bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinatorial Algorithms for String Sanitization
Authors: Bernardini Giulia , Chen Huiping , Conte Alessio , Grossi Roberto , Loukides Grigorios , Pisanti Nadia , Pissis Solon P. , Rosone Giovanna , Sweering Michelle 
Published: December 2020

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge (e.g., trips to mental health clinics from a string representing a user’s location history). In this article, we consider the problem of sanitizing a string by concealing the occurrences of sensitive patterns, while maintaining data utility, in two settings that are relevant to many common string processing tasks.
In the first setting, we aim to generate the minimal-length string that preserves the order of appearance and frequency of all non-sensitive patterns. Such a string allows accurately performing tasks based on the sequential nature and pattern frequencies of the string. To construct such a string, we propose a time-optimal algorithm, TFS-ALGO. We also propose another time-optimal algorithm, PFS-ALGO, which preserves a partial order of appearance of non-sensitive patterns but produces a much shorter string that can be analyzed more efficiently. The strings produced by either of these algorithms are constructed by concatenating non-sensitive parts of the input string. However, it is possible to detect the sensitive patterns by “reversing” the concatenation operations. In response, we propose a heuristic, MCSR-ALGO, which replaces letters in the strings output by the algorithms with carefully selected letters, so that sensitive patterns are not reinstated, implausible patterns are not introduced, and occurrences of spurious patterns are prevented. In the second setting, we aim to generate a string that is at minimal edit distance from the original string, in addition to preserving the order of appearance and frequency of all non-sensitive patterns. To construct such a string, we propose an algorithm, ETFS-ALGO, based on solving specific instances of approximate regular expression matching.
We implemented our sanitization approach that applies TFS-ALGO, PFS-ALGO, and then MCSR-ALGO, and experimentally show that it is effective and efficient. We also show that TFS-ALGO is nearly as effective at minimizing the edit distance as ETFS-ALGO, while being substantially more efficient than ETFS-ALGO.
Genetic Variants Associated with Therapy-Related Cardiomyopathy among Childhood Cancer Survivors of African Ancestry
Authors: Sapkota Yadav , Qin Na , Ehrhardt Matthew J. , Wang Zhaoming , Chen Yan , Wilson Carmen L. , Estepp Jeremie , Rai Parul , Hankins Jane S. , Burridge Paul W. , Jefferies John L. , Zhang Jinghui , Hudson Melissa M. , Robison Leslie L. , Armstrong Gregory T. , Mulrooney Daniel A. , Yasui Yutaka 
Published: December 2020

AbstractCardiomyopathy occurs at significantly higher rates in survivors of childhood cancer than the general population, but few studies have evaluated racial or ethnic disparities, and none have assessed potential genetic factors contributing to this outcome. In this study, childhood cancer survivors of African ancestry exposed to cardiotoxic therapies (anthracyclines and/or heart radiotherapy; n = 246) were compared with cardiotoxic-exposed survivors of European ancestry (n = 1,645) in the St. Jude Lifetime Cohort. Genetic variants were examined using whole-genome sequencing data among survivors of African ancestry, first based on ejection fraction (EF) as a continuous outcome, followed by clinical history of cardiomyopathy. Survivors of African ancestry showed 1.53- and 2.47-fold risks of CTCAE grade 2–4 and grade 3–4 cardiomyopathy than survivors of European ancestry. A novel locus at 1p13.2 showed significant association with EF (rs6689879*C: EF reduction = 4.2%; P = 2.8 × 10−8) in 246 survivors of African ancestry, which was successfully replicated in 1,645 survivors of European ancestry but with attenuated magnitude (EF reduction = 0.4%; P = 0.042). In survivors of African ancestry, rs6689879*C showed a 5.43-fold risk of cardiomyopathy and 1.31-fold risk in those of European ancestry. Among survivors of African ancestry with rs6689879*C and CTCAE grade 2–4 cardiomyopathy, the PHTF1 promoter region was hypomethylated. Similar results were observed in survivors of European ancestry, albeit with reduced magnitudes of hypomethylation among those with rs6689879*C and CTCAE grade 2–4 cardiomyopathy. PHTF1 was upregulated in human-induced pluripotent stem cell-derived cardiomyocytes from patients with doxorubicin-induced cardiomyopathy. These findings have potential implications for long-term cardiac surveillance and up-front cancer care for patients of African ancestry.Significance:Childhood cancer survivors of African ancestry are at higher risk of cardiomyopathy than those of European ancestry, and a novel locus at 1p13.2 is associated with therapy-related cardiomyopathy specifically in African-American survivors.See related commentary by Brown and Richard, p. 2272
Early-Life and Adult Adiposity, Adult Height, and Benign Breast Tissue Composition
Authors: Oh Hannah , Yaghjyan Lusine , Austin-Datta Rebecca J. , Heng Yujing J. , Baker Gabrielle M. , Sirinukunwattana Korsuk , Vellal Adithya D. , Collins Laura C. , Murthy Divya , Eliassen A. Heather , Rosner Bernard A. , Tamimi Rulla M. 
Published: December 2020

