bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient‐reported outcomes use during orthopaedic surgery clinic visits improves the patient experience
Authors: Bernstein David N. , Fear Kathleen , Mesfin Addisu , Hammert Warren C. , Mitten David J. , Rubery Paul T. , Baumhauer Judith F. 
Published: January 2019

AbstractObjectivesThe Patient‐Reported Outcomes Measurement Information System (PROMIS) is growing in popularity as healthcare shifts towards a value‐based system. However, it remains unclear if PROMIS use improves the patient experience. The aim of the present study was to determine if PROMIS use as part of routine orthopaedic clinical care is associated with improved patient experience, as measured by the Clinician and Group Consumer Assessment of Healthcare Providers and Systems (CGCAHPS) survey.MethodsAll patient visits to an orthopaedic surgery clinic at a single academic medical centre between February 2015 and September 2016 were reviewed. Accounting for known patient factors that have an impact on clinic visit satisfaction, CGCAHPS scores were compared between patients who had PROMIS used as part of their routine care and those who had not had PROMIS used as part of their routine care. A p‐value of <0.05 was considered significant.ResultsA total of 8,607 patient visits fitted our inclusion criteria. Of these, surgeons elected not to use PROMIS in 8,422 patient encounters, leaving 185 patient visits in which PROMIS was actively used. When PROMIS was used, patients were significantly more likely to feel that the provider had spent enough time with them, to recommend this provider office to another patient and to rate the provider significantly higher on a scale from 0 to 10. Although not significant, a trend was found between use of PROMIS and whether a patient felt that a provider explained health information in way that the patient understood.ConclusionsPROMIS use in an orthopaedic clinic visit can have a positive impact on the patient experience, which is currently part of a number of alternative payment models.
Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information
Authors: Khare Shruti , Bhasin Munmun , Sahoo Anusmita , Varadarajan Raghavan 
Published: January 2019

AbstractStructure prediction methods often generate a large number of models for a target sequence. Even if the correct fold for the target sequence is sampled in this dataset, it is difficult to distinguish it from other decoy structures. An attempt to solve this problem using experimental mutational sensitivity data for the CcdB protein was described previously by exploiting the correlation of residue depth with mutational sensitivity (r ~ 0.6). We now show that such a correlation extends to four other proteins with localized active sites, and for which saturation mutagenesis datasets exist. We also examine whether incorporation of predicted secondary structure information and the DOPE model quality assessment score, in addition to mutational sensitivity, improves the accuracy of model discrimination using a decoy dataset of 163 targets from CASP. Although most CASP models would have been subjected to model quality assessment prior to submission, we find that the DOPE score makes a substantial contribution to the observed improvement. We therefore also applied the approach to CcdB and four other proteins for which reliable experimental mutational data exist and observe that inclusion of experimental mutational data results in a small qualitative improvement in model discrimination relative to that seen with just the DOPE score. This is largely because of our limited ability to quantitatively predict effects of point mutations on in vivo protein activity. Further improvements in the methodology are required to facilitate improved utilization of single mutant data.
Expressional activation and functional roles of human endogenous retroviruses in cancers
Authors: Zhang Mengwen , Liang Jessie Qiaoyi , Zheng Shu 
Published: January 2019

SummaryHuman endogenous retroviruses (HERVs) are widely believed to be remnants of ancestral germ line infections by exogenous retroviruses. Although HERVs are deemed as “nonfunctional DNAs” due to loss of most of their viral protein coding capacity during evolution as part of the human genome, cumulative evidences are showing the expressional activation and potential roles of HERVs in diseases especially cancers. Work by other researchers and us has observed the dysregulation of HERVs in cancers, identified new HERV‐related genes, and revealed their potential importance in cancer development. Here, we summarized the current knowledge on the mechanisms of the expressional activation and functional roles of HERVs, with a focus on the H family HERV (HERV‐H), in carcinogenesis. HERV expression is regulated by external chemical or physical substances and exogenous virus infection, as well as host factors such as epigenetic DNA methylation, transcription factors, cytokines, and small RNAs. Diverse roles of HERVs have been proposed by acting in the forms of noncoding RNAs, proteins, and transcriptional regulators during carcinogenesis. However, much remains to be learnt about the contributions of HERVs to human cancers. More investigation is warranted to elucidate the functions of these “fossil remnants” yet important viral DNAs in the human genome.
Ligand‐Exchange of Low‐Temperature Synthesized CsPbBr3 Perovskite toward High‐Efficiency Light‐Emitting Diodes
Authors: Ye Fanghao , Zhang Huijun , Li Wei , Yan Yu , Cai Jinlong , Gurney Robert S. , Pearson Andrew J. , Liu Dan , Wang Tao 
Published: January 2019

