bluuebunny/crossref_metadata_2025_split huggingface dataset:
Value of the 21-gene expression assay in predicting locoregional recurrence rates in estrogen receptor-positive breast cancer: a systematic review and network meta-analysis
Authors: Davey Matthew G. , Cleere Eoin F. , O’Donnell John P. , Gaisor Sara , Lowery Aoife J. , Kerin Michael J. 
Published: April 2022

Abstract
Purpose
The Oncotype DX© 21-gene Recurrence Score (RS) estimates the risk of distant disease recurrence in early-stage estrogen receptor-positive, human epidermal growth factor receptor-2-negative (ER+/HER2− ) breast cancer. Using RS to estimate risk of locoregional recurrence (LRR) is less conclusive. We aimed to perform network meta-analysis (NMA) evaluating the RS in estimating LRR in ER+/HER2− breast cancer.

Methods
A NMA was performed according to PRISMA-NMA guidelines. Analysis was performed using R packages and Shiny.

Results
16 studies with 21,037 patients were included (mean age: 55.1 years (range: 22–96)). The mean RS was 17.1 and mean follow-up was 66.4 months. Using traditional RS cut-offs, 49.7% of patients had RS < 18 (3944/7935), 33.8% had RS 18–30 (2680/7935), and 16.5% had RS > 30 (1311/7935). Patients with RS 18–30 (risk ratio (RR): 1.76, 95% confidence interval (CI): 1.32–2.37) and RS > 30 (RR: 3.45, 95% CI: 2.63–4.53) were significantly more likely to experience LRR than those with RS < 18. Using TAILORx cut-offs, 16.2% of patients had RS < 11 (1974/12,208), 65.8% had RS 11–25 (8036/12,208), and 18.0% with RS > 30 (2198/12,208). LRR rates were similar for patients with RS 11–25 (RR: 1.120, 95% CI: 0.520–2.410); however, those with RS > 25 had an increased risk of LRR (RR: 2.490, 95% CI: 0.680–9.390) compared to those with RS < 11. There was a stepwise increase in LRR rates when applying traditional and TAILORx cut-offs (both P < 0.050).

Conclusion
RS testing accurately estimates LRR risk for patients being treated for early-stage ER+/HER2− breast cancer. Future prospective, randomized studies may validate the predictive value of RS in estimating LRR.
The Association between exposure to COVID-19, internalizing symptoms, and Dispositional Mindfulness in Adolescents: a longitudinal pre- and during-pandemic study
Authors: Royuela-Colomer Estíbaliz , Fernández-González Liria , Orue Izaskun , Calvete Esther 
Published: April 2022

AbstractThis study examined the association between contact with COVID-19 and internalizing symptoms in Spanish adolescents, and the moderation and mediation roles of dispositional mindfulness. Adolescents (N = 383; 58% female; Mage = 15.62, SD = 1.32) completed measures of dispositional mindfulness (MAAS-A) and internalizing symptoms (DASS-21), other stressors different from COVID-19, and contact with COVID-19 twice, in October 2019 and 2020. Three profiles emerged according to their contact with COVID-19: (1) little/no contact, (2) knowing someone close (outside home) who was infected, hospitalized, or died, and (3) being or someone at home being infected and/or hospitalized. Compared to little/no contact, both contact profiles predicted dispositional mindfulness and anxiety; and profile 2 predicted stress. Dispositional mindfulness mediated the association between both contact profiles and depression and stress. This study suggests that contact with COVID-19 predicts increased internalizing symptoms in adolescents, which could be partially explained by the decrease in mindfulness levels.
Rational planning strategies of urban structure, metro, and car use for reducing transport carbon dioxide emissions in developing cities
Authors: Yang Liu , Wang Yuanqing , Lian Yujun , Dong Xin , Liu Jianhong , Liu Yuanyuan , Wu Zhouhao 
Published: April 2022

