nils-herrmann/clean_scirepeval huggingface dataset:
Editorial: periprosthetic infection.

Periprosthetic infection is a common and challenging problem in current orthopaedic surgery practice. It can result in a devastating clinical outcome and be very costly to treat. In some cases, infection is lifelong. 
 
Any implant for arthroplasty or osteosynthesis may be subject to infection . However, the frequency and nature of such infection remain to be accurately characterised. Proposed definitions take into account only the objective criteria obtained from direct clinical observation or by diagnostic tools . Nevertheless, it is well known that months or even years after the apparent disappearance of infection, a new episode of local clinical sepsis can develop spontaneously. 
 
Prevention, on the one hand, and careful epidemiological surveillance on the other, of infections in the orthopaedic department can maintain the incidence of infection within a “tolerable” range. Despite this, diagnosis remains most solidly grounded by a retrospective review of clinical history, when the infection has already become apparent . Microbiological tests to confirm the existence of infection can fail due to false positive contamination, false negative (difficult to culture) microorganisms or antibiotic treatment. New developments in the diagnosis of infection are continually being presented, but none has yet proven infallible [4-6]. 
 
Even retrospective epidemiological short or medium-term follow up can fail to detect whether a patient will suffer in the future from periprosthetic infection, because this may develop at any time after the primary operation, either as a result of silent infection or due to newly-developed bacteraemia. 
 
The majority of these patients need more than one surgical debridement. An aggressive approach, meticulously removing necrotic or ischaemic infected soft tissue, together with peri-implant vascularisation enhancement, is the most effective basis for pharmacological treatment. Antibiotic administration consists of a single or, more frequently, a combination of antibiotics determined in accordance with the findings of a positive culture. It is currently accepted that treatment must be conducted by an orthopaedic surgeon in collaboration with a physician specialised in infectious diseases and in antibiotic management . Nevertheless, early or late antibiotic resistance may require treatment changes. If the infection continues, implant removal may be necessary, followed, in due course, by the insertion of a new implant. Nevertheless, the soundness of this procedure, known as two-stage revision, has yet to be fully established. 
 
The advantages and problems of medical and surgical techniques for the diagnosis and treatment of periprosthetic infection are analysed in this issue of the Open Orthopaedic Journal.

Field of study: Medicine
Feasibility and Features of a Staggered Undulator Constructed With HTS YBCO Bulks

A staggered undulator with high-temperature superconducting bulks might be a solution to achieve an undulator with an extremely short period for a synchrotron light source. YBCO bulk was thus selected to investigate the feasibility. This bulk (diameter 32 mm, thickness 2.5 mm) was used to build a staggered-magnet array structure and a mock-up staggered undulator of period 5 mm and fixed gap 4 mm was designed for this test. The potential generation of a sinusoidal field was tested in a 3-T magnetization system with field-cooling magnetization (FCM). The practicability of a HTS undulator is discussed in regard to the possibility of correction of the local field, repetition of field trapping and long-term stability. In addition, a field simulation concept was developed for designing the staggered undulator with YBCO bulks.

Field of study: Physics
Deep brain stimulation in obsessive-compulsive disorder

The use of deep brain stimulation in psychiatric disorders has received great interest owing to the small risk of the operation, the reversible nature of the technique, and the possibility of optimizing treatment postoperatively. Currently, deep brain stimulation in psychiatry is investigated for obsessive–compulsive disorder, Gilles de la Tourette's syndrome, and major depression. This chapter reviews the application of deep brain stimulation in obsessive–compulsive disorder. Preliminary results suggest that deep brain stimulation in obsessive–compulsive disorder can effectuate a decrease of 40–60% in at least half of the patients. Although various side effects occur, most of these are transitory and linked to specific stimulation parameters which can be changed. Because only a few studies have been performed with a limited number of patients in accordance with varying research protocols, appliance of deep brain stimulation to obsessive–compulsive disorder is still at an experimental stage. The speed of the effect of deep brain stimulation causes fundamental assumptions on the pathophysiology of obsessive–compulsive disorder.

Field of study: Medicine, Psychology
Cattaneo models for chemosensitive movement


We derive models for chemosensitive movement based on Cattaneo's law of heat propagation with finite speed. We apply the model to pattern formation as observed in experiments with Dictyostelium discoideum, with Salmonella typhimurium and with Escherichia coli. For Salmonella typhimurium we make predictions on pattern formation which can be tested in experiments. We discuss the relations of the Cattaneo models to classical models and we develop an effective numerical scheme.