AbstractCsPbX3 perovskite nanocrystals (NCs) are promising light‐emitting materials that have gained significant attention over the past few years. The synthesis of CsPbX3 NCs is usually performed in an inert environment under high temperature conditions; however, this requirement hinders commercial development. Low‐temperature preparation of CsPbX3 NCs with rationally designed surface ligands is crucial to the performance and stability of CsPbX3 light‐emitting diodes (LEDs). In this work, short‐chain ligand‐anchored CsPbBr3 NCs in ambient conditions at room temperature are synthesized and a ligand‐exchange strategy is employed, using longer‐chain acid/amine ligand pairs, resulting in the dramatic improvement of performance and stability of CsPbBr3 NCs LEDs. It is found that CsPbBr3 NCs anchored by oleic acid and oleylamine complex ligands result in the best LED performance, with the maximum luminance of 5033 Cd m−2, current efficiency of 18.6 Cd A−1, external quantum efficiency of 5.4%, turn‐on voltage of 3.2 V, and the best thermal stability under ambient conditions.
Second‐order feedback and climatic effects determine the dynamics of a small rodent population in a temperate forest of South America
Authors: Murúa Roberto , González Luz A. , Lima Mauricio 
Published: January 2019

AbstractThe multiannual cyclic fluctuations exhibited by arvicoline rodents in the Northern Hemisphere have attracted the attention of population ecologists. However, despite the abundant information on small rodent dynamics in South America, there are no studies reporting cyclic population dynamics. Here, we report evidence of cyclic population dynamics in a South American small rodent, the longhaired field mouse (Abrothrix longipilis) from southern temperate forests in Chile. The time‐series analyses showed that longhaired field mice dynamics are better represented by a second‐order autoregressive model characterized by 3‐year cyclic dynamics. The 3‐year cycles are clearly shown in the autocorrelation factor (ACF) pattern and in the dominant frequency of the spectral analysis. In addition, we determined nonlinear effects of the Antarctic Oscillation Index (AAOI). The results shown here pointed out that we need the integration of studies about cyclic small rodent populations from the different continents and beyond the Northern Hemisphere to resolve the enigma underlying the cyclic population dynamics exhibited by many small rodent species.
On the geometry and regularity of invariant sets of piecewise-affine automorphisms on the Euclidean space
Authors: GÜNTÜRK C. SİNAN , THAO NGUYEN T. 
Published: January 2019

In this paper, we derive geometric and analytic properties of invariant sets, including orbit closures, of a large class of piecewise-affine maps $T$ on $\mathbb{R}^{d}$. We assume that (i) $T$ consists of finitely many affine maps defined on a Borel measurable partition of $\mathbb{R}^{d}$, (ii) there is a lattice $\mathscr{L}\subset \mathbb{R}^{d}$ that contains all of the mutual differences of the translation vectors of these affine maps, and (iii) all of the affine maps have the same linear part that is an automorphism of $\mathscr{L}$. We prove that finite-volume invariant sets of such piecewise-affine maps always consist of translational tiles relative to this lattice, up to some multiplicity. When the partition is Jordan measurable, we show that closures of bounded orbits of $T$ are invariant and yield Jordan measurable tiles, again up to some multiplicity. In the latter case, we show that compact $T$-invariant sets also consist of Jordan measurable tiles. We then utilize these results to quantify the rate of convergence of ergodic averages for $T$ in the case of bounded single tiles.
Prandtl–Batchelor theorem for flows with quasiperiodic time dependence
Authors: Arbabi Hassan , Mezić Igor 
Published: January 2019

