bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unannotated splicing regulatory elements in deep intron space
Authors: Conboy John G. 
Published: April 2021

AbstractDeep intron space harbors a diverse array of splicing regulatory elements that cooperate with better‐known exon‐proximal elements to enforce proper tissue‐specific and development‐specific pre‐mRNA processing. Many deep intron elements have been highly conserved through vertebrate evolution, yet remain poorly annotated in the human genome. Recursive splicing exons (RS‐exons) and intraexons promote noncanonical, multistep resplicing pathways in long introns, involving transient intermediate structures that are greatly underrepresented in RNA‐seq datasets. Decoy splice sites and decoy exons act at a distance to inhibit splicing catalysis at annotated splice sites, with functional consequences such as exon skipping and intron retention. RNA:RNA bridges can juxtapose distant sequences within or across introns to activate deep intron splicing enhancers and silencers, to loop out exons to be skipped, or to select one member of a mutually exclusive set of exons. Similarly, protein bridges mediated by interactions among transcript‐bound RNA binding proteins (RBPs) can modulate splicing outcomes. Experimental disruption of deep intron elements serving any of these functions can abrogate normal splicing, strongly suggesting that natural mutations of deep intron elements can do likewise to cause human disease. Understanding noncanonical splicing pathways and discovering deep intron regulatory signals, many of which map hundreds to many thousands of nucleotides from annotated splice junctions, is of great academic interest for basic scientists studying alternative splicing mechanisms. Hopefully, this knowledge coupled with increased analysis of deep intron sequences will also have important medical applications, as better interpretation of deep intron mutations may reveal new disease mechanisms and suggest new therapies.This article is categorized under:
RNA Processing > Splicing Regulation/Alternative Splicing
Strong first order electroweak phase transition in 2HDM confronting future Z & Higgs factories
Authors: Su Wei , Williams Anthony G. , Zhang Mengchao 
Published: April 2021

Abstract
The electroweak phase transition can be made first order by extending the Standard Model (SM) Higgs sector with extra scalars. The same new physics can explain the matter-antimatter asymmetry of the universe by supplying an extra source of CP violation and sphaleron processes. In this paper we study the existence of strong first order electroweak phase transition (SFOEWPT) in the type-I and type-II two Higgs doublet models (2HDM). We focus on how the SFOEWPT requirements constraint the spectrum of non-SM Higgs. Through the parameter space scan, we find that SFOEWPT suggests an upper limit on the masses of heavy Higgs $$ {m}_{A/H/{H}^{\pm }} $$

m

A
/
H
/

H
±

, which is around 1 TeV. High temperature expansion and Higgs vacuum uplifting is used for an analytical understanding of our results. After taking into account the probe ability on SFOEWPT from theoretical constraints, Higgs and Z-pole precision measurements up to the one-loop level at future Higgs & Z factories, sizeable loop corrections require $$ {m}_{A/{H}^{\pm }}-{m}_H $$

m

A
/

H
±

−

m
H

∈ (100, 250) GeV to meet SFOEWPT condition for Type-II 2HDM, and $$ \left|{m}_{A/{H}^{\pm }}-{m}_H\right| $$

m

A
/

H
±

−

m
H

∈ (100, 350) GeV or $$ \left|{m}_A-{m}_{H/{H}^{\pm }}\right| $$

m
A

−

m

H
/

H
±

∈ (100, 350) GeV for Type-I 2HDM.
On the Spectrum of Hilbert Matrix Operator
Authors: Silbermann Bernd 
Published: April 2021

AbstractThe Hilbert matrix $$\begin{aligned} {\mathcal {H}}_\lambda =\left( \frac{1}{n+m+\lambda }\right) _{n,m=0}^{\infty }, \quad \lambda \ne 0,-1,-2, \ldots \, \end{aligned}$$

H
λ

=

1

n
+
m
+
λ

n
,
m
=
0

∞

,

λ
≠
0
,
-
1
,
-
2
,
…

generates a bounded linear operator in the Hardy spaces $$H^p$$

H
p

and in the $$l^p$$

l
p

-spaces. The aim of this paper is to study the spectrum of this operator in the spaces mentioned. In a sense, the presented investigation continues earlier works of various authors. More information concerning the history of the topic can be found in the introduction.
Full-Waveform Inversion for Imaging Faulted Structures: A Case Study from the Japan Trench Forearc Slope
Authors: Jamali Hondori Ehsan , Guo Chen , Mikada Hitoshi , Park Jin-Oh 
Published: April 2021