Field of study: Biology, Mathematics
Factors influencing latitudinal pattern of biodiversity: An example using Sabellidae (Annelida, Polychaeta)

The ‘latitudinal gradient of biodiversity’ hypothesis was tested utilising the geographical distribution of species taxa belonging to the family Sabellidae (Annelida: Polychaeta), one of the polychaete families studied by only a few specialists around the world. An increase in species richness towards the Tropical region was revealed, with an asymmetric distribution between the two hemispheres. Data show that most of the species were found in Northern latitudes, producing a Northern area much richer than the Southern one. The Atlantic-Mediterranean Region was particularly rich, with the number of species close to those from the Indo-Pacific Region. Mediterranean species richness is discussed in the light of the particular history of the basin, also emphasising the importance of naturalistic studies that have made the Mediterranean marine flora and fauna one of the best known in the world. The existence of ‘extrinsic factors’ that obscure the real pattern of distributions is hypothesised. Differences found between the two hemispheres could be attributed primarily to the higher number of specialists working in the Boreal Domains, including the Mediterranean area. Global trends produced by some representative genera are also discussed with respect to the distribution of the taxonomic specialists.

Field of study: Environmental science
Analysis of Fault Evolution on Road Traffic Network Under Disruptive Traffic Accident

This paper quantitatively analyzes statistical topology parameters of urban road network of Tongzhou based on complex network theory (CNT), and the value the degree, betweenness and strength are analyzed. Cascaded failure model is proposed based on the comprehensive consideration of the influence of road network topology and flow characteristics, and influence rule is analyzed with different disturbance values and different coupling strength. The results indicate that when the external perturbation is larger, the time of all nodes failure is earlier once the failure is triggered. Under attack, the threshold of the node-based largest betweenness damaged (1.6) is smaller than the node-based largest strength damaged (1.8). When the flow coupling coefficient is constant, no matter how the network topology coupling coefficient changes, the road network will have cascade failure. When the topology coupling coefficient is constant, the greater the flow coupling coefficient is, the more vulnerable the network to have cascading failures. The study is aimed at providing technical reference for control measures under sudden condition on road network.

Field of study: Engineering
TU-C-201-03: The Use of Checklists and Audit Tools for Safety and QA

Recent use of HDR has increased while planning has become more complex often necessitating 3D
image-based planning. While many guidelines for the use of HDR exist, they have not kept pace with the increased complexity of 3D
image-based planning. Furthermore, no comprehensive document exists to describe the wide variety of current HDR clinical indications. This educational session aims to summarize existing national and international guidelines for the safe implementation of an HDR program. A summary of HDR afterloaders available on the market and their existing applicators will be provided, with guidance on how to select the best fit for each institution’s needs. Finally, the use of checklists will be discussed as a means to implement a safe and efficient HDR program and as a method by which to verify the quality of an existing HDR program. This session will provide the perspective of expert HDR physicists as well as the perspective of a new HDR user.

1. 
Summarize national and international safety and staffing guidelines for HDR implementation
2. 
Discuss the process of afterloader and applicator selection for gynecologic, prostate, breast, interstitial, surface treatments
3. 
Learn about the use of an audit checklist tool to measure of quality control of a new or existing HDR program
4. 
Describe the evolving use of checklists within an HDR program

Field of study: Medicine, Physics
Dung beetle conservation biogeography in southern Africa: current challenges and potential effects of climatic change

Miocene, Pliocene and Pleistocene changes to the geomorphology, climate and vegetation of southern Africa are considered responsible for radical differences between southwest and northeast dung beetle assemblages (Coleoptera: Scarabaeidae: Scarabaeinae) leading to current endemism in Namibia, Botswana and South Africa. This bias is supported by distributional analysis of 437 species across vegetation regions and 2° × 2° squares of latitude and longitude using non-metric multidimensional scaling (NMDS) and minimum spanning trees (MST). The ordinal values for six NMDS dimensions showed significant correlations with annual rainfall, annual temperature, rainfall seasonality and altitude. Significant climatic differences were also shown between six regional centres defined and modelled for the subcontinent: winter/bimodal rainfall, southwest arid, southeast highlands, savanna, sandy savanna and east coast. Twenty-one, principal, subregional centres defined from further NMDS and MST analyses of regional data showed significant intra-regional differences in climatic attributes although published data suggest that soil, vegetation and dung type associations were frequent additional influences. Species showing the smallest ranges were centred primarily around the coast and bordering escarpments, which coincide with regions and subregions showing unique environmental conditions characterized by many endemic genera and species. Published land use data indicate that large parts of these regions are highly transformed or degraded, so that some species are facing strong current threats. Furthermore, published global climatic change data suggest that many endemic species could be further threatened, especially to the southwest where the late Cenozoic trend to unique climatic and environmental conditions could, potentially, be reversed in the future.

