Changing the name of the NBPF/DUF1220 domain to the Olduvai domain

We are jointly proposing a new name for a protein domain of approximately 65 amino acids that has been previously termed NBPF or DUF1220. Our two labs independently reported the initial studies of this domain, which is encoded almost entirely within a single gene family. The name Neuroblastoma Breakpoint Family (NBPF) was applied to this gene family when the first identified member of the family was found to be interrupted in an individual with neuroblastoma. Prior to this discovery, the PFAM database had termed the domain DUF1220, denoting it as one of many protein domains of unknown function. It has been PFAM’s intention to use “DUF” nomenclature to serve only as a temporary placeholder until more appropriate names are proposed based on research findings. We believe that additional studies of this domain, primarily from our laboratories over the past 10 years, have resulted in furthering our understanding of these sequences to the point where proposing a new name for this domain is warranted. Because of considerable data linking the domain to human-specific evolution, brain expansion and cognition, we believe a name reflecting these findings would be appropriate. With this in mind, we have chosen to name the domain (and the repeat that encodes it) Olduvai. The gene family will remain as NBPF for now. The primary domain subtypes will retain their previously assigned names (e.g. CON1-3; HLS1-3), and the three-domain block that expanded dramatically in the human lineage will be termed the Olduvai triplet. The new name refers to Olduvai Gorge, which is a site in East Africa that has been the source of major anthropological discoveries in the early-mid 1900’s. We also chose the name as a tribute to the scientists who made important contributions to the early studies of human origins and our African genesis

Long-term electrode behavior during treatment of arsenic contaminated groundwater by a pilot-scale iron electrocoagulation system.

Iron electrocoagulation (Fe-EC) is an effective technology to remove arsenic (As) from groundwater used for drinking. A commonly noted limitation of Fe-EC is fouling or passivation of electrode surfaces via rust accumulation over long-term use. In this study, we examined the effect of removing electrode surface layers on the performance of a large-scale (10,000 L/d capacity) Fe-EC plant in West Bengal, India. We also characterized the layers formed on the electrodes in active use for over 2 years at this plant. The electrode surfaces developed three distinct horizontal sections of layers that consisted of different minerals: calcite, Fe(III) precipitates and magnetite near the top, magnetite in the middle, and Fe(III) precipitates and magnetite near the bottom. The interior of all surface layers adjacent to the Fe(0) metal was dominated by magnetite. We determined the impact of surface layer removal by mechanical abrasion on Fe-EC performance by measuring solution composition (As, Fe, P, Si, Mn, Ca, pH, DO) and electrochemical parameters (total cell voltage and electrode interface potentials) during electrolysis. After electrode cleaning, the Fe concentration in the bulk solution increased substantially from 15.2 to 41.5 mg/L. This higher Fe concentration led to increased removal of a number of solutes. For As, the concentration reached below the 10 μg/L WHO MCL more rapidly and with less total Fe consumed (i.e. less electrical energy) after cleaning (128.4 μg/L As removed per kWh) compared to before cleaning (72.9 μg/L As removed per kWh). Similarly, the removal of P and Si improved after cleaning by 0.3 mg/L/kWh and 1.1 mg/L/kWh, respectively. Our results show that mechanically removing the surface layers that accumulate on electrodes over extended periods of Fe-EC operation can restore Fe-EC system efficiency (concentration of solute removed/kWh delivered). Since Fe release into the bulk solution substantially increased upon electrode cleaning, our results also suggest that routine electrode maintenance can ensure robust and reliable Fe-EC performance over year-long timescales

Precrop Functional Group Identity Affects Yield of Winter Barley but Less so High Carbon Amendments in a Mesocosm Experiment