Abstract

Background:
Early-life and adult anthropometrics are associated with breast density and breast cancer risk. However, little is known about whether these factors also influence breast tissue composition beyond what is captured by breast density among women with benign breast disease (BBD).

Methods:
This analysis included 788 controls from a nested case–control study of breast cancer within the Nurses' Health Study BBD subcohorts. Body fatness at ages 5 and 10 years was recalled using a 9-level pictogram. Weight at age 18, current weight, and height were reported via questionnaires. A deep-learning image analysis was used to quantify the percentages of epithelial, fibrous stromal, and adipose tissue areas within BBD slides. We performed linear mixed models to estimate beta coefficients (β) and 95% confidence intervals (CI) for the relationships between anthropometrics and the log-transformed percentages of individual tissue type, adjusting for confounders.

Results:
Childhood body fatness (level ≥ 4.5 vs. 1), BMI at age 18 (≥23 vs. &lt;19 kg/m2), and current adult BMI (≥30 vs. &lt;21 kg/m2) were associated with higher proportions of adipose tissue [β (95% CI) = 0.34 (0.03, 0.65), 0.19 (−0.04–0.42), 0.40 (0.12, 0.68), respectively] and lower proportions of fibrous stromal tissue [−0.05 (−0.10, 0.002), −0.03 (−0.07, 0.003), −0.12 (−0.16, −0.07), respectively] during adulthood (all Ptrend &lt; 0.04). BMI at age 18 was also inversely associated with epithelial tissue (Ptrend = 0.03). Adult height was not associated with any of the individual tissue types.

Conclusions:
Our data suggest that body fatness has long-term impacts on breast tissue composition.

Impact:
This study contributes to our understanding of the link between body fatness and breast cancer risk.
See related commentary by Oskar et al., p. 590
Phosphorylation and Driver Mutations in PI3Kα and PTEN Autoinhibition
Authors: Nussinov Ruth , Zhang Mingzhen , Tsai Chung-Jung , Jang Hyunbum 
Published: December 2020

Abstract
PI3K and PTEN are the second and third most highly mutated proteins in cancer following only p53. Their actions oppose each other. PI3K phosphorylates signaling lipid PIP2 to PIP3. PTEN dephosphorylates it back. Driver mutations in both proteins accrue PIP3. PIP3 recruits AKT and PDK1 to the membrane, promoting cell-cycle progression. Here we review phosphorylation events and mutations in autoinhibition in PI3K and PTEN from the structural standpoint. Our purpose is to clarify how they control the autoinhibited states. In autoinhibition, a segment or a subunit of the protein occludes its functional site. Protein–protein interfaces are often only marginally stable, making them sensitive to changes in conditions in living cells. Phosphorylation can stabilize or destabilize the interfaces. Driver mutations commonly destabilize them. In analogy to “passenger mutations,” we coin “passenger phosphorylation” to emphasize that the presence of a phosphorylation recognition sequence logo does not necessarily imply function. Rather, it may simply reflect a statistical occurrence. In both PI3K and PTEN, autoinhibiting phosphorylation events are observed in the occluding “piece.” In PI3Kα, the “piece” is the p85α subunit. In PTEN, it is the C-terminal segment. In both enzymes the stabilized interface covers the domain that attaches to the membrane. Driver mutations that trigger rotation of the occluding piece or its deletion prompt activation. To date, both enzymes lack specific, potent drugs. We discuss the implications of detailed structural and mechanistic insight into oncogenic activation and how it can advance allosteric precision oncology.
Site-Level Variability in 30-Day Patient Outcomes After Transcatheter Mitral Valve Repair in the United States
Authors: Malik Ali O. , Chhatriwalla Adnan K. , Saxon John , Hejjaji Vittal , Stebbins Amanda , Jones Philip G. , Cohen David J. , Arnold Suzanne V. , Vemulapalli Sreekanth , Wegermann Zachary K. , Kosinski Andrzej , Spertus John A. 
Published: December 2020

