nils-herrmann/clean_scirepeval huggingface dataset:
Seasonality of arbuscular mycorrhizal symbiosis and dark septate endophytes in a grassland site in southwest China.

Arbuscular mycorrhizal and dark septate endophytic fungal colonization in a grassland in Kunming, southwest China, was investigated monthly over one year. All plant roots surveyed were co-colonized by arbuscular mycorrhizal and dark septate endophytic fungi in this grassland. Both arbuscular mycorrhizal and dark septate endophytic fungal colonization fluctuated significantly throughout the year, and their seasonal patterns were different in each plant species. The relationships between environmental (climatic and edaphic) factors and fungal colonization were also studied. Correlation analysis demonstrated that arbuscular mycorrhizal colonization was significantly correlative with environmental factors (rainfall, sunlight hours, soil P, etc.), but dark septate endophytic fungal colonization was only correlative with relative humidity and sunlight hours.

Field of study: Biology, Environmental science
The superior ophthalmic vein approach for the treatment of carotid-cavernous fistulas: a novel technique using Onyx.

Endovascular therapy is the primary treatment option for carotid-cavernous fistulas (CCFs). Operative cannulation of the superior ophthalmic vein (SOV) provides a reasonable alternative route to the cavernous sinus when all transvenous and transarterial approaches have been unsuccessful. The role of the liquid embolic agent Onyx in the management of CCFs has not been well documented, especially when using an SOV approach. The purpose of this study is to assess the safety and efficacy of Onyx embolization of CCFs through a surgical cannulation of the SOV.



The authors retrospectively reviewed all patients with CCFs who were treated with Onyx through an SOV approach between April 2009 and April 2011. Traditional endovascular approaches had failed in all patients.



A total of 10 patients were identified, 1 with a Type A CCF, 5 with a Type B CCF, and 4 with a Type D CCF. All fistulas were embolized in 1 session. Onyx was the sole embolic agent used in 7 cases and was combined with coils in 3 other cases. Complete obliteration was achieved in 8 patients and a significant reduction in fistulous flow was achieved in 2 patients, which later progressed to near-complete occlusion on angiographic follow-up. All patients experienced a complete clinical recovery with excellent cosmetic results and were free from recurrence at their latest clinical follow-up evaluations.



Onyx embolization is an excellent therapy for CCFs in general, and through an SOV approach in particular. Direct operative cannulation of the SOV followed by Onyx embolization may be the best treatment option in patients with CCFs when all other endovascular approaches have been exhausted.

Field of study: Medicine
Estimating the predictive ability of genetic risk models in simulated data based on published results from genome-wide association studies

There is increasing interest in investigating genetic risk models in empirical studies, but such studies are premature when the expected predictive ability of the risk model is low. We assessed how accurately the predictive ability of genetic risk models can be estimated in simulated data that are created based on the odds ratios (ORs) and frequencies of single-nucleotide polymorphisms (SNPs) obtained from genome-wide association studies (GWASs).  We aimed to replicate published prediction studies that reported the area under the receiver operating characteristic curve (AUC) as a measure of predictive ability. We searched GWAS articles for all SNPs included in these models and extracted ORs and risk allele frequencies to construct genotypes and disease status for a hypothetical population. Using these hypothetical data, we reconstructed the published genetic risk models and compared their AUC values to those reported in the original articles.  The accuracy of the AUC values varied with the method used for the construction of the risk models. When logistic regression analysis was used to construct the genetic risk model, AUC values estimated by the simulation method were similar to the published values with a median absolute difference of 0.02 [range: 0.00, 0.04]. This difference was 0.03 [range: 0.01, 0.06] and 0.05 [range: 0.01, 0.08] for unweighted and weighted risk scores.  The predictive ability of genetic risk models can be estimated using simulated data based on results from GWASs. Simulation methods can be useful to estimate the predictive ability in the absence of empirical data and to decide whether empirical investigation of genetic risk models is warranted.