Field of study: Environmental science
Shallow donor generation in ZnO by remote hydrogen plasma

We investigate the effects of a remote hydrogen-plasma treatment on Hall parameters as well as on the bound exciton (BEx) photoluminescence (PL) for a variety of ZnO single crystals: bulk air-annealed, Li-doped, and epitaxially grown on sapphire. We present transport and spectroscopic evidence in favor of the hypothesis that hydrogen behaves as a shallow donor rather than a compensating center in ZnO. Specifically, we show that H-plasma-induced increases in I4 luminescence (photon energy: ∼3.363 eV at 4 K) correlate with increases in free-carrier concentrations from Hall-effect measurements.

Field of study: Materials science
Selenoprotein S is involved in maintenance and transport of multiprotein complexes.

SelS (Selenoprotein S) is a selenocysteine-containing protein with roles in ER (endoplasmic reticulum) function and inflammation. It has been implicated in ERAD (ER-associated protein degradation), and clinical studies revealed an association of its promoter polymorphism with cytokine levels and human diseases. However, the pathways and interacting proteins that could shed light on pathogenesis of SelS-associated diseases have not been studied systematically. We performed a large-scale affinity isolation of human SelS and its mutant forms and analysed the proteins that interact with them. All previously known SelS targets and nearly two hundred additional proteins were identified that were remarkably enriched for various multiprotein complexes. Subsequent chemical cross-linking experiments identified the specific interacting sites in SelS and its several targets. Most of these interactions involved coiled-coil domains. The data suggest that SelS participates in intracellular membrane transport and maintenance of protein complexes by anchoring them to the ER membrane.

Field of study: Biology, Computer science
Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD)

The deleterious amino acid substitution mutations in IL-10 receptor alpha gene are most frequently reported in several autoimmune diseases including early onset-inflammatory bowel disease (IBD). Despite the important role of IL-10 RA in maintaining immune homeostasis, the specific structural and functional implications of these mutations on protein phenotype, stability, ligand binding and post translational characteristics is not well explored. Therefore, this study performed the multidimensional computational analysis of IL10RA missense variations causative to pediatric or early onset inflammatory bowel disease (<5 years of age). Our computational algorithmic screening identified the deleterious nature of p. W45G, p. Y57C, p. W69G, p.T84I, p.Y91C, p.R101W, p.R117C, and p.R117H, IBD causative IL10-RA mutations. The sensitivity and specificity analysis of different computational methods showed that CADD outperform SIFT, PolyPhen 2.0, FATHMM, LRT, MetaLR, MetaSVM, PROVEAN and Condel in predicting the pathogenicity of IL10RA mutations. Our three-dimensional protein modeling assays showed that the point mutations cause major drifts in the structural plasticity of IL10 RA molecule and negatively influence its stability. Findings from molecular docking analysis have shown that these point mutations decrease the binding affinity of IL10RA toward IL10 and may likely to disturb the IL10 signaling pathway. This study provides an easy frame work for phenotypic characterization of mutant IL10RA molecule in terms of structure, flexibility and stability aspects. Our approach may also add a new dimension to conventional functional biology assays in quickly studying IL10 RA mutations and also for designing and developing inhibitors for mutant IL10RA molecule.

Field of study: Biology
Structural and biochemical characterization of the laminarinase ZgLamCGH16 from Zobellia galactanivorans suggests preferred recognition of branched laminarin.

Laminarin is a β-1,3-D-glucan displaying occasional β-1,6 branches. This storage polysaccharide of brown algae constitutes an abundant source of carbon for marine bacteria such as Zobellia galactanivorans. This marine member of the Bacteroidetes possesses five putative β-1,3-glucanases [four belonging to glycosyl hydrolase family 16 (GH16) and one to GH64] with various modular architectures. Here, the characterization of the β-glucanase ZgLamC is reported. The catalytic GH16 module (ZgLamCGH16) was produced in Escherichia coli and purified. This recombinant enzyme has a preferential specificity for laminarin but also a significant activity on mixed-linked glucan (MLG). The structure of an inactive mutant of ZgLamCGH16 in complex with a thio-β-1,3-hexaglucan substrate unravelled a straight active-site cleft with three additional pockets flanking subsites -1, -2 and -3. These lateral pockets are occupied by a glycerol, an acetate ion and a chloride ion, respectively. The presence of these molecules in the vicinity of the O6 hydroxyl group of each glucose moiety suggests that ZgLamCGH16 accommodates branched laminarins as substrates. Altogether, ZgLamC is a secreted laminarinase that is likely to be involved in the initial step of degradation of branched laminarin, while the previously characterized ZgLamA efficiently degrades unbranched laminarin and oligo-laminarins.