The classical Prandtl–Batchelor theorem (Prandtl, Proc. Intl Mathematical Congress, Heidelberg, 1904, pp. 484–491; Batchelor, J. Fluid Mech., vol. 1 (02), 1956, pp. 177–190) states that in the regions of steady 2D flow where viscous forces are small and streamlines are closed, the vorticity is constant. In this paper, we extend this theorem to recirculating flows with quasiperiodic time dependence using ergodic and geometric analysis of Lagrangian dynamics. In particular, we show that 2D quasiperiodic viscous flows, in the limit of zero viscosity, cannot converge to recirculating inviscid flows with non-uniform vorticity distribution. A corollary of this result is that if the vorticity contours form a family of closed curves in a quasiperiodic viscous flow, then at the limit of zero viscosity, vorticity is constant in the area enclosed by those curves at all times.
Spatiotemporal evolution of paludification associated with autogenic and allogenic factors in the black spruce–moss boreal forest of Québec, Canada
Authors: Le Stum-Boivin Éloïse , Magnan Gabriel , Garneau Michelle , Fenton Nicole J. , Grondin Pierre , Bergeron Yves 
Published: January 2019

AbstractPaludification is the most common process of peatland formation in boreal regions. In this study, we investigated the autogenic (e.g., topography) and allogenic (fire and climate) factors triggering paludification in different geomorphological contexts (glaciolacustrine silty-clayey and fluvioglacial deposits) within the Québec black spruce (Picea mariana)–moss boreal forest. Paleoecological analyses were conducted along three toposequences varying from a forest on mineral soil to forested and semi-open peatlands. Plant macrofossil and charcoal analyses were performed on basal peat sections (≤50 cm) and thick forest humus (<40 cm) to reconstruct local vegetation dynamics and fire history involved in the paludification process. Results show that primary paludification started in small topographic depressions after land emergence ca. 8000 cal yr BP within rich fens. Lateral peatland expansion and secondary paludification into adjacent forests occurred between ca. 5100 and 2300 cal yr BP and resulted from low-severity fires during a climatic deterioration. Fires that reduced or eliminated entirely the organic layer promoted the establishment ofSphagnumin microdepressions. Paludification resulted in the decline of some coniferous species such asAbies balsameaandPinus banksiana. The paleoecological approach along toposequences allowed us to understand the spatiotemporal dynamics of paludification and its impacts on the vegetation dynamics over the Holocene.
Petrogenesis and tectonic implications of Late Mesoproterozoic A1- and A2-type felsic lavas from the Huili Group, southwestern Yangtze Block
Authors: Wang Dong-Bing , Wang Bao-Di , Yin Fu-Guang , Sun Zhi-Ming , Liao Shi-Yong , Tang Yuan , Luo Liang , Liu Zheng 
Published: January 2019

AbstractThis paper presents new LA-ICP-MS zircon U–Pb chronology, whole-rock geochemical and zircon Hf isotopic data for the felsic lavas of the Huili Group from the southwestern Yangtze Block. LA-ICP-MS zircon U–Pb dating shows that these rocks were emplaced in Late Mesoproterozoic time (∼1028 to 1019 Ma). Relative to typical I-type and S-type granitoids, all the samples are characterized by low Sr and Eu, and high high-field-strength element contents, highTFeO/MgO, enriched rare earth element compositions and negative Eu anomalies, indicating that they share the geochemical signatures of A-type granitoid. They can be further divided into two groups: Group I and Group II. Group I are A1-type felsic rocks and were produced by fractional crystallization of alkaline basaltic magmas. The Group II felsic lavas belong to the A2-type and were derived by partial melting of a crustal source with mixing of mantle-derived magmas. Both Group I and Group II felsic lavas may erupt in a continental back-arc setting. The coexistence of A1- and A2-type rocks in the southwestern Yangtze Block suggests that they can occur in the same tectonic setting.
Southern right whales in the South-western Atlantic Ocean: proposed criteria to identify suitable areas of use in poorly known reproductive grounds
Authors: Figueiredo Giovanna Corrêa e , Goya Samara Cazzoli y , Santos Marcos César de Oliveira 
Published: January 2019