Field of study: Biology
Persistence, extinction, and critical patch number for island populations

Sufficient conditions are derived for persistence and extinction of a population inhabiting several islands. Discrete reaction-diffusion population models are analyzed which describe growth and diffusion of a population on a group of islands or a patch environment. A critical patch number is defined as the number of islands below which the population goes extinct on that group of islands. It is shown that population persistence on one island leads to population persistence for the entire archipelago. Both single-species and multi-species models are discussed.

Field of study: Biology, Mathematics
Growing season variability of net ecosystem CO 2 exchange and evapotranspiration of a sphagnum mire in the broad-leaved forest zone of

The spatial and temporal variability of net ecosystem exchange (NEE) of CO2 and evapotranspiration (ET) of a karst-hole sphagnum peat mire situated at the boundary between broad-leaved and forest‐steppe zones in the central part of European Russia in the Tula region was described using results from field measurements. NEE and ET were measured using a portable measuring system consisting of a transparent ventilated chamber combined with an infrared CO2/H2O analyzer, LI-840A (Li-Cor, USA) along a transect from the southern peripheral part of the mire to its center under sunny clear-sky weather conditions in the period from May to September of 2012 and in May 2013. The results of the field measurements showed significant spatial and temporal variability of NEE and ET that was mainly influenced by incoming solar radiation and ground water level. The seasonal patterns of NEE and ET within the mire were quite different. During the entire growing season the central part of the mire was a sink of CO2 for the atmosphere. NEE reached maximal values in June‐July. 6:8 4:2 mol m 2 s 1 /. The southern peripheral part of the mire, due to strong shading by the surrounding forest, was a sink of CO2 for the atmosphere in June‐July only. ET reached maximal values in the well-lighted central parts of the mire in May (0:34 0:20 mm h 1 ) mainly because of high air and surface temperatures and the very wet upper peat horizon and sphagnum moss. Herbaceous species made the maximum contribution to the total gross primary production (GPP) in both the central and the peripheral parts of the mire. The contribution of sphagnum to the total GPP of these plant communities was relatively small and ranged on sunny days of July‐August from 1:1 1:1 mgC g 1 of dry weight (DW) per hour in the peripheral zone of the mire to 0:6 0:2 mgC g 1 DW h 1 at the mire center. The sphagnum layer made the maximum contribution to total ET at the mire center.0:25 0:10 mm h 1 / and the herbaceous species on the peripheral part of the mire (0:03 0:03 mm h 1 ).

Field of study: Environmental science
A study of compressible turbulent reattaching free shear layers

An experimental investigation was conducted to study the two-dimensional, compressible, turbulent reattaching free shear layer formed by the geometrical separation of a Mach 2.46 flow with a turbulent boundary layer and a Reynolds number of 5.01 X 107/m from a 25.4 mm high backward-facing step. The wind tunnel test section was specifically designed to obtain a constant pressure separation at the step. A detailed survey of the flowfield was made utilizing a Schlieren system, static pressure taps, and a two-component coincident laser Doppler velocimeter. In contrast to incompressibl e reattaching free shear layers, significant increases in the turbulence level, shear stress, and turbulent triple products were observed within the reattachment region. Large turbulence structure and enhanced mixing were observed in the redeveloping region.

Field of study: Physics
Can Current Protocol Verification Techniques Guarantee Correctness?

In the past 15 years the alternating-bit protocol has been perhaps the most widely verified protocol, the benchmark of protocol verification techniques; is it really correct? We claim that the answer is negative. The problem is that existing concepts of correctness do not capture an important sense in which a protocol may be incorrect. Specifically, although protocol goals (e.g., delivering messages) may be attained eventually, the time periods to achieve these goals may increase indefinitely. A notion of correctness that allows one to consider the probability of reaching a goal as well as the time or computational effort required to achieve the goal is required. We suggest a novel approach to protocol correctness which unifies functional and performance considerations using a recently proposed probabilistic semantics for programs.