Nitrate leaching is a pressing environmental problem in intensive agriculture. Especially after the crop harvest, leaching risk is greatest due to decomposing plant residues, and low plant nutrient uptake and evapotranspiration. The specific crop also matters: grain legumes and canola commonly result in more leftover N than the following winter crop can take up before spring. Addition of a high carbon amendment (HCA) could potentially immobilize N after harvest. We set up a 2-year mesocosm experiment to test the effects of N fertilization (40 or 160 kg N/ha), HCA addition (no HCA, wheat straw, or sawdust), and precrop plant functional group identity on winter barley yield and soil C/N ratio. Four spring precrops were sown before winter barley (white lupine, faba bean, spring canola, spring barley), which were selected based on a functional group approach (colonization by arbuscular mycorrhizal fungi [AMF] and/or N2-fixing bacteria). We also measured a subset of faba bean and spring barley for leaching over winter after harvest. As expected, N fertilization had the largest effect on winter barley yield, but precrop functional identity also significantly affected the outcome. The non-AMF precrops white lupine and canola had on average a positive effect on yield compared to the AMF precrops spring barley and faba bean under high N (23% increase). Under low N, we found only a small precrop effect. Sawdust significantly reduced the yield compared to the control or wheat straw under either N level. HCAs reduced nitrate leaching over winter, but only when faba bean was sown as a precrop. In our setup, short-term immobilization of N by HCA addition after harvest seems difficult to achieve. However, other effects such as an increase in SOM or nutrient retention could play a positive role in the long term. Contrary to the commonly found positive effect of AMF colonization, winter barley showed a greater yield when it followed a non-AMF precrop under high fertilization. This could be due to shifts of the agricultural AMF community toward parasitism

Highly efficient room temperature spin injection in a metal-insulator-semiconductor light emitting diode

We demonstrate highly efficient spin injection at low and room temperature in an AlGaAs/GaAs semiconductor heterostructure from a CoFe/AlOx tunnel spin injector. We use a double-step oxide deposition for the fabrication of a pinhole-free AlOx tunnel barrier. The measurements of the circular polarization of the electroluminescence in the Oblique Hanle Effect geometry reveal injected spin polarizations of at least 24% at 80K and 12% at room temperature

Logic programming in the context of multiparadigm programming: the Oz experience

Oz is a multiparadigm language that supports logic programming as one of its major paradigms. A multiparadigm language is designed to support different programming paradigms (logic, functional, constraint, object-oriented, sequential, concurrent, etc.) with equal ease. This article has two goals: to give a tutorial of logic programming in Oz and to show how logic programming fits naturally into the wider context of multiparadigm programming. Our experience shows that there are two classes of problems, which we call algorithmic and search problems, for which logic programming can help formulate practical solutions. Algorithmic problems have known efficient algorithms. Search problems do not have known efficient algorithms but can be solved with search. The Oz support for logic programming targets these two problem classes specifically, using the concepts needed for each. This is in contrast to the Prolog approach, which targets both classes with one set of concepts, which results in less than optimal support for each class. To explain the essential difference between algorithmic and search programs, we define the Oz execution model. This model subsumes both concurrent logic programming (committed-choice-style) and search-based logic programming (Prolog-style). Instead of Horn clause syntax, Oz has a simple, fully compositional, higher-order syntax that accommodates the abilities of the language. We conclude with lessons learned from this work, a brief history of Oz, and many entry points into the Oz literature.Comment: 48 pages, to appear in the journal "Theory and Practice of Logic Programming

Efficacy of tofacitinib monotherapy in methotrexate-naive patients with early or established rheumatoid arthritis.

IntroductionTofacitinib is an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA). Tofacitinib monotherapy was previously shown to inhibit structural damage, reduce clinical signs and symptoms of RA, and improve physical functioning over 24 months in methotrexate (MTX)-naive adult patients with RA. In this post hoc analysis, we compared efficacy and safety of tofacitinib in patients with early (disease duration <1 year) versus established (≥1 year) RA.MethodsMTX-naive patients ≥18 years with active RA received tofacitinib monotherapy (5 or 10 mg two times a day, or MTX monotherapy, in a 24-month Phase 3 trial.ResultsOf 956 patients (tofacitinib 5 mg two times a day, n=373; tofacitinib 10 mg two times a day, n=397; MTX, n=186), 54% had early RA. Baseline disease activity and functional disability were similar in both groups; radiographic damage was greater in patients with established RA. At month 24, clinical response rates were significantly greater in patients with early versus established RA in the tofacitinib 5 mg two times a day group. Both tofacitinib doses had greater effects on clinical, functional and radiographic improvements at 1 and 2 years compared with MTX, independent of disease duration. No new safety signals were observed.ConclusionsTreatment response was generally similar in early and established RA; significantly greater improvements were observed at month 24 with tofacitinib 5 mg two times a day in early versus established RA. Tofacitinib 5 and 10 mg two times a day demonstrated greater efficacy versus MTX irrespective of disease duration. No difference in safety profiles was observed between patients with early or established RA.Trial registration numberNCT01039688; Results

