bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species
Authors: Marot-Lassauzaie Valérie , Goldberg Tatyana , Armenteros Jose Juan Almagro , Nielsen Henrik , Rost Burkhard 
Published: July 2021

AbstractThe native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. Do ten eukaryotic model organisms differ in theirlocation spectrum, i.e., the fraction of its proteome in each of seven major cellular compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes:Homo sapiens(human),Gorilla gorilla(gorilla),Pan troglodytes(chimpanzee),Mus musculus(mouse),Rattus norvegicus(rat),Drosophila melanogaster(fruit/vinegar fly),Anopheles gambiae(African malaria mosquito),Caenorhabitis elegans(nematode),Saccharomyces cerevisiae(baker’s yeast), andSchizosaccharomyces pombe(fission yeast). The two largest classes were predicted to be the nucleus and the cytoplasm together accounting for 47–62% of all proteins, while 7–21% of the proteins were predicted in the plasma membrane and 4–15% to be secreted. Overall, the predicted location spectra were largely similar. However, in detail, the differences sufficed to plot trees (UPGMA) and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states (location classes). The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons. Most interestingly, known phylogenetic relations were reproduced better by paralog-only than by ortholog-only trees.
INFRAFRONTIER quality principles in systemic phenotyping
Authors: Ehlich Hilke , Cater Heather L. , Flenniken Ann M. , Goncalves Da Cruz Isabelle , Mura Anne-Marie , Ntafis Vasileios , Raess Michael , Selloum Mohammed , Stoeger Claudia , Suchanova Sarka , Vuolteenaho Reetta , Brown Steve D. M. , Hérault Yann , Hinttala Reetta , Hrabě de Angelis Martin , Kollias George , Kontoyiannis Dimitris L. , Malissen Bernard , McKerlie Colin , Sedláček Radislav , Wells Sara E. , Zarubica Ana , Rozman Jan , Sorg Tania 
Published: July 2021

AbstractImproving reproducibility and replicability in preclinical research is a widely discussed and pertinent topic, especially regarding ethical responsibility in animal research. INFRAFRONTIER, the European Research Infrastructure for the generation, phenotyping, archiving, and distribution of model mammalian genomes, is addressing this issue by developing internal quality principles for its different service areas, that provides a quality framework for its operational activities. This article introduces the INFRAFRONTIER Quality Principles in Systemic Phenotyping of genetically altered mouse models. A total of 11 key principles are included, ranging from general requirements for compliance with guidelines on animal testing, to the need for well-trained personnel and more specific standards such as the exchange of reference lines. Recently established requirements such as the provision of FAIR (Findable, Accessible, Interoperable, Reusable) data are also addressed. For each quality principle, we have outlined the specific context, requirements, further recommendations, and key references.
On the Number of Forests and Connected Spanning Subgraphs
Authors: Borbényi Márton , Csikvári Péter , Luo Haoran 
Published: July 2021

AbstractLet F(G) be the number of forests of a graph G. Similarly let C(G) be the number of connected spanning subgraphs of a connected graph G. We bound F(G) and C(G) for regular graphs and for graphs with a fixed average degree. Among many other things we study $$f_d=\sup _{G\in {\mathcal {G}}_d}F(G)^{1/v(G)}$$

f
d

=

sup

G
∈

G
d

F

(
G
)

1
/
v
(
G
)

, where $${\mathcal {G}}_d$$

G
d

is the family of d-regular graphs, and v(G) denotes the number of vertices of a graph G. We show that $$f_3=2^{3/2}$$

f
3

=

2

3
/
2

, and if $$(G_n)_n$$

(

G
n

)

n

is a sequence of 3-regular graphs with the length of the shortest cycle tending to infinity, then $$\lim _{n\rightarrow \infty }F(G_n)^{1/v(G_n)}=2^{3/2}$$

lim

n
→
∞

F

(

G
n

)

1
/
v
(

G
n

)

=

2

3
/
2

. We also improve on the previous best bounds on $$f_d$$

f
d

for $$4\le d\le 9$$

4
≤
d
≤
9

.
Vitamin D supplementation in people with IBS has no effect on symptom severity and quality of life: results of a randomised controlled trial
Authors: Williams Claire E. , Williams Elizabeth A. , Corfe Bernard M. 
Published: July 2021

Abstract
Purpose
Several small trials suggest a benefit of vitamin D supplementation in irritable bowel syndrome (IBS). The generalisability of these reports is limited by their design and scale. This study aimed to assess whether vitamin D supplementation improved IBS symptoms in a UK community setting.

