources have been used for various types of plasma processing, such as, etching and thin film deposition. The critical parameter for effective plasma processing is high plasma density. One type of high density plasma source is Microwave sheath-Voltage combination Plasma (MVP). In the present investigation, a better design of MVP source is reported, in which over-dense plasma is generated for low input microwave powers. The results indicate that the length of plasma column increases significantly with increase in input microwave power.
Rapid Gist Perception of Meaningful Real-Life Scenes: Exploring Individual and Gender Differences in Multiple Categorization Tasks
Authors: Vanmarcke Steven , Wagemans Johan
Published: January 2015

In everyday life, we are generally able to dynamically understand and adapt to socially (ir)elevant encounters, and to make appropriate decisions about these. All of this requires an impressive ability to directly filter and obtain the most informative aspects of a complex visual scene. Such rapid gist perception can be assessed in multiple ways. In the ultrafast categorization paradigm developed by Simon Thorpe et al. (1996), participants get a clear categorization task in advance and succeed at detecting the target object of interest (animal) almost perfectly (even with 20 ms exposures). Since this pioneering work, follow-up studies consistently reported population-level reaction time differences on different categorization tasks, indicating a superordinate advantage (animal versus dog) and effects of perceptual similarity (animals versus vehicles) and object category size (natural versus animal versus dog). In this study, we replicated and extended these separate findings by using a systematic collection of different categorization tasks (varying in presentation time, task demands, and stimuli) and focusing on individual differences in terms of e.g., gender and intelligence. In addition to replicating the main findings from the literature, we find subtle, yet consistent gender differences (women faster than men).
Visual Attention at the Tip of the Tongue
Authors: Barnett-Cowan Michael , Soeizi Matin , DeSouza Joseph F. X.
Published: January 2015

The brain shifts attention by selectively modulating sensory information about relevant environmental features. It has been shown that eye, head, trunk and limb position can bias spatial attention. This leads to the interesting question: Does the brain only recruit bodily information that is explicitly related to orienting behaviour to direct attention, or more generally? We tested whether tongue position, which does not explicitly functionally relate to orienting behaviour, biases attention in a visual search task. Thirty-six participants completed three visual search trial blocks of increased difficulty each consisting of three tongue positions for 50 trials. Response times and error rates were used to assess whether tongue position modulates visual attention. Results show that sensorimotor information from the tongue modulates attention in a difficult visual search task: faster responses to visual search targets presented ipsilateral with the tongue; slower responses when contralateral. In line with cognition being generally embodied, the tongue plays a surprising role in directing attention.
Atypical correlation of otolith strontium : calcium and barium : calcium across a marine–freshwater life history transition of a diadromous fish
Authors: Hamer Paul , Henderson Angela , Hutchison Michael , Kemp Jodie , Green Corey , Feutry Pierre
Published: January 2015

Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr:Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr:Ca and Ba:Ca, however, showed the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35–45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4mgL–1) of the freshwater resulted in the Sr:Ca being substantially higher than the marine water. Importantly, the otolith Sr:Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr:Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr:Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element:Ca ratios and that inferences of marine–freshwater habitat use from otolith Sr:Ca alone can be problematic without an understanding of water chemistry.
Plant litter diversity affects invertebrate shredder activity and the quality of fine particulate organic matter in streams
Authors: Fernandes Isabel , Duarte Sofia , Cássio Fernanda , Pascoal Cláudia
Published: January 2015