GP trainees’ perceptions on learning EBM using conversations in the workplace : a video-stimulated interview study

Background To be able to practice evidence-based medicine (EBM) when making decisions for individual patients, it is important to learn how to combine the best available evidence with the patient's preferences and the physician's clinical expertise. In general practice training, these skills can be learned at the workplace using learning conversations: meetings between the supervising general practitioner (GP) and GP trainee to discuss medical practice, selected topics or professional performance. This study aimed to give insight into the perceptions of GP trainees on their EBM learning processes during learning conversations. Methods We held semi-structured video-stimulated elicitation interviews (n = 22) with GP trainees affiliated to GP training institutes in the Netherlands and Belgium. GP trainees were shown fragments of their learning conversations, enabling reflection during the interview. Taking an inductive approach, interview recordings were transcribed verbatim and analysed with NVivo software. Results GP trainees perceived learning conversations as useful for learning and discussing EBM. Multiple EBM learning activities were identified, such as discussing evidence together, relating evidence to cases in daily practice and discussing the supervisor's experience and the specific local context in the light of what the evidence recommends. However, for learning to occur, trainees need and expect specific behaviour, both from their supervisors and themselves. Supervisors should supply well-substantiated answers that are applicable in practice and give the trainee confirmation. In turn, the trainee needs to prepare well in order to ask focused, in-depth questions. A safe space allowing equal and open discussion between trainee and supervisor is perceived as an essential context for optimal EBM learning. Conclusions Our findings show that trainees find learning conversations useful for EBM learning in general practice. To bring EBM learning to its full potential, attention should be paid to optimising the behavioural and contextual factors found relevant to enhancing EBM learning

Electrical Spin Injection in a Ferromagnetic / Tunnel Barrier/ Semiconductor Heterostructure

We demonstrate experimentally the electrical ballistic electron spin injection from a ferromagnetic metal / tunnel barrier contact into a semiconductor III-V heterostructure. We introduce the Oblique Hanle Effect technique for reliable optical measurement of the degree of injected spin polarization. In a CoFe / Al2O3 / GaAs / (Al,Ga)As heterostructure we observed injected spin polarization in excess of 8 % at 80K.Comment: 5 pages, 4 figure

Thermomagnetic history effects in SmMn2_2Ge2_2

The intermetallic compound SmMn$_2$Ge$_2$, displaying multiple magnetic phase transitions, is being investigated in detail for its magnetization behavior near the 145 K first order ferromagnetic to antiferromagnetic transition occuring on cooling, in particular for thermomagnetic history effects in the magnetization data. The most unusual finding is that the thermomagnetic irreversibility, [= M$^{FCW}$(T)-M$^{ZFC}$(T)] at 135 K is higher in intermediate magnetic field strengths. By studying the response of the sample (i.e., thermomagnetic irreversibility and thermal hysteresis) to different histories of application of magnetic field and temperature, we demonstrate how the supercooling and superheating of the metastable magnetic phases across the first order transition at 145 K contribute to overall thermomagnetic irreversibility.Comment: 15 pages, 5 figures, to appear in Physical Review

Quantized spin wave modes in magnetic tunnel junction nanopillars

We present an experimental and theoretical study of the magnetic field dependence of the mode frequency of thermally excited spin waves in rectangular shaped nanopillars of lateral sizes 60x100, 75x150, and 105x190 nm2, patterned from MgO-based magnetic tunnel junctions. The spin wave frequencies were measured using spectrally resolved electrical noise measurements. In all spectra, several independent quantized spin wave modes have been observed and could be identified as eigenexcitations of the free layer and of the synthetic antiferromagnet of the junction. Using a theoretical approach based on the diagonalization of the dynamical matrix of a system of three coupled, spatially confined magnetic layers, we have modeled the spectra for the smallest pillar and have extracted its material parameters. The magnetization and exchange stiffness constant of the CoFeB free layer are thereby found to be substantially reduced compared to the corresponding thin film values. Moreover, we could infer that the pinning of the magnetization at the lateral boundaries must be weak. Finally, the interlayer dipolar coupling between the free layer and the synthetic antiferromagnet causes mode anticrossings with gap openings up to 2 GHz. At low fields and in the larger pillars, there is clear evidence for strong non-uniformities of the layer magnetizations. In particular, at zero field the lowest mode is not the fundamental mode, but a mode most likely localized near the layer edges.Comment: 16 pages, 4 figures, (re)submitted to PR