Methods
This was a randomised, double-blind, placebo-controlled study. Participants were recruited from the community in winter months between December 2017 and March 2019. 135 participants received either vitamin D (3,000 IU p.d.) or placebo for 12 weeks. The primary outcome measure was change in IBS symptom severity; secondary outcomes included change in IBS-related quality of life.

Results
The participants were analysed on an intent-to-treat basis. 60% of participants were vitamin D deficient or insufficient at baseline. Although vitamin D levels increased in the intervention arm relative to placebo (45.1 ± 32.88 nmol/L vs 3.1 ± 26.15 nmol/L; p < 0.001). There was no difference in the change of IBS symptom severity between the active and placebo trial arms (− 62.5 ± 91.57 vs – 75.2 ± 84.35, p = 0.426) over time. Similarly there was no difference between trial arms in τhe change in quality of life (− 7.7 ± 25.36 vs – 11.31 ± 25.02, p = 0.427).

Conclusions
There is no case for advocating use of vitamin D in the management of IBS symptoms. The prevalence of vitamin D insufficiency suggests routine screening and supplementation should be implemented in this population for general health reasons.
This trial was retrospectively registered with ISRCTN (ISRCTN13277340) on 24th April 2018 after recruiting had been initiated.
The voyage of the ‘Guyot Stone’ from the Swiss Alps to Neuchâtel and Princeton
Authors: Bernoulli Daniel , Capuzzo Nicola 
Published: July 2021

AbstractIn 1890, former students of Arnold Guyot at the University of Neuchàtel dedicated a ‘large glacial boulder from Neuchâtel’ to his memory, now in front of Guyot Hall at Princeton University. We established that this block originated with all certainty from Upper Carboniferous conglomerates of the Salvan–Dorénaz Basin, the relics of which crop out in the Alps of western Switzerland and eastern France. During the Last Glacial Maximum, the boulder travelled from the lower Rhône Valley on the back of the Pleistocene Rhône Glacier to Neuchâtel from where, later, it crossed the Atlantic and was transported to Princeton. Guyot’s name is familiar to geologists because of the term ‘guyot’, introduced 1946 by Harry Hess for ‘curious flat-topped peaks scattered over millions of square miles in the Pacific basin’, many of which are now known to represent drowned carbonate platforms.
Olfaction in patients with Parkinson’s disease: a new threshold test analysis through turning points trajectories
Authors: Cecchini Maria Paola , Mantovani Elisa , Federico Angela , Zanini Alice , Ottaviani Sarah , Masala Carla , Tinazzi Michele , Tamburin Stefano 
Published: July 2021

AbstractOlfactory deficit is a widely documented non-motor symptom in Parkinson’s disease (PD). Abnormal turning points trajectories through olfactory threshold testing have been recently reported in patients with olfactory dysfunction, who seem to adapt faster to olfactory stimuli, but data on PD patients are lacking. The aim of this study is to perform olfactory threshold test and explore the turning points trajectories in PD patients in comparison to normal controls. We recruited 59 PD patients without dementia, and no conditions that could influence evaluation of olfaction and cognition. Sixty healthy subjects served as controls. Patients and controls underwent a comprehensive olfactory evaluation with the Sniffin’ Sticks extended test assessing threshold, discrimination and identification and a full neuropsychological evaluation. Besides, threshold test data were analyzed examining all the turning points trajectories. PD patients showed a different olfactory threshold test pattern, i.e., faster olfactory adaptation, than controls with no effect of age. Normosmic PD patients showed different olfactory threshold test pattern, i.e., better threshold score, than normosmic controls. Visuospatial dysfunction was the only factor that significantly influenced this pattern. Olfactory threshold trajectories suggested a possible adaptation phenomenon in PD patients. Our data offered some new insights on normosmic PD patients, which appear to be a subset with a specific psychophysical profile. The analysis of the turning points trajectories, through an olfactory threshold test, could offer additional information on olfactory function in PD patients. Future larger studies should confirm these preliminary findings.
Which birds participate in mass concentrations of Bramblings Fringilla montifringilla?—Ring recoveries, biometry, age and sex composition
Authors: Jenni Lukas 
Published: July 2021