There is evidence that loss of riparian plant diversity alters the availability and quality of resources in streams, but little is known about how such effects change with time after loss of diversity. We used a microcosm approach with leaves of alder, oak and eucalypt previously colonised by microbes in a mixed forest stream to test how loss of litter diversity and time (2 and 6 months after loss of diversity) affect leaf consumption by invertebrate shredders, the elemental composition of shredder tissues, and the quality of fine particulate organic matter (FPOM). The number and identity of leaf species affected leaf consumption and FPOM production by shredders. Effects of leaf species diversity were positive and became more frequent with time after loss of diversity. Carbon (C) and nitrogen (N) composition of invertebrate tissues changed with the leaf identity. FPOM quality (C:N ratio) was positively correlated with leaf quality. Leaf consumption by the animals decreased linearly with the increase in C:N imbalance between leaf litter and invertebrate tissues. Our results suggest that changes in plant litter diversity affect the activity of shredders (leaf consumption and FPOM production), and the quality of food resources (FPOM and shredders) to higher trophic levels in streams; such effects are likely to become stronger with time after loss of plant diversity.
Age and growth of the white shark, Carcharodon carcharias, in the western North Atlantic Ocean
Authors: Natanson Lisa J. , Skomal Gregory B.
Published: January 2015

Age and growth estimates for the white shark (Carcharodon carcharias) in the western North Atlantic Ocean (WNA) were derived from band pair counts on the vertebral centra of 81 specimens collected between 1963 and 2010. We used two previously published criteria to interpret band pairs and assessed the validity of each method using Δ14C levels from a recent bomb radiocarbon validation study and existing Δ14C reference chronologies in the WNA. Although both criteria produced age estimates consistent, to varying degrees, with different reference chronologies, only one was considered valid when life history information was used to select the appropriate reference chronology and minimum/maximum ages based on bomb carbon values were taken into consideration. These age estimates, validated up to 44 years, were used to develop a growth curve for the species, which was best described using the Schnute general model (sexes combined). These results indicate that white sharks grow more slowly and live longer than previously thought.
Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in
Arabidopsis thaliana
Authors: Bond Donna M. , Baulcombe David C.
Published: January 2015

Significance

Using virus-induced gene silencing (VIGS) in wild-type and mutant
Arabidopsis
, we characterize a novel mechanism associated with the de novo establishment of heritable epigenetic marks in plants. Once established by this novel mechanism, the epigenetic mark is then reinforced by the previously characterized PolIV pathway of RNA-directed DNA methylation. A similar transition from the novel mechanism to the PolIV pathway is likely to explain many epigenetic phenomena in which RNA-directed DNA methylation is established de novo, including transposon silencing and paramutation. A practical benefit of our work is the identification of a mutant plant genotype in which the maintenance mechanism of epigenetic VIGS is reinforced. This genotype would aid the use of epigenetic VIGS for dissection of gene structure and function.
Fermi surface reconstruction and multiple quantum phase transitions in the antiferromagnet CeRhIn
5
Authors: Jiao Lin , Chen Ye , Kohama Yoshimitsu , Graf David , Bauer E. D. , Singleton John , Zhu Jian-Xin , Weng Zongfa , Pang Guiming , Shang Tian , Zhang Jinglei , Lee Han-Oh , Park Tuson , Jaime Marcelo , Thompson J. D. , Steglich Frank , Si Qimiao , Yuan H. Q.
Published: January 2015

Significance

Conventional, thermally driven continuous phase transitions are described by universal critical behavior that is independent of microscopic details of a specific material. An analogous description is lacking for phase transitions that are driven at absolute zero temperature by a nonthermal control parameter. Classification of quantum-driven phase transitions is a fundamental but open problem that arises in diverse contexts and multiple classes of materials. Here we report the first observation, to our knowledge, of a sharp Fermi surface reconstruction while applying a strong magnetic field to suppress an antiferromagnetic transition to zero temperature. These experiments demonstrate that direct measurements of the Fermi surface can distinguish theoretically proposed models of quantum criticality and point to a universal description of quantum phase transitions.
Clofazimine shortens the duration of the first-line treatment regimen for experimental chemotherapy of tuberculosis
Authors: Tyagi Sandeep , Ammerman Nicole C. , Li Si-Yang , Adamson John , Converse Paul J. , Swanson Rosemary V. , Almeida Deepak V. , Grosset Jacques H.
Published: January 2015