AbstractUrbanization and intense vessel traffic in coastal areas are obstacles for right whales when selecting breeding and calving grounds. Human activities might be the main cause for the recently observed drop in right whale sightings along the south-eastern coast of Brazil. Information concerning the biology and the activities that can potentially affect the presence of individuals along the coast are essential for management purposes, as well as for the recovery of the species stocks after a period of whaling pressure. This study correlated the occurrence of right whales in the northern limit of the breeding ground in the South-western Atlantic Ocean with local geomorphology, degree of urbanization and oceanographic features to better identify suitable areas for use by these whales. The study area was divided into 14 sub-areas based on local coastal geomorphology and discharge of large rivers. The following five ranking criteria were applied to each sub-area: presence of whaling stations and whaling activity in the past; presence and activity of ports; protection from swell, coastal slope and composition of the bottom substrate. The sub-areas that offered conditions conducive to the presence of right whales received higher scores. The proposed criteria were validated by overlapping the ranking scores with the records of right whales sighted in each sub-area. In south-eastern Brazil, protected areas with sandy bottom and gentle slope were associated with more sightings of female-calf pairs. The criteria can be used as a primary diagnostic indicating suitable sub-areas for right whales in poorly known breeding grounds.
Comparison of an in-house developed monitor unit double-check program for 3D conformal radiation therapy and treatment planning system verification
Authors: Slassi Noureddine , Ouabi Hmad , El Khayati Naïma 
Published: January 2019

AbstractAimThe treatment planning system (TPS) plays a key role in radiotherapy treatments; it is responsible for the accurate determination of the monitor unit (MU) needed to be delivered to treat a patient with cancer. The main goal of radiotherapy is to sterilise the tumour; however, any imprecise dose delivered could lead to deadly consequences. The TPS has a quality assurance tool, an independent program to double check the MU, evaluate patient plan correctness and search for any potential error.Materials and methodsIn this work, a comparison was carried out between a MU calculated by TPS and an independent in-house-developed monitor unit calculation program (MUCP). The program, written in Cplusplus (C++ Object-Oriented), requires a database of several measured quantities and uses a recently developed physically based method for field equivalence calculation. The ROOT CERN data analysis library has been used to establish fit functions, to extend MUCP use to a variety of photon beams. This study presents a new approach to checking MU correctness calculated by the TPS for a water-like tissue equivalent medium, using our MUCP, as the majority of previous studies on the MU independent checks were based on the Clarkson method. To evaluate each irradiated region, four calculation points corresponding to relative depths under the water phantom were tested for several symmetric, asymmetric, irregular symmetric and asymmetric field cases. A comparison of MU for each radiation fields from readings of the TPS and the MUCP was undertaken.ResultsA satisfactory agreement has been obtained and within the required standards (3%). Additional experimental measurements of dose deposited in a water phantom showed a deviation of &lt;1·6%.FindingsThe MUCP is a useful tool for basic and complex MU verification for 3D conformal radiation therapy plans.
Estimating Contributions of Sea Ice and Land Snow to Climate Feedback
Authors: Duan Lei , Cao Long , Caldeira Ken 
Published: January 2019