Background:
Clinical trials have demonstrated health status benefit of transcatheter mitral valve repair (TMVr) with MitraClip in patients with mitral valve regurgitation. Real-world site-level variability in health status outcomes for TMVr, and factors associated with this variability, are unknown.

Methods:

All patients undergoing TMVr procedure with MitraClip between November 2013 and March 2019 in the Transcatheter Valve Therapy Registry were included. Health status was measured at baseline and 30 days with the Kansas City Cardiomyopathy Questionnaire (KCCQ) Overall Summary (OS) score. Site-level variability in 30-day change in KCCQ-OS was examined by calculating the median odds ratio from a hierarchical logistic regression model, with ≥20-point improvement as the dependent variable. To define the extent to which patient characteristics, procedural characteristics (residual mitral valve regurgitation, periprocedural bleeding), site volume, and patients’ baseline health status accounted for variability in outcomes, the proportion of variability (
R

2

) explained by sequentially adding these variables to the model was quantified.

Results:

Across 339 sites, 12 415 patients (mean age 79.0±9.5 years, 46.1%. females, 89.5% White) completed baseline and 30-day health status assessments. Mean KCCQ-OS score was 43.0±24.4 at baseline and 67.0±24.9 at 30-day follow-up. Across sites, the proportion of patients achieving a ≥20-point improvement in KCCQ-OS ranged from 12.5% to 100% and the adjusted median odds ratio was 1.58 (95% CI, 1.46–1.69). The greatest contribution to the variability in health status outcomes was from patients’ baseline KCCQ-OS score (
R

2

=25%) with <1% of the variability explained by patient and procedural characteristics, and annual site volume.

Conclusions:
There is moderate variation across sites in their patients’ achievement of health status benefits from TMVr, with patient’s baseline health status accounting for the largest proportion of this variation. This underscores the importance of patient selection in supporting more consistent health status benefit from TMVr.
The Effect of Social Information Use Without Learning on the Evolution of Social Behavior
Authors: Borg James M. , Channon Alastair 
Published: December 2020

Abstract
In a recent article by Borg and Channon it was shown that social information alone, decoupled from any within-lifetime learning, can result in improved performance on a food-foraging task compared to when social information is unavailable. Here we assess whether access to social information leads to significant behavioral differences both when access to social information leads to improved performance on the task, and when it does not: Do any behaviors resulting from social information use, such as movement and increased agent interaction, persist even when the ability to discriminate between poisonous and non-poisonous food is no better than when social information is unavailable? Using a neuroevolutionary artificial life simulation, we show that social information use can lead to the emergence of behaviors that differ from when social information is unavailable, and that these behaviors act as a promoter of agent interaction. The results presented here suggest that the introduction of social information is sufficient, even when decoupled from within-lifetime learning, for the emergence of pro-social behaviors. We believe this work to be the first use of an artificial evolutionary system to explore the behavioral consequences of social information use in the absence of within-lifetime learning.
A Thermodynamic Perspective on Steady-State Tropical Cyclones
Authors: Rousseau-Rizzi Raphaël , Rotunno Richard , Bryan George 
Published: December 2020