Field of study: Computer science
Congress and National Science Policy

The recent efforts by Congress to reassert some of its constitutional prerogatives, which began with the reaction against involvement in Vietnam and continues in the wake of the Watergate affair, have made the role of the legislative branch a more lively issue than it has been at perhaps any other time in this century. The degree of legislative involvement affects many areas of government policy, including the complex of issues and activities that together make up "science policy." The role of Congress in setting and maintaining science policy has never been very well defined or delimited. Congressional influence has often been felt in specific cases, such as the development of atomic energy, the Apollo project, and controversial and expensive weapons systems. In general, however, the pattern and direction of federally supported research and development has been set in the executive branch and embodied in the budget presented annually to Congress. As the deployment of scientific resources becomes a critical instrument of government in virtually every area of public concern, science policy has come to be regarded as one of the vital levers of social action. For this reason, it is entirely possible that Congress may take advantage of the present climate of political uncertainty to try to assert more authority in this area of public policy than it has had either the will or the opportunity to do since the end of World War II.

Field of study: Political science
An Aromatic Macromolecule as a Nano Drug Carrier: Polyether Dendrimer / Poly(2-hydroxyethyl methacrylate)

Highly branched, functionalized polymers have the potential to act as efficient drug carrier systems. The aromatic polyether dendrimers are spherical, highly ordered, multibranched, nanometre-sized macromolecules having positively charged ether groups on the surface under physiological conditions. In this study, we have synthesized a kind of dendrimer/poly(2-hydroxy ethyl methacrylate) nanocomposite/5-aminosalicylic acid (5-ASA) for oral drug delivery. The aromatic polyether dendrimer (generation 2, hyperbranched polyether with -CH2OH functionality, 3,5-Dihydroxybenzoic acid core) was prepared from generation 2, hyperbranched polyether dendrimer with -COOCH3 form in excellent yield. FT-IR, 1H-NMR and DSC studies suggest that the monomer predominantly forms a complex with polyether dendrimers because of the interaction between the –CH2OH end groups of dendrimer and the –OH group of 2-hydroxyethyl methacrylate monomer.

Field of study: Materials science
Taxing Perks and Interpreting Statutes: Pepper v Hart

There are two kinds of perks: the licit and the illicit.' Licit perquisites can take a variety of forms: the company car, private health care, cheap loans, the use of assets owned by the employer, and subsidised travel and accommodation. They also offer a variety of advantages. From the employee's perspective, such perks represent (since tax is payable on them) the purchase of benefits which they might otherwise be unable to afford, or afford only at a cost to their disposable income that would require saving elsewhere. From the employer's perspective, it is often more cost effective to provide a perk than an increase in salary that would, after tax, allow the employee to purchase the perk in the retail market. This is especially so where the employer wants the employee to have the perk, for example the cottage on the estate whose responsibility it is for the employee to maintain,2 in order to do the job. Employers can buy in bulk and may, as in the case of fleet purchasing of company cars, be able to exert considerable leverage on motor manufacturers and traders.3 Another significant saving for employers is the provision to their employees of the service which they are in the business of providing; what Nicholls LJ (as he then was) in the Court of Appeal referred to as 'in-house' as opposed to 'external' benefits.4 Air and rail travel, and places at public schools and the like, are good examples. Employees can be given free or reduced cost access to a service which the employer has presumably costed on the basis that it is the non-employee user who is paying. A train has to travel from Cardiff to London: the addition of a few non-paying BR employees as passengers does not on the face of it affect the cost to BR of providing that service to the general public. The teachers at a public school as in Pepper v Hart,5 which is the focus for this comment may have the opportunity to place their children there at a cost which is marginal to the school, but is, of course, a considerable saving to them. Perks have traditionally been used as the means for increasing an employee's total remuneration (and for distinguishing grades of employee) but without

Field of study: Law
Establishing a process of irradiating small animal brain using a CyberKnife and a microCT scanner.