AbstractUnderstanding transport carbon dioxide (CO2) emission impact factors’ effects is important for the rational planning strategy making in reducing the emissions. This study determines transport emission impact factors’ heterogeneous effects and proposes urban and transport planning strategies in typical developing cities. Quantile regression is applied to overcome the insufficiency of factors’ mean effects and to avoid the biased estimations when the outcome variable is non-normally distributed and heteroscedastic. It is found that, from the low emitters at the 10th quantile to the high emitters at the 90th quantile, transport emissions’ increasing rates are 8.8 times and 79.6 times that of car availability and home-to-center/subcenter distance (HCD/HSD), respectively. When commute distance reaches 5.8 km or farther, and car availability percentage is 41.2% or greater, the effects that metro services have on reducing emissions decrease by 37.8%. Polycentric and satellite city forms can greatly reduce emission increases, which are caused by HCD growth when HCD is more than 10–15 km. According to these findings, the following planning strategies are recommended, including limiting oil-fueled car use to about 40% among the urban residents, forming employment and life circles within a 5–6 km radius, allocating better public transit services around metro stations, providing high service levels of bicycle lanes, pedestrian streets, and greenways to attract more transfers to metros, controlling urban radius within 10–15 km under the monocentric pattern, and fostering polycentric structures and satellite cities when city continuously sprawls. This study can provide empirical evidence and reference value globally.
Linkage map construction using limited parental genotypic information
Authors: Cuevas Hugo E. , Vermerris Wilfred 
Published: April 2022

AbstractGenetic linkage maps based on single nucleotide polymorphisms (SNPs) represent an essential tool for a variety of genomic analyses. Today, next-generation sequencing (NGS) enables rapid genotyping of different mapping populations based on thousands of SNPs and the construction of highly saturated linkage maps. Nevertheless, missing data in the genotyping of the parental lines creates a bottleneck that determines the number of SNPs that can be used for the linkage map. As a proof of concept, a highly saturated genetic linkage map was constructed using the imputed genotypic data of a recombinant inbred line (RIL) population and the limited genotypic information of its parental lines. Two ABH genotype files were created from a pseudo-parental genotypic data set that includes all the SNPs present in the RIL population. In the first ABH file pseudo-parental 1 was considered parental A, while in the second pseudo-parental 1 was considered parental B. These two duplicate ABH genotype files were merged by chromosome and subjected to linkage map analysis. Since the ABH data were duplicated, two mirrored linkage groups were generated per chromosome. The correct linkage map was identified and selected based on the partial genotypic data of the parental lines. This strategy was effective for constructing a highly saturated linkage map of 33,421 SNPs based on the genotyping of 205 RILs and a limited number of 100 SNPs present in the parental lines. This strategy enables the use of all the NGS SNP data obtained from a low-coverage sequencing experiment in the mapping population.
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction
Authors: Grosjean Harold , Işık Mehtap , Aimon Anthony , Mobley David , Chodera John , von Delft Frank , Biggin Philip C 
Published: April 2022

AbstractA novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The SAMPL challenges prospectively assess the predictive power of methods involved in computer-aided drug design. Application of various methods to fragment molecules are now widely used in the search for new drugs. However, there is little in the way of systematic validation specifically for fragment-based approaches. We have performed a large crystallographic high-throughput fragment screen against the therapeutically relevant second bromodomain of the Pleckstrin-homology domain interacting protein (PHIP2) that revealed 52 different fragments bound across 4 distinct sites, 47 of which were bound to the pharmacologically relevant acetylated lysine (Kac) binding site. These data were used to assess computational screening, binding pose prediction and follow-up enumeration. All submissions performed randomly for screening. Pose prediction success rates (defined as less than 2 Å root mean squared deviation against heavy atom crystal positions) ranged between 0 and 25% and only a very few follow-up compounds were deemed viable candidates from a medicinal-chemistry perspective based on a common molecular descriptors analysis. The tight deadlines imposed during the challenge led to a small number of submissions suggesting that the accuracy of rapidly responsive workflows remains limited. In addition, the application of these methods to reproduce crystallographic fragment data still appears to be very challenging. The results show that there is room for improvement in the development of computational tools particularly when applied to fragment-based drug design.
Meta-interpretive learning as metarule specialisation
Authors: Patsantzis S. , Muggleton S. H. 
Published: April 2022