Significance

The infectious disease tuberculosis (TB) is a major public health problem that affects millions of people worldwide. TB treatment consists of a multidrug regimen that needs to be taken for a minimum of 6 mo, and lack of adherence to this regimen is associated with treatment failure and emergence of drug resistance. In a mouse model of TB chemotherapy, we have found that inclusion of the antileprosy drug clofazimine in the first-line regimen for TB reduces the duration of treatment necessary to achieve relapse-free cure from 6 mo to 3 mo. Our data suggest that clofazimine, a drug already known to be safe for long-term administration to patients with leprosy, has the potential to significantly shorten the duration of TB treatment.
Flies expand the repertoire of protein structures that bind ice
Authors: Basu Koli , Graham Laurie A. , Campbell Robert L. , Davies Peter L.
Published: January 2015

Significance

A previously unidentified insect antifreeze protein has been characterized in a fly. It is present in the adult stage of midges that emerge from fresh water in the spring and need protection from occasional night frosts. The mature protein has 79 residues and is small and repetitive enough to be reliably modeled as a tightly wound solenoid structure. Each tandem repeat of 10 residues forms a coil of the solenoid that is cross-braced by a disulfide bond. This fold orients a row of seven stacked tyrosine side chains to make a flat surface, which is the predicted ice-binding site of the protein. This protein has no homologs in the database and has, therefore, recently evolved to protect its host from freezing.
Control of stem cell self-renewal and differentiation by the heterochronic genes and the cellular asymmetry machinery in
Caenorhabditis elegans
Authors: Harandi Omid F. , Ambros Victor R.
Published: January 2015

Significance

Transitions between asymmetric (self-renewal) and symmetric (proliferative) divisions for stem cells are precisely regulated during development and tissue regeneration.
Caenorhabditis elegans
heterochronic genes encode evolutionarily conserved developmental regulators, including
lin-4
(lineage defect) and
let-7
(lethal defects) microRNAs and the stem cell factor LIN-28 that control patterns of stem cell self-renewal and proliferation. It is not known how these developmental regulators interface with the machinery of division asymmetry. We report that, in
C. elegans
, the timing of transitions between asymmetric and symmetric stem cell divisions reflects developmental modulation of the LIT-1/POP-1/APR-1 (loss of intestine/posterior pharynx defect/APC related) asymmetry machinery by the heterochronic genes. These findings illuminate how evolutionarily conserved cellular asymmetry machinery can be coupled to microRNA-regulated developmental pathways for robust stem cell maintenance and proliferation.
Semilocal density functional obeying a strongly tightened bound for exchange
Authors: Sun Jianwei , Perdew John P. , Ruzsinszky Adrienn
Published: January 2015

Significance

Efficient calculation of the properties of atoms, molecules, and solids on the computer requires a semilocal approximation to the density functional for the exchange-correlation energy, which becomes thereby a single integral over three-dimensional space. A recent, strongly tightened lower bound on the exchange energy has been built into the approximation “meta-generalized gradient approximations made very simple,” or MGGA-MVS, with accurate results for heats of formation, energy barriers, and weak interactions of molecules, and for lattice constants of solids. This would not have been possible without the use of a third ingredient (the local kinetic energy density) in addition to the standard two (the local electron density and its gradient). This third ingredient permits accurate energies even with the drastically tightened bound.
Asymmetric synthesis of 3-azide-4-fluoro-l-phenylalanine
Authors: Adachi Masaatsu , Nakajima Mado , Isobe Minoru
Published: January 2015

The asymmetric synthesis of N-Fmoc-protected 3-azide-4-fluoro-l-phenylalanine as a photoactive phenylalanine analog has been achieved by Schöllkopf’s alkylation.
Engineering aspects of rate-related processes in food manufacturing
Authors: Adachi Shuji
Published: January 2015

Many rate-related phenomena occur in food manufacturing processes. This review addresses four of them, all of which are topics that the author has studied in order to design food manufacturing processes that are favorable from the standpoint of food engineering. They include chromatographic separation through continuous separation with a simulated moving adsorber, lipid oxidation kinetics in emulsions and microencapsulated systems, kinetic analysis and extraction in subcritical water, and water migration in pasta.
Rapid separation of seed gliadins by reversed-phase ultra performance liquid chromatography (RP-UPLC) and its application in wheat cultivar and germplasm identification
Authors: Han Caixia , Lu Xaiobing , Yu Zitong , Li Xiaohui , Ma Wujun , Yan Yueming
Published: January 2015

