bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerating Adolescent Vocabulary Growth: Development of an Individualized, Web-Based, Vocabulary Instruction Program
Authors: Adlof Suzanne M. , Baron Lauren S. , Scoggins Joanna , Kapelner Adam , McKeown Margaret G. , Perfetti Charles A. , Miller Elaine , Soterwood Jeanine , Petscher Yaacov 
Published: October 2019

Purpose
Improving vocabulary knowledge is important for many adolescents, but there are few evidence-based vocabulary instruction programs available for high school students. The purpose of this article is to describe the iterative development of the DictionarySquared research platform, a web-based vocabulary program that provides individualized vocabulary instruction, and to report the results of 2 pilot studies examining the feasibility of implementation and potential effectiveness with high school students.

Method
We describe our theory of change and 5 phases of iterative development. In Phases 1 and 2, we evaluated the initial implementation of DictionarySquared and revised the instructional materials. In Phase 3, we conducted a feasibility study involving 169 high school students who used the program for 4 weeks. Student usage data and feedback from teachers were used to guide program revisions in Phase 4. In Phase 5, we examined potential effectiveness for 264 high school students who were assigned to use the program for 1 semester.

Results
Results of the Phase 3 study indicated that implementation of the program was feasible, although usage was below assigned levels. Results of the Phase 5 study indicated that the duration of active program usage significantly predicted posttest vocabulary scores on the proximal assessment after controlling for pretest standardized vocabulary scores. Analyses using propensity score matching revealed positive, but nonsignificant, gains on standardized assessments between pre- and posttests.

Conclusion
Together, the results of early-stage pilot studies are promising and suggest that a more rigorous test of efficacy is warranted. Successful implementation of the DictionarySquared research program, as well as lessons learned from the program development process, will expand the range of evidence-based treatment options that clinicians and educators can use to improve adolescent vocabulary and reading comprehension skills.

Supplemental Material

https://doi.org/10.23641/asha.9765161
Pyridox(am)ine 5′-Phosphate Oxidase Deficiency: Severe Prenatal Presentation with Hypoxic Ischemic Encephalopathy
Authors: Alghamdi Malak , Arold Stefan T. , Hasan Hamdi , Bashiri Fahad 
Published: October 2019

AbstractPyridox(am)ine 5′-phosphate oxidase (PNPO) deficiency is a rare autosomal recessive vitamin-responsive epileptic encephalopathy that manifests with a clinically and electrographically observable antiepileptic response to pyridoxine or pyridoxal 5′-phosphate (P5P). We report a preterm infant who presented with fetal distress and hypoxic ischemic encephalopathy (HIE) as well as seizures that responded to pyridoxine in the first day of life. The patient was diagnosed with PNPO deficiency and homozygosity for a missense-mutation in exon 7 of the PNPO gene, c.673 c > T (Arg225Cys), which disrupts the P5P binding site on PNPO. P5P with folinic acid achieved good control of the seizures. Riboflavin was introduced in the second year of life. The patient continued to have episodes of breakthrough seizures with sickness. P5P therapy resulted in marked seizure cessation but did not improve neurocognitive function in this patient, who had significant global psychomotor delay at the age of 3 years despite early treatment. We conclude from this report and other reports that HIE is a co-occurring condition with some inborn errors of metabolism. Therefore, PNPO deficiency should be investigated and P5P trial should be considered in case of presumed HIE particularly with familial recurrence of epileptic encephalopathy and refractory seizure.
Convergence analysis of (statistical) inverse problems under conditional stability estimates
Authors: Werner Frank , Hofmann Bernd 
Published: October 2019

Abstract
Conditional stability estimates require additional regularization for obtaining stable approximate solutions if the validity area of such estimates is not completely known. In this context, we consider ill-posed nonlinear inverse problems in Hilbert scales satisfying conditional stability estimates characterized by general concave index functions. For that case, we exploit Tikhonov regularization and provide convergence and convergence rates of regularized solutions for both deterministic and stochastic noise. We further discuss a priori and a posteriori parameter choice rules and illustrate the validity of our assumptions in different model and real world situations.
Revisiting assessments of ecosystem drought recovery
Authors: Liu Laibao , Gudmundsson Lukas , Hauser Mathias , Qin Dahe , Li Shuangcheng , Seneviratne Sonia I 
Published: October 2019