AbstractIn Meta-interpretive learning (MIL) the metarules, second-order datalog clauses acting as inductive bias, are manually defined by the user. In this work we show that second-order metarules for MIL can be learned by MIL. We define a generality ordering of metarules by $$\theta$$
θ
-subsumption and show that user-defined sort metarules are derivable by specialisation of the most-general matrix metarules in a language class; and that these matrix metarules are in turn derivable by specialisation of third-order punch metarules with variables quantified over the set of atoms and for which only an upper bound on their number of literals need be user-defined. We show that the cardinality of a metarule language is polynomial in the number of literals in punch metarules. We re-frame MIL as metarule specialisation by resolution. We modify the MIL metarule specialisation operator to return new metarules rather than first-order clauses and prove the correctness of the new operator. We implement the new operator as TOIL, a sub-system of the MIL system Louise. Our experiments show that as user-defined sort metarules are progressively replaced by sort metarules learned by TOIL, Louise’s predictive accuracy and training times are maintained. We conclude that automatically derived metarules can replace user-defined metarules.
Hyperbolic trees for efficient routing computation
Authors: Heszberger Zalán 
Published: April 2022

AbstractComplex system theory is increasingly applied to develop control protocols for distributed computational and networking resources. The paper deals with the important subproblem of finding complex connected structures having excellent navigability properties using limited computational resources. Recently, the two-dimensional hyperbolic space turned out to be an efficient geometry for generative models of complex networks. The networks generated using the hyperbolic metric space share their basic structural properties (like small diameter or scale-free degree distribution) with several real networks. In the paper, a new model is proposed for generating navigation trees for complex networks embedded in the two-dimensional hyperbolic plane. The generative model is not based on known hyperbolic network models: the trees are not inferred from the existing links of any network; they are generated from scratch instead and based purely on the hyperbolic coordinates of nodes. We show that these hyperbolic trees have scale-free degree distributions and are present to a large extent both in synthetic hyperbolic complex networks and real ones (Internet autonomous system topology, US flight network) embedded in the hyperbolic plane. As the main result, we show that routing on the generated hyperbolic trees is optimal in terms of total memory usage of forwarding tables.
Intelligence and scientific expertise
Authors: Barrotta Pierluigi , Gronda Roberto 
Published: April 2022

AbstractIn this article we develop a pragmatist-inspired notion of intelligence that should lead to a better understanding of the notion of scientific expertise. The notion of intelligence is drawn from Dewey and is therefore used here in its technical sense. Our thesis is that scientific knowledge is a necessary but not sufficient condition for scientific expertise; intelligence should also be added. Conceived of as the capacity to apply general knowledge to particulars, we reach the conclusion that intelligence is a necessary requirement for scientific experts in the wake of Dewey’s logic of inquiry. In particular, we argue that an all-important task that scientific experts are asked to accomplish, and which puts their expertise to the test, is to transform indeterminate situations into problematic situations, and that such a goal can only be achieved if scientific experts succeed in paying attention to all the contingent and precarious aspects that make the situation they face unique.
Johnston versus Johnston
Authors: Kowalczyk Kacper 
Published: April 2022

AbstractPersonites are like continuant people but shorter-lived. Johnston argues that personites do not exist since otherwise personites would have the same moral status as persons, which is untenable. I argue that Johnston’s arguments fail. To do that I propose an alternative way to understand intrinsicness and I clarify the meaning of reductionism about persons. I also argue that a plausible ethical theory is possible even if personites have the same moral status as persons. My arguments draw on Johnston’s earlier debate with Parfit about personal identity and the place of ordinary concerns in a naturalistic world. I also describe an important but metaphysics-free problem that arises from Johnston’s discussion.
Skilled performance in Contact Improvisation: the importance of interkinaesthetic sense of agency
Authors: Deans Catherine , Pini Sarah 
Published: April 2022