To separate gliadin from wheat flour, a novel and stability-indicating reversed-phase ultra performance liquid chromatography (RP-UPLC) method is established and optimized. A comparative analysis of routine capillary electrophoresis (CE), reversed-phase high-performance liquid chromatography (RP-HPLC), and RP-UPLC was performed and the results showed that the resolution and efficiency of RP-UPLC were significantly higher than those of CE and RP-HPLC. Characteristic RP-UPLC patterns of different bread wheat variety and related species were readily identified. These results demonstrated that our RP-UPLC procedure resulted in significant improvements in sensitivity, speed, and resolution, and thus is highly useful in wheat cultivar and germplasm identification.
MD-2 is required for disulfide HMGB1–dependent TLR4 signaling
Authors: Yang Huan , Wang Haichao , Ju Zhongliang , Ragab Ahmed A. , Lundbäck Peter , Long Wei , Valdes-Ferrer Sergio I. , He Mingzhu , Pribis John P. , Li Jianhua , Lu Ben , Gero Domokos , Szabo Csaba , Antoine Daniel J. , Harris Helena E. , Golenbock Doug T. , Meng Jianmin , Roth Jesse , Chavan Sangeeta S. , Andersson Ulf , Billiar Timothy R. , Tracey Kevin J. , Al-Abed Yousef
Published: January 2015

Innate immune receptors for pathogen- and damage-associated molecular patterns (PAMPs and DAMPs) orchestrate inflammatory responses to infection and injury. Secreted by activated immune cells or passively released by damaged cells, HMGB1 is subjected to redox modification that distinctly influences its extracellular functions. Previously, it was unknown how the TLR4 signalosome distinguished between HMGB1 isoforms. Here we demonstrate that the extracellular TLR4 adaptor, myeloid differentiation factor 2 (MD-2), binds specifically to the cytokine-inducing disulfide isoform of HMGB1, to the exclusion of other isoforms. Using MD-2–deficient mice, as well as MD-2 silencing in macrophages, we show a requirement for HMGB1-dependent TLR4 signaling. By screening HMGB1 peptide libraries, we identified a tetramer (FSSE, designated P5779) as a specific MD-2 antagonist preventing MD-2–HMGB1 interaction and TLR4 signaling. P5779 does not interfere with lipopolysaccharide-induced cytokine/chemokine production, thus preserving PAMP-mediated TLR4–MD-2 responses. Furthermore, P5779 can protect mice against hepatic ischemia/reperfusion injury, chemical toxicity, and sepsis. These findings reveal a novel mechanism by which innate systems selectively recognize specific HMGB1 isoforms. The results may direct toward strategies aimed at attenuating DAMP-mediated inflammation while preserving antimicrobial immune responsiveness.
Multidisciplinary Intervention for Childhood Feeding Difficulties
Authors: Marshall Jeanne , Hill Rebecca J. , Ware Robert S. , Ziviani Jenny , Dodrill Pamela
Published: January 2015

Objective:

The aim of the study was to determine whether operant conditioning (OC) or systematic desensitization (SysD) intervention resulted in more improvements in dietary variety/intake, and more reductions in difficult mealtime behaviors.

Methods:

Children 2 to 6 years with autism spectrum disorder or with a nonmedically complex history were recruited. Feeding difficulties were confirmed based on clinical assessment. Participants were randomized to receive 10 OC or SysD sessions (parents could opt for intervention once per week, or intensively within a week). Immersive parent education was delivered across both arms. A 3‐month review was provided to measure outcomes postintervention.

Results:

In total, 68 participants (87%) completed the study. There were no significant differences in outcome measures between the OC and SysD intervention groups from baseline to 3‐month review. When the data were combined across both groups, however, significant improvements in primary outcome measures were observed (P < 0.05). Although not statistically significant, it was considered clinically significant that participants in the OC arm demonstrated more increases in dietary variety (mean difference 3.3 foods, 95% confidence interval −0.1 to 6.8, P = 0.06) compared with the SysD arm. There were limited differences in response observed between the autism spectrum disorder and nonmedically complex history groups, and the intensive and weekly arms.