Establish and validate a process of accurately irradiating small animals using the CyberKnife G4 System (version 8.5) with treatment plans designed to irradiate a hemisphere of a mouse brain based on microCT scanner images.



These experiments consisted of four parts: (1) building a mouse phantom for intensity modulated radiotherapy (IMRT) quality assurance (QA), (2) proving usability of a microCT for treatment planning, (3) fabricating a small animal positioning system for use with the CyberKnife's image guided radiotherapy (IGRT) system, and (4)in vivo verification of targeting accuracy. A set of solid water mouse phantoms was designed and fabricated, with radiochromic films (RCF) positioned in selected planes to measure delivered doses. After down-sampling for treatment planning compatibility, a CT image set of a phantom was imported into the CyberKnife treatment planning system--MultiPlan (ver. 3.5.2). A 0.5 cm diameter sphere was contoured within the phantom to represent a hemispherical section of a mouse brain. A nude mouse was scanned in an alpha cradle using a microCT scanner (cone-beam, 157 × 149 pixels slices, 0.2 mm longitudinal slice thickness). Based on the results of our positional accuracy study, a planning treatment volume (PTV) was created. A stereotactic body mold of the mouse was "printed" using a 3D printer laying UV curable acrylic plastic. Printer instructions were based on exported contours of the mouse's skin. Positional reproducibility in the mold was checked by measuring ten CT scans. To verify accurate dose delivery in vivo, six mice were irradiated in the mold with a 4 mm target contour and a 2 mm PTV margin to 3 Gy and sacrificed within 20 min to avoid DNA repair. The brain was sliced and stained for analysis.



For the IMRT QA using a set of phantoms, the planned dose (6 Gy to the calculation point) was compared to the delivered dose measured via film and analyzed using Gamma analysis (3% and 3 mm). A passing rate of 99% was measured in areas of above 40% of the prescription dose. The final inverse treatment plan was comprised of 43 beams ranging from 5 to 12.5 mm in diameter (2.5 mm size increments are available up to 15 mm in diameter collimation). Using the Xsight Spine Tracking module, the CyberKnife system could not reliably identify and track the tiny mouse spine; however, the CyberKnife system could identify and track the fiducial markers on the 3D mold.In vivo positional accuracy analysis using the 3D mold generated a mean error of 1.41 mm ± 0.73 mm when fiducial markers were used for position tracking. Analysis of the dissected brain confirmed the ability to target the correct brain volume.



With the use of a stereotactic body mold with fiducial markers, microCT imaging, and resolution down-sampling, the CyberKnife system can successfully perform small-animal radiotherapy studies.

Field of study: Medicine, Physics
Research on CAD/PDM Integration Based on Designing Knowledge Base

In order to satisfy the requirements for quick product customized design,the knowledge-based integration of computer aided design (CAD) and product data management (PDM) was researched.The knowledge structure which is composed of product requirement decision knowledge,product structure knowledge,product configuration knowledge,product characteristic knowledge and product designing resources was constructed on the basis of product's information model,the decision tree and weighted clustering algorithm were used to knowledge inference and designing decision,thus realizes knowledge-based data exchange between CAD and PDM system and improve the efficiency of product design.Finally the designing of gear-box was used to verify integrated system's support to product designing process.

Field of study: Materials science
Nutrition for the critically ill.

Standard IV therapy for a critically ill patient is a form of semi-starvation. The rate of complications and mortality can be as much as 50% higher in malnourished patients. Assessing patients' nutritional state as it was before the surgery or illness by asking about eating patterns indicates how severely a patient may react to further malnourishment. Even more important is assessment of the patient's immune defense system. Rate of hypermetabolism in the critically ill will indicate the amounts of nutrients needed and when. Enteral feeding is best, where possible. The physician must know the exact contents of whatever liquid diet is being used. If parenteral nutrition is used, stringent aseptic technique must be employed.