AbstractTheories for the maximum intensity of tropical cyclones (TCs) assume steady state. However, many TCs in simulations that run for tens of days tend to decay considerably from an early steady state in the core (CS), before stabilizing at a final equilibrium steady state (ES). This decay raises the question of whether CS or ES should be used as a comparison to the maximum intensity theories. To understand the differences between CS and ES, we investigate why TCs decay and attempt to simulate a TC with steady intensity over a 100-day period. Using the axisymmetric Cloud Model 1, we find that the CS TC decay is due to a large-scale drying of the subsidence region. Such a drying is very pronounced in axisymmetric models because shallow-to-midlevel convection is not represented accurately enough to moisten air in the subsidence region. Simulations with an added moisture relaxation term in the subsidence region and dry cyclones without any moisture both remain in a steady state for over 100 days, without decaying appreciably after the spinup period. These simulations indicate that the decay in TC simulations is due to the irreversible removal of precipitation combined with the lack of a moistening mechanism in the subsidence region. Once either of these conditions is removed, the decay disappears and the CS and ES intensities become essentially equivalent.
Households with unimproved water sources in Ethiopia: spatial variation and point-of-use treatment based on 2016 Demographic and Health Survey
Authors: Damtew Yohannes Tefera , Geremew Abraham 
Published: December 2020

Abstract
Background
Improved water sources are not equally available in all geographical regions. Populations dependent on unsafe water sources are recommended to treat their water at point-of-use using adequate methods to reduce associated health problems. In Ethiopia, the spatial distribution of households using unimproved water sources have been incomplete or ignored in most of the studies. Moreover, evidence on the point-of-use water treatment practice of households dependent on such water sources is scarce. Therefore, the current study is intended to analyze the spatial distribution of unimproved water sources by wealth quintiles at country level and point-of-use treatment (POU) practices using nationally representative data.

Method
The data of 2016 Ethiopian Demographic and Health Survey (EDHS) conducted on 16650 households from 643 clusters were used for the analysis. For spatial analysis, the raw and spatially smoothed coverage data was joined to the geographic coordinates based on EDHS cluster identification code. Global spatial autocorrelation was performed to analyze whether the pattern of unimproved water coverage is clustered, dispersed, or random across the study areas. Once a positive global autocorrelation was confirmed, a local spatial autocorrelation analysis was applied to detect local clusters. The POU water treatment is analyzed based on reported use of either boiling, chlorine (bleach), filtration, or solar disinfection (SODIS).

Results
There were 5005 households using unimproved water sources for drinking purposes. Spatial variation of unimproved water coverage was observed with high coverage observed at Amhara, Afar, Southern Nations Nationalities and People and Somalia regions. Disparity in unimproved water coverage between wealth quintiles was also observed. The reported point-of-use water treatment practice among these households is only 6.24%. The odds of POU water treatment among household heads with higher education status is 2.5 times higher (95% CI = 1.43-4.36) compared to those who did not attend education.

Conclusion
An apparent clustering trend with high unimproved water coverage was observed between regions and among wealth quintiles hence indicates priority areas for future resource allocation and the need for regional and national policies to address the issue. Promoting households to treat water prior to drinking is essential to reduce health problems.
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Authors: Canzler Sebastian , Hackermüller Jörg 
Published: December 2020

AbstractBackgroundGaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods. A plethora of different tools and algorithms have been developed so far. Among those, the gene set enrichment analysis (GSEA) proved to control both type I and II errors well. In recent years the call for a combined analysis of multiple omics layers became prominent, giving rise to a few multi-omics enrichment tools. Each of these has its own drawbacks and restrictions regarding its universal application.ResultsHere, we present the package aiding to calculate a combined GSEA-based pathway enrichment on multiple omics layers. The package queries 8 different pathway databases and relies on the robust GSEA algorithm for a single-omics enrichment analysis. In a final step, those scores will be combined to create a robust composite multi-omics pathway enrichment measure. supports 11 different organisms and includes a comprehensive mapping of transcripts, proteins, and metabolite IDs.ConclusionsWith we introduce a highly versatile tool for multi-omics pathway integration that minimizes previous restrictions in terms of omics layer selection, pathway database availability, organism selection and the mapping of omics feature identifiers. is publicly available under the GPL-3 license athttps://github.com/yigbt/multiGSEAand at bioconductor:https://bioconductor.org/packages/multiGSEA.
Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa)
Authors: Li Jun , Zhou Yinyin , Zhou Zihua , Lin Chuanxu , Wei Jinkuan , Qin Yanpin , Xiang Zhiming , Ma Haitao , Zhang Yang , Zhang Yuehuan , Yu Ziniu 
Published: December 2020