AbstractThe BramblingFringilla montifringillacombines several special features of migration and wintering: differential migration according to age and sex groups, large differences in winter densities as a response to food availability, and flocking behaviour as a response to local mass fructification of the beechFagussp. resulting in roosts of several million birds. This study examines (a) whether Bramblings participating in mass concentrations originate from different, or additional, breeding grounds compared with birds present in normal winters, and (b) how differential migration according to age and sex groups combines with irruptive migration and with congregations in mass roosts, i.e., whether the benefits from mass concentrations differ between age and sex groups. Wing biometry (wing length, lengths of outer primaries, and wing pointedness) did not vary geographically, as shown by museum skins, and was therefore not helpful to reveal differences in origin between birds of mass concentrations and normal winters. The extent of the post-juvenile moult was smaller in mass concentration birds and suggests that slightly later-born juveniles, i.e., born further east or north, participate in mass concentrations. Ringing recoveries could not demonstrate a difference in breeding range origin of Bramblings which participate in mass concentrationsversusBramblings in normal winters in Switzerland. However, this may be due to insufficient recoveries of ringed birds. A rough estimate suggests that the number of Bramblings migrating SW on a broad front across Europe could be sufficient to form mass concentrations of up to 10 million birds which are halted by a large area of beech mast. Across Europe, the proportion of juvenile males decreased towards south (i.e., with increasing migration distance) in autumn migrants and wintering birds, while adult females showed the opposite pattern, and adult males and juvenile females were intermediate. Mass concentrations in Switzerland were composed of significantly more adults, especially adult males, and fewer juveniles, particularly juvenile females, while the sex–age composition outside mass concentrations was similar to normal winters. Adults and females likely benefit from wintering further south where snow is less likely to cover food of this ground-feeding finch. On the other hand, the costs of migration are probably substantial in terms of direct costs or indirectly in terms of reaching the breeding grounds, so that juvenile males prefer to winter closer to the breeding area than adults. Feeding in large flocks in beech mast areas incurs the high risk of being cut off from this food by snowfall. Adult males are apparently best adapted to this risk, and hence predominate in mass concentrations.
Designing convolutional neural networks with constrained evolutionary piecemeal training
Authors: Sapra Dolly , Pimentel Andy D. 
Published: July 2021

AbstractThe automated architecture search methodology for neural networks is known as Neural Architecture Search (NAS). In recent times, Convolutional Neural Networks (CNNs) designed through NAS methodologies have achieved very high performance in several fields, for instance image classification and natural language processing. Our work is in the same domain of NAS, where we traverse the search space of neural network architectures with the help of an evolutionary algorithm which has been augmented with a novel approach of piecemeal-training. In contrast to the previously published NAS techniques, wherein the training with given data is considered an isolated task to estimate the performance of neural networks, our work demonstrates that a neural network architecture and the related weights can be jointly learned by combining concepts of the traditional training process and evolutionary architecture search in a single algorithm. The consolidation has been realised by breaking down the conventional training technique into smaller slices and collating them together with an integrated evolutionary architecture search algorithm. The constraints on architecture search space are placed by limiting its various parameters within a specified range of values, consequently regulating the neural network’s size and memory requirements. We validate this concept on two vastly different datasets, namely, the CIFAR-10 dataset in the domain of image classification, and PAMAP2 dataset in the Human Activity Recognition (HAR) domain. Starting from randomly initialized and untrained CNNs, the algorithm discovers models with competent architectures, which after complete training, reach an accuracy of of 92.5% for CIFAR-10 and 94.36% PAMAP2. We further extend the algorithm to include an additional conflicting search objective: the number of parameters of the neural network. Our multi-objective algorithm produces a Pareto optimal set of neural networks, by optimizing the search for both the accuracy and the parameter count, thus emphasizing the versatility of our approach.
The Value of Surprise in Science
Authors: French Steven , Murphy Alice 
Published: July 2021