Conclusions:

Favorable results were observed regardless of intervention, intensity, or etiological group. Results suggest that, when delivered to a protocol by experienced therapists and coupled with parent education, these 2 intervention approaches are effective. Further research is required in exploring these interventions across other subgroups, and examining outcomes for longer periods.
The Gastrointestinal Endoscopy Competency Assessment Tool for Pediatric Colonoscopy
Authors: Walsh Catharine M. , Ling Simon C. , Mamula Petar , Lightdale Jenifer R. , Walters Thomas D. , Yu Jeffrey J. , Carnahan Heather
Published: January 2015

Objectives:

Validated assessment tools are required to support competency‐based education. We aimed to assess the reliability and validity of the Gastrointestinal Endoscopy Competency Assessment Tool for Pediatric Colonoscopy (GiECATKIDS), an instrument developed by 41 North American experts using Delphi methodology.

Methods:

GiECATKIDS consists of a 7‐item global rating scale (GRS) and an 18‐item checklist (CL). An attending physician assessed 104 colonoscopies performed at 3 North American hospitals by 56 endoscopists, including 25 novices (<50 previous procedures), 21 intermediates (50–250), and 10 advanced endoscopists (>500). Another observer rated procedures to assess interrater reliability using intraclass correlation coefficient (ICC). Test–retest reliability was measured with ICC comparing endoscopists' first and second procedure scores. Discriminative validity was examined by comparing experience level with scores. Concurrent validity was assessed by correlating scores with colonoscopy experience, cecal and terminal ileal intubation rates, and physician global assessment.

Results:

Interrater reliability of the GiECATKIDS was high (total: ICC = 0.88; GRS: ICC = 0.79; CL: ICC = 0.89). Test–retest reliability was excellent (total: ICC = 0.94; GRS: ICC = 0.94; CL: ICC = 0.84). GiECATKIDS total, GRS, and CL scores differed significantly among novice, intermediate, and advanced endoscopists (P < 0.001). There was a significant positive correlation (P < 0.001) between scores and number of previous colonoscopies (total: ρ = 0.91, GRS: ρ = 0.92, CL: ρ = 0.84), cecal intubation rate (total: ρ = 0.82, GRS: ρ = 0.85, CL: ρ = 0.77), ileal intubation rate (total: ρ = 0.82, GRS: ρ = 0.82, CL: ρ = 0.80), and physician global assessment (total: ρ = 0.95, GRS: ρ = 0.94, CL: ρ = 0.89).

Conclusions:

The GiECATKIDS demonstrates strong reliability and validity as a measure of performance of pediatric colonoscopy that can be used to support training and assessment.
Lactobacillus rhamnosus GG Dosage Affects the Adjuvanticity and Protection Against Rotavirus Diarrhea in Gnotobiotic Pigs
Authors: Wen Ke , Liu Fangning , Li Guohua , Bai Muqun , Kocher Jacob , Yang Xingdong , Wang Haifeng , Clark‐Deener Sherrie , Yuan Lijuan
Published: January 2015

Objectives:

The use of immunostimulatory strains of probiotics as adjuvants has been increasingly recognized as a promising approach in enhancing vaccine immunogenicity; however, dose effects of probiotic adjuvants are not well defined. In the present study, we examined dose effects of a commonly used probiotic strain, Lactobacillus rhamnosus GG (LGG), on immunomodulation with 2 different dosages.

Methods:

Neonatal gnotobiotic pigs were inoculated with 2 oral doses of attenuated human rotavirus (AttHRV) vaccines and fed with 5 doses (LGG5X; total 2.1 × 106 colony‐forming units) or 9 doses (LGG9X; total 3.2 × 106 colony‐forming units) of LGG, starting at 3 days of age.