AbstractFull-waveform inversion (FWI) of limited-offset marine seismic data is a challenging task due to the lack of refracted energy and diving waves from the shallow sediments, which are fundamentally required to update the long-wavelength background velocity model in a tomographic fashion. When these events are absent, a reliable initial velocity model is necessary to ensure that the observed and simulated waveforms kinematically fit within an error of less than half a wavelength to protect the FWI iterative local optimization scheme from cycle skipping. We use a migration-based velocity analysis (MVA) method, including a combination of the layer-stripping approach and iterations of Kirchhoff prestack depth migration (KPSDM), to build an accurate initial velocity model for the FWI application on 2D seismic data with a maximum offset of 5.8 km. The data are acquired in the Japan Trench subduction zone, and we focus on the area where the shallow sediments overlying a highly reflective basement on top of the Cretaceous erosional unconformity are severely faulted and deformed. Despite the limited offsets available in the seismic data, our carefully designed workflow for data preconditioning, initial model building, and waveform inversion provides a velocity model that could improve the depth images down to almost 3.5 km. We present several quality control measures to assess the reliability of the resulting FWI model, including ray path illuminations, sensitivity kernels, reverse time migration (RTM) images, and KPSDM common image gathers. A direct comparison between the FWI and MVA velocity profiles reveals a sharp boundary at the Cretaceous basement interface, a feature that could not be observed in the MVA velocity model. The normal faults caused by the basal erosion of the upper plate in the study area reach the seafloor with evident subsidence of the shallow strata, implying that the faults are active.
Do pre-operative radiologic assessment predict postoperative outcomes in patients with insertional Achilles tendinopathy?: a retrospective database study
Authors: Baumbach Sebastian Felix , Hörterer Hubert , Oppelt Sonja , Szeimies Ulrike , Polzer Hans , Walther Markus 
Published: April 2021

Abstract
Introduction
Diagnosis and treatment of insertional tendinopathy of the Achilles tendon (IAT) remains a challenge. The aim of this study was to assess the influence of pre-operative radiological pathologies on the patient-reported outcomes following open debridement of all pathologies for IAT.

Materials and methods
In this IRB-approved retrospective correlation and comparative study, patients with pre-operative imaging were identified from the authors’ retrospective IAT database comprising of 118 patients. All were treated by a standardized surgical treatment strategy utilizing a midline, transachillary approach and debridement of all pathologies. A total of fifteen radiologic parameters were measured on radiographs (RX) and MRI. The patient-reported outcomes were assessed using the Victorian Institute of Sport Assessment-Achilles questionnaire (VISA-A-G) and the general health questionnaire SF-12 at a minimum follow-up of 12 months. The data are presented as mean ± SD (95% CI).

Results
88 patients (74.6%) with an average age of 50 ± 12 (47–52) years were included. Radiographs were available in 68 patients and MRI in 53. The mean follow-up was 3.8 ± 1.9 (3.4–4.3) years. The overall VISA-A-G was 81 ± 22 (77–86), the SF-12 PCS 54 ± 7 (52–55), and the SF-12 MCS 52 ± 9 (50–54) points. None of the assessed radiological parameters had a significant influence on the patient-reported outcome following surgical treatment for IAT.

Conclusion
In this retrospective correlation study, no significant association was found between preoperative radiographic and MRI radiologic parameters for IAT and postoperative patient-reported outcomes (VISA-A-G and SF-12).
Anatomy of the sonographic post-cesarean uterus
Authors: Al Naimi Ammar , Wolnicki Bartosch , Mouzakiti Niki , Reinbach Tiana , Louwen Frank , Bahlmann Franz 
Published: April 2021

Abstract
Purpose
We aim to describe the sonographic uterine anatomy after a cesarean section (CS), test the reproducibility of predefined measurements from the BSUM study, and report the distribution of these measurements.