AbstractScientific results are often presented as ‘surprising’ as if that is a good thing. Is it? And if so, why? What is the value of surprise in science? Discussions of surprise in science have been limited, but surprise has been used as a way of defending the epistemic privilege of experiments over simulations. The argument is that while experiments can ‘confound’, simulations can merely surprise (Morgan, 2005). Our aim in this paper is to show that the discussion of surprise can be usefully extended to thought experiments and theoretical derivations. We argue that in focusing on these features of scientific practice, we can see that the surprise-confoundment distinction does not fully capture surprise in science. We set out how thought experiments and theoretical derivations can bring about surprises that can be disruptive in a productive way, and we end by exploring how this links with their future fertility.
A Refined Well-Posedness Result for the Modified KdV Equation in the Fourier–Lebesgue Spaces
Authors: Chapouto Andreia 
Published: July 2021

AbstractWe study the well-posedness of the complex-valued modified Korteweg-de Vries equation (mKdV) on the circle at low regularity. In our previous work (2021), we introduced the second renormalized mKdV equation, based on the conservation of momentum, which we proposed as the correct model to study the complex-valued mKdV outside $$H^\frac{1}{2}({\mathbb {T}})$$

H

1
2

(
T
)

. Here, we employ the method introduced by Deng et al. (Commun Math Phys 384(1):1061–1107, 2021) to prove local well-posedness of the second renormalized mKdV equation in the Fourier–Lebesgue spaces $${\mathcal {F}}L^{s,p}({\mathbb {T}})$$

F

L

s
,
p

(
T
)

for $$s\ge \frac{1}{2}$$

s
≥

1
2

and $$1\le p <\infty $$

1
≤
p
<
∞

. As a byproduct of this well-posedness result, we show ill-posedness of the complex-valued mKdV without the second renormalization for initial data in these Fourier–Lebesgue spaces with infinite momentum.
Misconceptions, Knowledge, and Attitudes Towards the Phenomenon of Radioactivity
Authors: Morales López Ana Isabel , Tuzón Marco Paula 
Published: July 2021

AbstractThe teaching of the phenomenon of radioactivity is considered a key ingredient in the path towards developing critical thinking skills in many secondary science education curricula. Despite being one of the basic concepts in general physics courses, the scientific teaching literature of the last 40 years reports a great deal of misconceptions and conceptual errors related to radioactivity that seemingly appear regardless of the educational level and context. This study reports the first cross-sectional diagnostic study in Spain to secondary education students and pre-service teachers. Data were collected in the year 2019 through a questionnaire adapted from a previously validated one to explore the main misconceptions, attitudes, and knowledge status on the topic on a sample of 191 secondary school students and 29 Physics-and-Chemistry trainee teachers in the Spanish region of Valencia. Open and closed questions were used to categorize the entity itself, its properties, and the main misconceptions related to radioactivity. The responses were analysed using conventional statistical methods. The results indicate an evolution from a widespread dissenting notion on the phenomenon, which is staunchly related to danger, hazard, and destruction in the lowest educational levels, towards a more rational, relative, and multidimensional perspective in the highest ones. On the other hand, the ideas, emotions, and attitudes of the inquired individuals are in good agreement with the main misconceptions reported in the literature.
A Delphi Study Investigating Clinicians’ Views on Access to, Delivery of, and Adaptations of MBCT in the UK Clinical Settings
Authors: Williams Kate , Hartley Samantha , Taylor Peter 
Published: July 2021