Results:

Both LGG feeding regimens enhanced the protection rate of AttHRV vaccine against diarrhea on virulent human rotavirus challenge. LGG5X, but not LGG9X, significantly enhanced rotavirus‐specific intestinal memory B‐cell responses to AttHRV; LGG5X also significantly enhanced virus‐specific intestinal immunoglobulin A (IgA) antibody‐secreting cell responses. Both regimens significantly enhanced rotavirus‐specific serum IgA antibody responses to AttHRV. They also enhanced rotavirus‐specific interferon‐γ–producing effector/memory T‐cell responses to AttHRV vaccine, with LGG9X being more effective than LGG5X, and both regimens downregulated CD4+CD25−FoxP3+ regulatory T (Treg) cell responses in most lymphoid tissues examined prechallenge and postchallenge and maintained the CD4+CD25+FoxP3+ Treg population in the ileum and intraepithelial lymphocyte postchallenge. LGG9X, however, did not significantly reduce total CD4+CD25−FoxP3+ Treg frequencies in the intestine and transforming growth factor‐β–producing and interleukin (IL)‐10–producing Treg frequencies in the blood.

Conclusions:

These results indicate that LGG at both dosages functioned as effective probiotic adjuvant for AttHRV vaccine, but different dosages differentially modulated immune responses to favor either the mucosal IgA response (LGG5X) or the T‐cell response (LGG9X).
Infliximab “Top‐Down” Strategy is Superior to “Step‐Up” in Maintaining Long‐Term Remission in the Treatment of Pediatric Crohn Disease
Authors: Lee Yoo Min , Kang Ben , Lee Yoon , Kim Mi Jin , Choe Yon Ho
Published: January 2015

Objectives:

We aimed to compare the efficacy of remission maintenance between infliximab “top‐down” and “step‐up” strategies in moderate to severe pediatric Crohn disease during 3 years. We also aimed to determine prognostic factors that may influence the relapse‐free rate in these patients.

Methods:

The present study was a retrospective review of a prospective cohort, based on an infliximab treatment protocol for pediatric Crohn disease used at Samsung Medical Center. A total of 31 patients (group A) were treated with early infliximab induction (“top‐down” strategy) and 20 patients (group B) refractory to conventional therapy underwent infliximab treatment (“step‐up” strategy). The efficacy of infliximab treatment was assessed by relapse‐free rate and remission period rate for 3 years. A total of 11 prognostic factors that may influence the relapse‐free rate were further analyzed.

Results:

The relapse‐free rates at 3 years were 35.5% (95% confidence interval [CI] 0.194–0.519) in group A and 15.0% (95% CI 0.037–0.335) in group B (P = 0.0094). Overall remission period rate for 3 years also showed a significant difference between the 2 groups (92.1% ± 7.2% vs 78.3% ± 16.6%; P = 0.005). Multivariable analysis revealed that the duration from the initial diagnosis to infliximab infusion was the only factor associated with relapse‐free remission for 3 years (hazard ratio = 1.077; 95% CI 1.025–1.131).

Conclusions:

“Top‐down” strategy had a longer remission period compared with the “step‐up” strategy in pediatric Crohn disease during a study period of 3 years, based on relapse‐free rate and remission period rate. Earlier introduction of infliximab is recommended in pediatric patients with moderate to severe Crohn disease.
Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages
Authors: Pollock Laura J. , Rosauer Dan F. , Thornhill Andrew H. , Kujala Heini , Crisp Michael D. , Miller Joseph T. , McCarthy Michael A.
Published: January 2015

Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of using PD in spatial prioritization could be extended to any clade or area that has spatial and phylogenetic data. Our results demonstrate the relevance of PD to regional conservation policy by highlighting that small but strategically located areas disproportionally impact the preservation of evolutionary lineages.
Global evolutionary isolation measures can capture key local conservation species in Nearctic and Neotropical bird communities
Authors: Redding David W. , Mooers Arne O. , Şekercioğlu Çağan H. , Collen Ben
Published: January 2015