Methods
This is a descriptive observational study where 200 women with a history of only one CS were recruited 12–24 months postoperatively. A 5–13 MHz micro-convex transvaginal transducer was used for the acquisition of volumetric datasets for evaluating the CS scars. We defined 15 distinct measurements including the residual myometrial thickness (RMT). RMT ratio was calculated as a percentage of RMT to the assumed pre-cesarean anterior uterine wall thickness. A P value below 0.05 is utilized for significant statistical analysis.

Results
Patients were included on average 18.5 months post-cesarean. The uterus was anteflexed in 82.5% and retroflexed in 17.5%. Myometrial defects at the site of CS manifest in two forms, either as a niche or as fibrosis. Patients are classified into four groups: those with isolated niches (45%), combined niches and fibrosis (38.5%), isolated fibrosis (11%), and lacking both (5%). The median RMT ratio for these groups was 63.09, 40.93, 59.84, and 100% with a standard deviation of 16.73, 12.95, 16.59, and 0, respectively. The interclass correlation coefficient (ICC) remained above 0.9 for all distinct measurements among these groups except for those of RMT, where ICC varied between 0.47 and 0.96. The RMT ratio shows a constant ICC at 0.94 regardless of the group.

Conclusion
The post-cesarean uterus is often anteflexed, and a myometrial loss of about 50% is normally expected. The pattern of this loss is in the form of a predominantly sharp-edged and echogenic niche, fibrosis, or a combination of both. The proposed RMT ratio takes these changes into consideration and results in a reproducible quantification. We hypothesize that different adverse outcomes could be attributed to the different scar patterns.
Untangling the relationship between negative illness perceptions and worse quality of life in patients with advanced cancer—a study from the population-based PROFILES registry
Authors: Jabbarian Lea J. , Rietjens Judith A. C. , Mols Floortje , Oude Groeniger Joost , van der Heide Agnes , Korfage Ida J 
Published: April 2021

Abstract
Purpose
Quality of life (QoL) is an important yet complex outcome of care in patients with advanced cancer. QoL is associated with physical and psychosocial symptoms and with patients’ illness perceptions (IPs). IPs are modifiable cognitive constructs developed to make sense of one’s illness. It is unclear how IPs influence patients’ QoL. A better understanding of this relationship can inform and direct high quality care aimed at improving patients’ QoL. We therefore investigated the mediating role of anxiety and depression in the association of IPs with QoL.

Methods
Data from 377 patients with advanced cancer were used from the PROFILES registry. Patients completed measures on IPs (BIPQ), QoL (EORTC QLQ-C30), and symptoms of anxiety and depression (HADS). Mediation analyses were conducted to decompose the total effect of IPs on QoL into a direct effect and indirect effect.

Results
All IPs but one (“Comprehensibility”) were negatively associated with QoL (p<0.001); patients with more negative IPs tended to have worse QoL. The effect was strongest for patients who felt that their illness affected their life more severely (“Consequences”), patients who were more concerned about their illness (“Concern”), and patients who thought that their illness strongly affected them emotionally (“Emotions”). Anxiety mediated 41–87% and depression mediated 39–69% of the total effect of patients’ IPs on QoL.

Conclusion
Negative IPs are associated with worse QoL. Anxiety and depression mediate this association. Targeting symptoms of anxiety and depression, through the modification of IPs, has the potential to improve QoL of patients with advanced cancer.
Automatically evaluating the quality of textual descriptions in cultural heritage records
Authors: Lorenzini Matteo , Rospocher Marco , Tonelli Sara 
Published: April 2021

AbstractMetadata are fundamental for the indexing, browsing and retrieval of cultural heritage resources in repositories, digital libraries and catalogues. In order to be effectively exploited, metadata information has to meet some quality standards, typically defined in the collection usage guidelines. As manually checking the quality of metadata in a repository may not be affordable, especially in large collections, in this paper we specifically address the problem of automatically assessing the quality of metadata, focusing in particular on textual descriptions of cultural heritage items. We describe a novel approach based on machine learning that tackles this problem by framing it as a binary text classification task aimed at evaluating the accuracy of textual descriptions. We report our assessment of different classifiers using a new dataset that we developed, containing more than 100K descriptions. The dataset was extracted from different collections and domains from the Italian digital library “Cultura Italia” and was annotated with accuracy information in terms of compliance with the cataloguing guidelines. The results empirically confirm that our proposed approach can effectively support curators (F1$$\sim $$∼ 0.85) in assessing the quality of the textual descriptions of the records in their collections and provide some insights into how training data, specifically their size and domain, can affect classification performance.
Geographical Python Teaching Resources: geopyter
Authors: Reades Jonathan , Rey Sergio J. 
Published: April 2021