AbstractIn this study, we use the National Center for Atmospheric Research Community Earth System Model to investigate the contribution of sea ice and land snow to the climate sensitivity in response to increased atmospheric carbon dioxide content. We focus on the overall effect arising from the presence or absence of sea ice and/or land snow. We analyze our results in terms of the radiative forcing and climate feedback parameter. We find that the presence of sea ice and land snow decreases the climate feedback parameter (and thus increases climate sensitivity). Adjusted radiative forcing from added carbon dioxide is comparatively less sensitive to the presence of sea ice or land snow. The effect of sea ice on the climate feedback parameter decreases as sea ice cover diminishes at higher CO2 concentration. However, the influence of both sea ice and land snow on the climate feedback parameter remains substantial under the CO2 concentration range considered here (to eight times preindustrial CO2 content). Approximately, one quarter of the effect of sea ice and land snow on the climate feedback parameter is a consequence of the effect of these components on longwave feedback that is mainly associated with cloud change. Polar warming in response to added CO2 is approximately doubled by the presence of sea ice and land snow. Relative to the case in which sea ice and land snow are absent in the model, in response to increased CO2 concentrations, the presence of sea ice and land snow results in an increase in global mean warming by over 40%.
Feasible future global scenarios for human life evaluations
Authors: Barrington-Leigh Christopher , Galbraith Eric 
Published: January 2019

AbstractSubjective well-being surveys show large and consistent variation among countries, much of which can be predicted from a small number of social and economic proxy variables. But the degree to which these life evaluations might feasibly change over coming decades, at the global scale, has not previously been estimated. Here, we use observed historical trends in the proxy variables to constrain feasible future projections of self-reported life evaluations to the year 2050. We find that projected effects of macroeconomic variables tend to lead to modest improvements of global average life evaluations. In contrast, scenarios based on non-material variables project future global average life evaluations covering a much wider range, lying anywhere from the top 15% to the bottom 25% of present-day countries. These results highlight the critical role of non-material factors such as social supports, freedoms, and fairness in determining the future of human well-being.
Coordinative metabolism of glutamine carbon and nitrogen in proliferating cancer cells under hypoxia
Authors: Wang Yuanyuan , Bai Changsen , Ruan Yuxia , Liu Miao , Chu Qiaoyun , Qiu Li , Yang Chuanzhen , Li Binghui 
Published: January 2019

AbstractUnder hypoxia, most of glucose is converted to secretory lactate, which leads to the overuse of glutamine-carbon. However, under such a condition how glutamine nitrogen is disposed to avoid over-accumulating ammonia remains to be determined. Here we identify a metabolic flux of glutamine to secretory dihydroorotate, which is indispensable to glutamine-carbon metabolism under hypoxia. We found that glutamine nitrogen is necessary to nucleotide biosynthesis, but enriched in dihyroorotate and orotate rather than processing to its downstream uridine monophosphate under hypoxia. Dihyroorotate, not orotate, is then secreted out of cells. Furthermore, we found that the specific metabolic pathway occurs in vivo and is required for tumor growth. The identified metabolic pathway renders glutamine mainly to acetyl coenzyme A for lipogenesis, with the rest carbon and nitrogen being safely removed. Therefore, our results reveal how glutamine carbon and nitrogen are coordinatively metabolized under hypoxia, and provide a comprehensive understanding on glutamine metabolism.
Mechano-chemical decomposition of organic friction modifiers with multiple reactive centres induces superlubricity of ta-C
Authors: Kuwahara Takuya , Romero Pedro A. , Makowski Stefan , Weihnacht Volker , Moras Gianpietro , Moseler Michael 
Published: January 2019

AbstractSuperlubricity of tetrahedral amorphous carbon (ta-C) coatings under boundary lubrication with organic friction modifiers is important for industrial applications, but the underlying mechanisms remain elusive. Here, combined experiments and simulations unveil a universal tribochemical mechanism leading to superlubricity of ta-C/ta-C tribopairs. Pin-on-disc sliding experiments show that ultra- and superlow friction with negligible wear can be achieved by lubrication with unsaturated fatty acids or glycerol, but not with saturated fatty acids and hydrocarbons. Atomistic simulations reveal that, due to the simultaneous presence of two reactive centers (carboxylic group and C=C double bond), unsaturated fatty acids can concurrently chemisorb on both ta-C surfaces and bridge the tribogap. Sliding-induced mechanical strain triggers a cascade of molecular fragmentation reactions releasing passivating hydroxyl, keto, epoxy, hydrogen and olefinic groups. Similarly, glycerol’s three hydroxyl groups react simultaneously with both ta-C surfaces, causing the molecule’s complete mechano-chemical fragmentation and formation of aromatic passivation layers with superlow friction.