Field of study: Chemistry
The TROPOMI surface UV algorithm

The TROPOspheric Monitoring Instrument (TROPOMI) is the only payload of the
Sentinel-5 Precursor (S5P), which is a polar-orbiting satellite mission of
the European Space Agency (ESA). TROPOMI is a nadir-viewing spectrometer
measuring in the ultraviolet, visible, near-infrared, and the shortwave
infrared that provides near-global daily coverage. Among other things,
TROPOMI measurements will be used for calculating the UV radiation reaching
the Earth's surface. Thus, the TROPOMI surface UV product will contribute to
the monitoring of UV radiation by providing daily information on the
prevailing UV conditions over the globe. The TROPOMI UV algorithm builds on
the heritage of the Ozone Monitoring Instrument (OMI) and the Satellite
Application Facility for Atmospheric Composition and UV Radiation (AC SAF)
algorithms. This paper provides a description of the algorithm that will be
used for estimating surface UV radiation from TROPOMI observations. The
TROPOMI surface UV product includes the following UV quantities: the UV
irradiance at 305, 310, 324, and 380  nm ; the erythemally weighted UV;
and the vitamin-D weighted UV. Each of these are available as (i) daily dose or
daily accumulated irradiance, (ii) overpass dose rate or irradiance, and
(iii) local noon dose rate or irradiance. In addition, all quantities are
available corresponding to actual cloud conditions and as clear-sky values,
which otherwise correspond to the same conditions but assume a cloud-free
atmosphere. This yields 36 UV parameters altogether. The TROPOMI UV algorithm
has been tested using input based on OMI and the Global Ozone Monitoring
Experiment-2 (GOME-2) satellite measurements. These preliminary results
indicate that the algorithm is functioning according to expectations.

Field of study: Environmental science
Equivalent optical resonators.

1450 APPLIED OPTICS / Vol. 23, No. 10 / 15 May 1984 concerning the significance of these equivalent systems and the different g-parameters characterizing a lens-type reso­ nator. It is the aim of this Letter to discuss briefly the meaning of an equivalent resonator and the relations between g-parameter, mode structure, and beam divergence. To understand the misinterpretations, some details of resonator theory have to be remembered. Let us start with the well-known stable spherical resonator. For the sake of simplicity a 1-D system is considered. The integral equation reads

Field of study: Physics
EXAFS and thermodynamics of Fe(II) spin transition polymeric compounds.

We have studied the temperature variations of the EXAFS spectra of three Fe(II)/triazole-based spin transition polymeric compounds compared to a monomer belonging to the same family. These compounds have various temperatures of transition and hysteresis loop widths. In the three polymers, the Fe-Fe-Fe alignment, detected by a multiple scattering signal at the double Fe-Fe distance, is preserved through the spin transition. For the four compounds, we have studied the variations versus temperature of the Debye-Waller factors for both FeN6 (first shell) and Fe-Fe-Fe (multiple scattering path, only for the polymers). We report a strong increase of (sigma2(FeN6) through the spin transition for the monomer and two of the polymeric species. For the polymers an increase of sigma2(Fe-Fe-Fe) is also observed. These observations confirm the results available in the literature, and we confirm the interpretation as an increase of the vibrational part of the DW. For one particular polymer, we observe an unexpected behaviour: no significant increase of the Debye-Waller factor from low spin to high spin states. The EXAFS study of these non mono-crystalline species is the only way to discuss the local structure-thermodynamics properties relationships, and particularly the so-called cooperative effect in the spin transition process.

Field of study: Physics
Ensambles de aves en el desierto de Atacama, norte grande de Chile

Se evaluo la riqueza y composicion de especies de aves en el desierto de Atacama, Norte Grande de Chile, entre 1996 y 1998. Mediante transectos lineales se estimo la riqueza de especies de aves en 9 localidades del desierto de Atacama agrupadas en cuatro zonas ecologicas: Desierto Litoral, Desierto Interior, Tropical Marginal y Tropical de Altura. La riqueza total de aves fue de 80 especies distribuidas en 51 generos y 26 familias. La riqueza total observada corresponde al 52% de las aves historicamente descritas para el desierto del Norte Grande de Chile. Las zonas ecologicas del desierto litoral y tropical de altura poseen elementos avifaunisticos unicos para cada zona. Las aves insectivoras predominaron entre los demas gremios troficos (40% del total de especies). La predominancia de los diferentes gremios troficos parece estar determinada por el tipo de habitat utilizado para alimentarse. Nuestros resultados permitirian sugerir que la riqueza de especies de aves en el desierto de Atacama, Norte Grande de Chile, estaria d eterminada por la heterogeneidad del habitat e inmigracion de especies provenientes de zonas adyacentes al desierto de Atacama.

Field of study: Biology, Environmental science