AbstractIn exploring skilled performance in Contact Improvisation (CI), we utilize an enactive ethnographic methodology combined with an interdisciplinary approach to examine the question of how skill develops in CI. We suggest this involves the development of subtleties of awareness of intra- and interkinaesthetic attunement, and a capacity for interkinaesthetic negative capability—an embodied interpersonal ‘not knowing yet’—including an ease with being off balance and waiting for the next shift or movement to arise, literally a ‘playing with’ balance, falling, nearly falling, momentum and gravity. We draw on insights from an interdisciplinary approach, including from a developmental perspective concerning the experience of dyadic interpersonal embodied skill development in both infancy and CI. Building on Ravn and Høffding’s (2021) definition of expertise in improvisation as an “oscillatory process of assuming and relinquishing agency” we propose that a key aspect of expertise in CI involves oscillation between levels and processes of interkinaesthetic sense of agency. These interdisciplinary insights also elucidate limitations within current conceptualisations of sense of agency, including the relationship between sense of agency and sense of control.
Limits to evidential pluralism: multi-method large-N qualitative analysis and the primacy of mechanistic studies
Authors: Runhardt Rosa W. 
Published: April 2022

AbstractEvidential pluralists, like Federica Russo and Jon Williamson, argue that causal claims should be corroborated by establishing both the existence of a suitable correlation and a suitable mechanism complex. At first glance, this fits well with mixed method research in the social sciences, which often involves a pluralist combination of statistical and mechanistic evidence. However, statistical evidence concerns a population of cases, while mechanistic evidence is found in individual case studies. How should researchers combine such general statistical evidence and specific mechanistic evidence? This article discusses a very recent answer to this question, ‘multi-method large-N qualitative analysis’ or multi-method LNQA, popular in political science and international relations studies of rare events like democratic transitions and cease-fire agreements. Multi-method LNQA combines a comprehensive study of all (or most) relevant event cases with statistical analysis, in an attempt to solve the issues of generalization faced by other types of qualitative research, such as selection bias and lack of representativeness. I will argue that the kind of general causal claim that multi-method LNQA is after, however, is crucially different from the average treatment effect found in statistical analysis and can in fact only be supported with mechanistic evidence. I conclude from this that mixed method research, and thereby evidential pluralism, may be inappropriate in this context.
Non-contrast-enhanced silent magnetic resonance angiography for assessing cerebral aneurysms after PulseRider treatment
Authors: Suzuki Tomoaki , Hasegawa Hitoshi , Ando Kazuhiro , Shibuya Kohei , Takahashi Haruhiko , Saito Shoji , Oishi Makoto , Fujii Yukihiko 
Published: April 2022

Abstract
Purpose
Conventional time-of-flight (TOF) magnetic resonance angiography (MRA) failed to depict clear visualization of coiled cerebral aneurysms with PulseRider due to metal-induced susceptibility artifacts. Our aim was to overcome the metal artifact using a novel imaging technique of non-contrast-enhanced ultrashort echo-time magnetic resonance angiography (UTE-MRA).

Materials and methods
Five unruptured intracranial aneurysms were treated using PulseRider and the patients underwent silent MRA (UTE-MRA). The images were compared with TOF-MRA and digital subtraction angiography (DSA).

Results
Silent MRA can visualize the residual cavity of the coiled aneurysms, which was not well visualized and rather defective when using TOF-MRA. While a segment of the proximal marker composed of stainless steel was poorly visualized, the other parts of the parent artery and the arteries of bifurcation, including the aneurysmal neck, were clearly visualized, equivalent to that of DSA.

Conclusions
UTE-MRA achieves better visualization of cerebral aneurysms after PulseRider treatment than TOF-MRA.
On an Involution in the Class of Non-negative Hermitian Matrix Measures on a Compact Interval
Authors: Fritzsche Bernd , Kirstein Bernd , Mädler Conrad 
Published: April 2022

AbstractWe study a particular involution in the class $${\mathcal {M}^\succcurlyeq _{q}({[\alpha ,\beta ]})}$$

M

q
≽

(

[
α
,
β
]

)

of all Non-negative Hermitian $${q\times q}$$

q
×
q

measures on a compact interval $${[\alpha ,\beta ]}$$

[
α
,
β
]

of $$\mathbb {R}$$
R
. Several connections to the matricial version of the Hausdorff moment problem on $${[\alpha ,\beta ]}$$

[
α
,
β
]

are investigated in terms of $${[\alpha ,\beta ]}$$

[
α
,
β
]

-Stieltjes transforms as well as in the language of matricial Hausdorff moment sequences and associated matricial canonical moments.
A study on spatial variation of water flow at confluence connected to non-orthogonal channels
Authors: Jeong Yong-Wook , Jeong Woochang 
Published: April 2022