Abstractgeopyter, an acronym of Geographical Python Teaching Resources, provides a hub for the distribution of ‘best practice’ in computational and spatial analytic instruction, enabling instructors to quickly and flexibly remix contributed content to suit their needs and delivery framework and encouraging contributors from around the world to ‘give back’ whether in terms of how to teach individual concepts or deliver whole courses. As such, geopyter is positioned at the confluence of two powerful streams of thought in software and education: the free and open-source software movement in which contributors help to build better software, usually on an unpaid basis, in return for having access to better tools and the recognition of their peers); and the rise of Massive Open Online Courses, which seek to radically expand access to education by moving course content online and providing access to students anywhere in the world at little or no cost. This paper sets out in greater detail the origins and inspiration for geopyter, the design of the system and, through examples, the types of innovative workflows that it enables for teachers. We believe that tools like geopyter, which build on open teaching practices and promote the development of a shared understanding of what it is to be a computational geographer represent an opportunity to expand the impact of this second wave of innovation in instruction while reducing the demands placed on those actively teaching in this area.
A hybrid data envelopment analysis—artificial neural network prediction model for COVID-19 severity in transplant recipients
Authors: Revuelta Ignacio , Santos-Arteaga Francisco J. , Montagud-Marrahi Enrique , Ventura-Aguiar Pedro , Di Caprio Debora , Cofan Frederic , Cucchiari David , Torregrosa Vicens , Piñeiro Gaston Julio , Esforzado Nuria , Bodro Marta , Ugalde-Altamirano Jessica , Moreno Asuncion , Campistol Josep M. , Alcaraz Antonio , Bayès Beatriu , Poch Esteban , Oppenheimer Federico , Diekmann Fritz 
Published: April 2021

AbstractIn an overwhelming demand scenario, such as the SARS-CoV-2 pandemic, pressure over health systems may outburst their predicted capacity to deal with such extreme situations. Therefore, in order to successfully face a health emergency, scientific evidence and validated models are needed to provide real-time information that could be applied by any health center, especially for high-risk populations, such as transplant recipients. We have developed a hybrid prediction model whose accuracy relative to several alternative configurations has been validated through a battery of clustering techniques. Using hospital admission data from a cohort of hospitalized transplant patients, our hybrid Data Envelopment Analysis (DEA)—Artificial Neural Network (ANN) model extrapolates the progression towards severe COVID-19 disease with an accuracy of 96.3%, outperforming any competing model, such as logistic regression (65.5%) and random forest (44.8%). In this regard, DEA-ANN allows us to categorize the evolution of patients through the values of the analyses performed at hospital admission. Our prediction model may help guiding COVID-19 management through the identification of key predictors that permit a sustainable management of resources in a patient-centered model.
Genetic testing results in Slovenian male breast cancer cohort indicate the BRCA2 7806-2A > G founder variant could be associated with higher male breast cancer risk
Authors: Strojnik Ksenija , Krajc Mateja , Dragos Vita Setrajcic , Stegel Vida , Novakovic Srdjan , Blatnik Ana 
Published: April 2021

Abstract
Purpose
To analyze the prevalence of pathogenic/likely pathogenic variants (P/LPVs) in BRCA1 and BRCA2 genes in the largest cohort of Slovenian male breast cancer (MBC) patients to date and to explore a possible correlation between the Slovenian founder variant BRCA2:c.7806-2A > G and predisposition to MBC.

Methods
We performed a retrospective analysis of 81 MBC cases who underwent genetic counseling and/or testing between January 1999 and May 2020. To explore a possible genotype–phenotype correlation, we performed additional analyses of 203 unrelated families with P/LPVs in BRCA2 and 177 cases of female breast cancer (FBC) in carriers of P/LPVs in BRCA2.