AbstractObjectivesMindfulness-based cognitive therapy (MBCT) is a well-evidenced relapse-prevention intervention for depression with a growing evidence-base for use in other clinical populations. The UK initiatives have outlined plans for increasing access to MBCT in clinical settings, although evidence suggests that access remains limited. Given the increased popularity and access to MBCT, there may be deviations from the evidence-base and potential risks of harm. We aimed to understand what clinicians believe should be best clinical practice regarding access to, delivery of, and adaptations to MBCT.MethodsWe employed a two-stage Delphi methodology. First, to develop statements around best practices, we consulted five mindfulness-based experts and reviewed the literature. Second, a total of 59 statements were taken forward into three survey rating rounds.ResultsTwenty-nine clinicians completed round one, with 25 subsequently completing both rounds two and three. Forty-four statements reached consensus; 15 statements did not. Clinicians agreed with statements regarding sufficient preparation for accessing MBCT, adherence to the evidence-base and good practice guidelines, consideration of risks, sufficient access to training, support, and resources within services, and carefully considered adaptations. The consensus was not reached on statements which reflected a lack of evidence-base for specific clinical populations or the complex decision-making processes involved in delivering and making adaptations to MBCT.ConclusionsOur findings highlight the delicate balance of maintaining a client-centred and transparent approach whilst adhering to the evidence-base in clinical decisions around access to, delivery of, and adaptations in MBCT and have important wide-reaching implications.
A survey on multiscale mollifier decorrelation of seismic data
Authors: Blick C. , Eberle S. 
Published: July 2021

AbstractIn this survey paper, we present a multiscale post-processing method in exploration. Based on a physically relevant mollifier technique involving the elasto-oscillatory Cauchy–Navier equation, we mathematically describe the extractable information within 3D geological models obtained by migration as is commonly used for geophysical exploration purposes. More explicitly, the developed multiscale approach extracts and visualizes structural features inherently available in signature bands of certain geological formations such as aquifers, salt domes etc. by specifying suitable wavelet bands.
Interpretation of pressure interference tests for wells connected by a large hydraulic fracture
Authors: Escobar Freddy Humberto , Prada Erik Felipe , Suescún-Díaz Daniel 
Published: July 2021

AbstractShale formations are being exploited in several places around the world. Thus, an adequate characterization of such formations is recommended. In this work, two interpretation methodologies—TDS technique and conventional analysis—are implemented for determining the fracture permeability, from interference tests, between two wells connected by a large hydraulic fracture. Therefore, equations have been developed for both interpretation techniques and tested with synthetic examples. The estimated fracture permeabilities closely match the values initially used for the simulation of the tests.
Classroom aerosol dispersion: desk spacing and divider impacts
Authors: Dacunto P. , Moser D. , Ng A. , Benson M. 
Published: July 2021

AbstractA study of aerosol dispersion was conducted in a university classroom using a CO2 tracer gas emitted from three source locations in a steady release, one source location per test. The tracer gas emitted from the single source location represented the potentially infectious aerosol droplets emitted from a single student and was thus a way to examine the influence of one sick student on the rest of the class. Two parameters were adjusted during the testing—the spacing of the desks, which included a spread and compressed configuration, and the inclusion of three-sided clear dividers attached to the student desk surfaces. Tracer dispersion was measured through the use of monitors in 13 locations within the classroom, with eight monitors representing seated student locations, four monitors representing a standing instructor along the classroom front, and one monitor at the return vent in the ceiling. As expected, spacing strongly influenced concentration levels at desks adjacent to the source location. The use of dividers reduced overall student and instructor location tracer concentrations when compared to desks without dividers in most cases. Finally, the influence of air change differences on the results was noted with consistent trends. The experimental construct provides a systematic means for classroom testing that may be broadly applicable to various configurations of classrooms beyond the one tested.
Graphic abstract