AbstractMost studies on the flood flow characteristics at a confluence focus on channels connected orthogonally or at right angle, but studies on non-orthogonally connected channels remain limited. In this study, hydraulic-model experiments and numerical simulations are conducted to analyze the spatial variation of water flow in and around a confluence connected to non-orthogonal channels. Comparison of the measured and simulated water depth distributions in and around the confluence indicates that the results are in relatively good agreement. In the experiment where the angle between two upstream channels is 45°, the water flow pattern in and around the confluence corresponds approximately to Type I proposed by (Mignot et al. J Hydraul Res 46:723–738, 2008). However, it was found that there is no any flow type to correspond to the water flow pattern measured in the case of the angle of 135°. For analyzing the variation of the water depth in and around the confluence with inflow, numerical simulation is performed by setting the inflow ratio of the two inlet channels to one, three, and six, respectively.
Evaluation of the adsorption efficiency of carcinogenic PAHs on microplastic (polyester) fibers—preliminary results
Authors: Wiśniowska Ewa , Włodarczyk-Makuła Maria 
Published: April 2022

AbstractPaper presents the results of investigations on sorption capacity of selected carcinogenic polycyclic aromatic hydrocarbons (PAHs) on microplastics fibers. Accumulation of organic micropollutants such as PAHs is indicated as one of the important problems in the case of microplastics present in surface water, including sea water. Concentrations of the micropollutants can reach even several mg/kg of microplastics. An unrecognized problem are sorption capacities of microfibers towards PAHs. Recent research works indicate that microfibers are commonly present in sewage sludge. Content of the fibers in this waste material can reach over 23000 particles per 1 kg of sludge dry matter. The fibers mainly come from cloth washing. It is obvious that the adsorption capacity of the fibers can affect the concentration of PAHs in sewage sludge. The aim of the study was to evaluate sorption capacities of polyester fibers towards PAHs. Adsorption of PAHs were provided under static conditions. After 24 h of adsorption 1255 μg/g of carcinogenic PAHs was adsorbed onto the polyster fibers. Amount of 6-ring PAHs was equal to 154 μg/g, whereas 5- i 4- ring ones, 562 and 539 μg/g, respectively. The results have confirmed that hydrophobic PAHs can be adsorbed onto polystyrene fibers and as a result cumulate in sewage sludge.
A comparative biodistribution study of polymeric and lipid-based nanoparticles
Authors: Åslund Andreas K. O. , Vandebriel Rob J. , Caputo Fanny , de Jong Wim H. , Delmaar Christiaan , Hyldbakk Astrid , Rustique Emilie , Schmid Ruth , Snipstad Sofie , Texier Isabelle , Vernstad Kai , Borgos Sven Even F. 
Published: April 2022

AbstractBiodistribution of nanoencapsulated bioactive compounds is primarily determined by the size, shape, chemical composition and surface properties of the encapsulating nanoparticle, and, thus, less dependent on the physicochemical properties of the active pharmaceutical ingredient encapsulated. In the current work, we aimed to investigate the impact of formulation type on biodistribution profile for two clinically relevant nanoformulations. We performed a comparative study of biodistribution in healthy rats at several dose levels and durations up to 14-day post-injection. The studied nanoformulations were nanostructured lipid carriers incorporating the fluorescent dye IR780-oleyl, and polymeric nanoparticles containing the anticancer agent cabazitaxel. The biodistribution was approximated by quantification of the cargo in blood and relevant organs. Several clear and systematic differences in biodistribution were observed, with the most pronounced being a much higher (more than 50-fold) measured concentration ratio between cabazitaxel in all organs vs. blood, as compared to IR780-oleyl. Normalized dose linearity largely showed opposite trends between the two compounds after injection. Cabazitaxel showed a higher brain accumulation than IR780-oleyl with increasing dose injected. Interestingly, cabazitaxel showed a notable and prolonged accumulation in lung tissue compared to other organs. The latter observations could warrant further studies towards a possible therapeutic indication within lung and conceivably brain cancer for nanoformulations of this highly antineoplastic compound, for which off-target toxicity is currently dose-limiting in the clinic.
Graphical abstract