Abstract
Background
Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mechanisms underlying gonad development and gametogenesis remain unclear in Tridacna squamosa, a large-size bivalve of great ecological value. They are protandrous simultaneous hermaphrodites, with the male gonad maturing first, eventually followed by the female gonads. In this study, nine gonad libraries representing resting, male and hermaphrodite stages in T. squamosa were performed to identify the molecular mechanisms.

Results
Sixteen thousand four hundred ninety-one unigenes were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 5091 and 7328 unigenes were assigned to Gene Ontology categories and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database, respectively. A total of 4763 differentially expressed genes (DEGs) were identified by comparing male to resting gonads, consisting of 3499 which were comparatively upregulated in males and 1264 which were downregulated in males. Six hundred-ninteen DEGs between male and hermaphroditic gonads were identified, with 518 DEGs more strongly expressed in hermaphrodites and 101 more strongly expressed in males. GO (Gene Ontology) and KEGG pathway analyses revealed that various biological functions and processes, including functions related to the endocrine system, oocyte meiosis, carbon metabolism, and the cell cycle, were involved in regulating gonadal development and gametogenesis in T. squamosa. Testis-specific serine/threonine kinases 1 (TSSK1), TSSK4, TSSK5, Doublesex- and mab-3-related transcription factor 1 (DMRT1), SOX, Sperm surface protein 17 (SP17) and other genes were involved in male gonadal development in Tridacna squamosal. Both spermatogenesis- (TSSK4, spermatogenesis-associated protein 17, spermatogenesis-associated protein 8, sperm motility kinase X, SP17) and oogenesis-related genes (zona pellucida protein, Forkhead Box L2, Vitellogenin, Vitellogenin receptor, 5-hydroxytryptamine, 5-hydroxytryptamine receptor) were simultaneously highly expressed in the hermaphroditic gonad to maintain the hermaphroditism of T. squamosa.

Conclusion
All these results from our study will facilitate better understanding of the molecular mechanisms underlying giant clam gonad development and gametogenesis, which can provided a base on obtaining excellent gametes during the seed production process for giant clams.
Standardization of an LNA-based TaqMan assay qPCR analysis for Aspiculuris tetraptera DNA in mouse faeces
Authors: Isayama Keishiro , Watanabe Kenji , Okamoto Mariko , Murata Tomoaki , Mizukami Yoichi 
Published: December 2020

Abstract
Background
Aspiculuris tetraptera, as a parasitic pinworm, is most frequently detected in laboratory mice, and transmission is mediated by the eggs contained in the faeces of infected mice. A highly sensitive and quantitative faeces-based diagnostic tool would be useful for the early detection of A. tetraptera to inhibit the expansion of infection. In this study, we developed a quantitative assay that exhibits high sensitivity in detecting A. tetraptera in faeces using PCR techniques.

Results
Endpoint PCR demonstrated the detection of A. tetraptera DNA in 0.5 ng genomic DNA extracted from the faeces of infected mice. To quantitatively detect the small amount of A. tetraptera DNA, locked nucleic acid (LNA)-based primers and LNA-based TaqMan probes were used for the quantitative PCR assay (qPCR). The combination of LNA-based DNA increased detection sensitivity by more than 100-fold compared to using normal oligo DNAs. The copy number of the A. tetraptera DNA detected was positively related to the infected faeces-derived genomic DNA with a simple linearity regression in the range of 20 pg to 15 ng of the genomic DNA. To more conveniently detect infection using faeces, the LNA-based TaqMan assay was applied to the crude fraction of the faeces without DNA purification. An assay using ethanol precipitation of the faeces yielded results consistent with those of direct microscopic observation.

Conclusion
The LNA-TaqMan assay developed in this study quantitatively detects A. tetraptera infection in mouse faeces.