Understanding how to prioritize among the most deserving imperilled species has been a focus of biodiversity science for the past three decades. Though global metrics that integrate evolutionary history and likelihood of loss have been successfully implemented, conservation is typically carried out at sub-global scales on communities of species rather than among members of complete taxonomic assemblages. Whether and how global measures map to a local scale has received little scrutiny. At a local scale, conservation-relevant assemblages of species are likely to be made up of relatively few species spread across a large phylogenetic tree, and as a consequence there are potentially relatively large amounts of evolutionary history at stake. We ask to what extent global metrics of evolutionary history are useful for conservation priority setting at the community level by evaluating the extent to which three global measures of evolutionary isolation (evolutionary distinctiveness (ED), average pairwise distance (APD) and the pendant edge or unique phylogenetic diversity (PD) contribution) capture community-level phylogenetic and trait diversity for a large sample of Neotropical and Nearctic bird communities. We find that prioritizing the most ED species globally safeguards more than twice the total PD of local communities on average, but that this does not translate into increased local trait diversity. By contrast, global APD is strongly related to the APD of those same species at the community level, and prioritizing these species also safeguards local PD and trait diversity. The next step for biologists is to understand the variation in the concordance of global and local level scores and what this means for conservation priorities: we need more directed research on the use of different measures of evolutionary isolation to determine which might best capture desirable aspects of biodiversity.
Incorporating evolutionary history into conservation planning in biodiversity hotspots
Authors: Buerki Sven , Callmander Martin W. , Bachman Steven , Moat Justin , Labat Jean-Noël , Forest Félix
Published: January 2015

There is increased evidence that incorporating evolutionary history directly in conservation actions is beneficial, particularly given the likelihood that extinction is not random and that phylogenetic diversity (PD) is lost at higher rates than species diversity. This evidence is even more compelling in biodiversity hotspots, such as Madagascar, where less than 10% of the original vegetation remains. Here, we use the Leguminosae, an ecologically and economically important plant family, and a combination of phylogenetics and species distribution modelling, to assess biodiversity patterns and identify regions, coevolutionary processes and ecological factors that are important in shaping this diversity, especially during the Quaternary. We show evidence that species distribution and community PD are predicted by watershed boundaries, which enable the identification of a network of refugia and dispersal corridors that were perhaps important for maintaining community integrity during past climate change. Phylogenetically clustered communities are found in the southwest of the island at low elevation and share a suite of morphological characters (especially fruit morphology) indicative of coevolution with their main dispersers, the extinct and extant lemurs. Phylogenetically over-dispersed communities are found along the eastern coast at sea level and may have resulted from many independent dispersal events from the drier and more seasonal regions of Madagascar.
Two cases of community acquired Legionella pneumophila non‐serogroup 1 in patients undergoing extra corporeal membrane oxygenation for severe respiratory failure
Authors: Thomas Stephanie , Hassan Ibrahim , Barker Julian , Ashworth Alan , Barnes Anita , Feddy Lee , Fedor Igor , Hayes Tim , Malagon Ignacio , Stirling Sarah , Szentgyorgyi Lajos , Mutton Ken , Harrison Timothy
Published: January 2015

Introduction:

The Legionellaceae are fastidious Gram‐negative bacteria that reside in aquatic environments. They are a cause of severe community acquired pneumonia. Legionella pneumophila serogroup 1 is responsible for 70–90 % of human infection, with cases caused by some of the other 15 serogroups accounting for the rest. Most hospitals use the Legionella urinary antigen test for detection of legionellosis; however, this will only reliably detect L. pneumophila serogroup 1.

Case presentation:

We report two cases of severe community acquired pneumonia in patients requiring extracorporeal membrane oxygenation, referred to our adult Severe Respiratory Failure Unit. Legionella urinary antigen was negative in both cases. As clinical presentation strongly suggested Legionnaires’ disease (LD), respiratory samples were sent to the reference laboratory for PCR, which confirmed L. pneumophila non‐serogroup 1 in both cases. Case 1 was subsequently confirmed by culture and confirmed as L. pneumophila serogroup 5. Case 2 was culture‐negative.