Field of study: Medicine
Bacterial activity and production in near-surface estuarine and freshwater sediments

Two indices of bacterial production, thymidine incorporation and the frequency of divided and dividing cells were measured, along with a suite of measurements of aerobic and anaerobic bacterial activity, to investigate the relationship between bacterial cell production and organic carbon mineralisation at three different sediment sites: a sheltered intertidal estuarine mudflat (Kingoodie Bay), a riverside mudbank (Ashleworth Quay) and an intertidal mudflat in a hydraulically dynamic estuary (Aust Warth). Organic carbon mineralisation was dominated by anaerobic processes at all three sites: sulfate reduction at the two estuarine sites (equivalent to 76% and 61% of oxygen uptake) and methanogenesis at the freshwater site (56%). Although all three sites had similar bacterial population sizes, activities in Kingoodie Bay were 2–3 times higher than at Aust Warth or Ashleworth Quay. Thymidine incorporation rates and Numbers of Dividing and Divided Cells correlated strongly at all three sites. Thymidine incorporation rates were spatially uncoupled from zones of principal anaerobic activity, providing in situ evidence that sulfate-reducing bacteria and methanogens do not incorporate radiolabelled thymidine into DNA during growth. Cell yield was lower in the anaerobic zone, as subsurface peaks in anaerobic mineralisation were not matched by increases in bacterial productivity. However, as anaerobic degradation processes were so dominant, anaerobic productivity still accounted for the majority of cell production.

Field of study: Biology, Environmental science
Effects of exogenous fat emulsion (Intralipid) on chemotactic function of monocytes and polymorphonuclear cells in sepsis.

Effects of exogenous fat emulsion (Intralipid) on the chemotactic function of monocytes and polymorphonuclear (PMN) cells were studied in vivo with rats. Abdominal sepsis was induced in Sprague Dawley rats by cecal ligation and puncture. Following a bolus infusion of the fat emulsion or saline, chemotactic function of monocytes and PMN cells was evaluated in animals divided into the following four groups: Group I, non-septic rats receiving saline infusion (NS-S); Group II, non-septic rats receiving the fat emulsion (NS-F); Group III, septic rats receiving saline (S-S); Group IV, septic rats receiving the fat emulsion (S-F). Results of the study revealed that monocyte function was suppressed by the sepsis, whether saline or the fat emulsion was infused, and administration of the fat emulsion resulted in suppression of monocyte chemotaxis both in the non-septic and the septic rats. Although in this study chemotactic function of PMN cells was not significantly suppressed by the sepsis, administration of the fat emulsion again led to a suppression of PMN cell function, in both the non-septic and the septic rats. Results of the study confirmed that administration of an exogenous fat emulsion may suppress the chemotactic function of the monocytes and PMN cells and, in the presence of severe sepsis, infusion of the fat emulsion may lead to a further deterioration of immunologic function of the host. Special care, therefore, should be taken against the use of exogenous fat emulsion in septic individuals or in those at risk of infection.

Field of study: Biology
Superconductor-Insulator Transition and the Crossover to Non Equilibrium in two-dimensional Indium - Indium-Oxide composite.

Magnetic-field tuned superconductor to insulator transition was observed in a novel hybrid system of granular superconducting indium, deposited on indium oxide thin film, which exhibits global superconductivity at low magnetic fields. We have used annealing to tune the coupling to lie just at the borderline where superconductivity in the underlying InOx is suppressed, which is also close to the metal-insulator transition of the InOx. The hybrid system exhibits a "giant" magnetoresistance above the H-SIT, with critical behavior that manifests the duality between Cooper pairs and vortices.

Field of study: Physics
Report of the Council for the session 2004–2005

As I come to the end of my period of office as President of the Royal Statistical Society I am constantly reminded of the enormous effort that is put into the running of the Society by many individual volunteers and the staff of Errol Street, admirably led as always by Ivor Goddard. I want to express my personal gratitude to them and to the Society's Honorary Officers. Without the efforts of these individuals the Society would not be the success that it undoubtedly is.

Field of study: Mathematics