Results
Detection rate of P/LPVs in the BRCA1 and BRCA2 genes was 24.7% (20/81) with 95% of them in BRCA2 gene. The only two recurrent P/LPVs were BRCA2:c.7806-2A > G and BRCA2:c.3975_3978dupTGCT (9 and 5 MBC cases, respectively). In families with BRCA2:c.7806-2A > G, the incidence of MBC cases was higher compared to families with other P/LPVs in BRCA2; however, the difference did not reach statistical significance (17.8% vs. 8.9%, p = 0.105). BRCA2:c.7806-2A > G was detected in both families with multiple cases of MBC. This splice-site variant represented a significantly higher proportion of all BRCA2 P/LPVs detected in MBC carriers compared to FBC carriers (47.4% vs. 26%, p = 0.049).

Conclusion
We observed a high mutation detection rate and conclude this may be due to the prevalent BRCA2:c.7806-2A > G variant in Slovenia. Our results indicate a possible association between this variant and higher risk of breast cancer in males compared to other identified P/LPVs in BRCA2.
Peddling promise? An analysis of private umbilical cord blood banking company websites in Canada
Authors: Marcon Alessandro R. , Murdoch Blake , Caulfield Timothy 
Published: April 2021

AbstractPrivate umbilical cord blood banking is growing around the world. A family’s decision to bank cord blood publicly or privately can be influenced by numerous sources including healthcare practitioners, personal networks, the popular press, social media and marketing discourse from private entities. Issues have been raised concerning how private banks market their services, particularly with regards to the likelihood of use and for what purposes cord blood can be used. The objective of this study was to analyze the marketing on the seven company websites offering private cord blood storage in Canada. We performed a mix of content and general qualitative analysis on the seven websites. Our analysis shows substantial hype around cord blood uses, amplifying the promise of speculative uses and distorting the likelihood of use. Findings show that this promotional messaging often deploys communication strategies which draw on testimonials and emotionally-charged narratives. Questions should be asked about whether the promissory aspects of these websites constitute breaches of Canadian law or regulation. Careful monitoring of the private cord blood space is important for ensuring that the Canadian public is adequately and accurately informed of the services being offered.
A deep study of the high–energy transient sky
Authors: Guidorzi C. , Frontera F. , Ghirlanda G. , Stratta G. , Mundell C. G. , Virgilli E. , Rosati P. , Caroli E. , Amati L. , Pian E. , Kobayashi S. , Ghisellini G. , Fryer C. , Valle M. Della , Margutti R. , Marongiu M. , Martone R. , Campana R. , Fuschino F. , Labanti C. , Orlandini M. , Stephen J. B. , Brandt S. , Silva R. Curado da , Laurent P. , Mochkovitch R. , Bozzo E. , Ciolfi R. , Burderi L. , Di Salvo T. 
Published: April 2021

AbstractThe coming decades will establish the exploration of the gravitational wave (GW) Universe over a broad frequency range by ground and space interferometers. Meanwhile, wide-field, high-cadence and sensitive surveys will span the electromagnetic spectrum from radio all the way up to TeV, as well as the high-energy neutrino window. Among the numerous classes of transients, γ–ray bursts (GRBs) have direct links with most of the hot topics that will be addressed, such as the strong gravity regime, relativistic shocks, particle acceleration processes, equation of state of matter at nuclear density, and nucleosynthesis of heavy elements, just to mention a few. Other recently discovered classes of transients that are observed throughout cosmological distances include fast radio bursts (FRBs), fast blue optical transients (FBOTs), and other unidentified high-energy transients. Here we discuss how these topics can be addressed by a mission called ASTENA (Advanced Surveyor of Transient Events and Nuclear Astrophysics, see Frontera et al. 18). Its payload combines two instruments: (i) an array of wide-field monitors with imaging, spectroscopic, and polarimetric capabilities (WFM-IS); (ii) a narrow field telescope (NFT) based on a Laue lens operating in the 50–600 keV range with unprecedented angular resolution, polarimetric capabilities, and sensitivity.