Conclusion:

Legionella is an important pathogen. Recognition of the potential for non‐serogroup 1 strains to cause severe LD should prompt requests for further investigations including Legionella PCR in patients who present with suggestive symptoms when the urine antigen is negative. Reliance on the urine antigen test may result in a potentially serious under‐recognition of L. pneumophila non‐serogroup 1 and lead to mis‐diagnoses and inappropriate antimicrobial treatment.
BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies
Authors: Borck Guntram , Hög Friederike , Dentici Maria Lisa , Tan Perciliz L. , Sowada Nadine , Medeira Ana , Gueneau Lucie , Thiele Holger , Kousi Maria , Lepri Francesca , Wenzeck Larissa , Blumenthal Ian , Radicioni Antonio , Schwarzenberg Tito Livio , Mandriani Barbara , Fischetto Rita , Morris-Rosendahl Deborah J. , Altmüller Janine , Reymond Alexandre , Nürnberg Peter , Merla Giuseppe , Dallapiccola Bruno , Katsanis Nicholas , Cramer Patrick , Kubisch Christian
Published: January 2015

RNA polymerase III (Pol III) synthesizes tRNAs and other small noncoding RNAs to regulate protein synthesis. Dysregulation of Pol III transcription has been linked to cancer, and germline mutations in genes encoding Pol III subunits or tRNA processing factors cause neurogenetic disorders in humans, such as hypomyelinating leukodystrophies and pontocerebellar hypoplasia. Here we describe an autosomal recessive disorder characterized by cerebellar hypoplasia and intellectual disability, as well as facial dysmorphic features, short stature, microcephaly, and dental anomalies. Whole-exome sequencing revealed biallelic missense alterations of BRF1 in three families. In support of the pathogenic potential of the discovered alleles, suppression or CRISPR-mediated deletion of brf1 in zebrafish embryos recapitulated key neurodevelopmental phenotypes; in vivo complementation showed all four candidate mutations to be pathogenic in an apparent isoform-specific context. BRF1 associates with BDP1 and TBP to form the transcription factor IIIB (TFIIIB), which recruits Pol III to target genes. We show that disease-causing mutations reduce Brf1 occupancy at tRNA target genes in Saccharomyces cerevisiae and impair cell growth. Moreover, BRF1 mutations reduce Pol III–related transcription activity in vitro. Taken together, our data show that BRF1 mutations that reduce protein activity cause neurodevelopmental anomalies, suggesting that BRF1-mediated Pol III transcription is required for normal cerebellar and cognitive development.
Genome-wide discovery of human splicing branchpoints
Authors: Mercer Tim R. , Clark Michael B. , Andersen Stacey B. , Brunck Marion E. , Haerty Wilfried , Crawford Joanna , Taft Ryan J. , Nielsen Lars K. , Dinger Marcel E. , Mattick John S.
Published: January 2015

During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.
A KNOTTED1-LIKE HOMEOBOX Protein Regulates Abscission in Tomato by Modulating the Auxin Pathway
Authors: Ma Chao , Meir Shimon , Xiao Langtao , Tong Jianhua , Liu Qing , Reid Michael S. , Jiang Cai-Zhong
Published: January 2015

A gene encoding a KNOTTED1-LIKE HOMEOBOX PROTEIN1 (KD1) is highly expressed in both leaf and flower abscission zones. Reducing the abundance of transcripts of this gene in tomato (Solanum lycopersicum) by both virus-induced gene silencing and stable transformation with a silencing construct driven by an abscission-specific promoter resulted in a striking retardation of pedicel and petiole abscission. In contrast, Petroselinum, a semidominant KD1 mutant, showed accelerated pedicel and petiole abscission. Complementary DNA microarray and quantitative reverse transcription-polymerase chain reaction analysis indicated that regulation of abscission by KD1 was associated with changed abundance of genes related to auxin transporters and signaling components. Measurement of auxin content and activity of a DR5::β-glucuronidase auxin reporter assay showed that changes in KD1 expression modulated the auxin concentration and response gradient in the abscission zone.