Abstract
The time taken for ecosystems to recover from drought (drought recovery time) is critically important for the ecosystem state. However, recent literature presents contradictory conclusions on this feature: one study concludes that drought recovery time in the tropics and high northern latitudes is shortest (<4 months) but another concludes that it is longest (>12 months) in these regions. Here we explore the reasons for these contradictory results and revisit assessments of drought recovery time. We find that the study period, drought identification method and recovery level definition are main factors contributing to the contradictory conclusions. Further, we emphasize that including droughts that did not decrease ecosystem production or using a period of abnormal water availability to define ecosystem recovery level can strongly bias drought recovery time estimates. Based on our refined methods, we find the drought recovery time is also longest in some tropical regions but not in high northern latitudes during 1901–2010. Our study helps to resolve the recent controversy and provides insight for future drought recovery assessments.
Changes in the trends of vegetation net primary productivity in China between 1982 and 2015
Authors: Feng Yuhao , Zhu Jianxiao , Zhao Xia , Tang Zhiyao , Zhu Jiangling , Fang Jingyun 
Published: October 2019

Abstract
China has been experiencing significant climate and land use changes over the past decades. The way in which these changes, particularly a warming hiatus and national ecological restoration projects that occurred almost concurrently in the late 1990s, have influenced vegetation net primary productivity (NPP), is not well documented. Here, we estimated annual and seasonal changes in China’s NPP between 1982 and 2015 using the Carnegie-Ames-Stanford Approach model and examined their shifting years (SHYs) caused by the switch in climatic factors and the restoration projects. Our analyses revealed that the growth of annual, spring and summer NPP stalled in 1997 or 1998, while the trend of autumn NPP increased in 1992 at the national scale. We also showed that the changes in the NPP trends were more sensitive to the warming hiatus in spring and autumn, as well as in the temperate monsoonal region and the Tibetan Plateau, while the larger trend of autumn NPP in eastern China after the SHY was strongly coupled with increased monsoonal precipitation. Although the starting years of the restoration projects were partially consistent with the SHYs of the NPP trends, the projects were likely playing minor roles in enhancing NPP increase. Our findings can be applied for ecological risk assessment and future management of ecological restoration projects in the context of global change.
Shorebird feeding specialists differ in how environmental conditions alter their foraging time
Authors: van der Kolk Henk-Jan , Ens Bruno J , Oosterbeek Kees , Bouten Willem , Allen Andrew M , Frauendorf Magali , Lameris Thomas K , Oosterbeek Thijs , Deuzeman Symen , de Vries Kelly , Jongejans Eelke , van de Pol Martijn 
Published: October 2019

AbstractFeeding specialization is a common cause of individual variation. Fitness payoffs of specialization vary with environmental conditions, but the underlying behavioral mechanisms are poorly understood. Such mechanistic knowledge, however, is crucial to reliably predict responses of heterogeneous populations to environmental change. We quantified spatiotemporal allocation of foraging behavior in wintering Eurasian oystercatchers (Haematopus ostralegus), a species in which feeding specialization can be inferred from bill shape. We combined global positioning system (GPS) and accelerometer data to quantify foraging time of 64 individuals for every tidal period in one or two winter seasons. Individuals varied widely in foraging time (3.7–6.5 h per tidal period) and individuals that spend more time foraging had lower inferred survival. Feeding specialization appeared a major determinant of individual variation in foraging time and its spatiotemporal allocation. Visually hunting worm specialists foraged more during day time and complemented intertidal foraging with grassland foraging when the exposure of intertidal flats was limited and nights were well illuminated. Shellfish specialists increased total foraging time in cold weather, whereas foraging time of worm specialists decreased as frosty grasslands became inaccessible. Our results imply that worm specialists may be most sensitive to cold snaps and daytime disturbance, whereas shellfish specialists are most sensitive to high water levels. These behavioral responses can be implemented in population models to predict the vulnerability of heterogeneous populations to environmental change and, thereby, provide a shortcut to long-term population studies that require fitness data across many years and conditions to make similar projections.
Managing batch effects in microbiome data
Authors: Wang Yiwen , LêCao Kim-Anh 
Published: October 2019

Abstract
Microbial communities have been increasingly studied in recent years to investigate their role in ecological habitats. However, microbiome studies are difficult to reproduce or replicate as they may suffer from confounding factors that are unavoidable in practice and originate from biological, technical or computational sources. In this review, we define batch effects as unwanted variation introduced by confounding factors that are not related to any factors of interest. Computational and analytical methods are required to remove or account for batch effects. However, inherent microbiome data characteristics (e.g. sparse, compositional and multivariate) challenge the development and application of batch effect adjustment methods to either account or correct for batch effects. We present commonly encountered sources of batch effects that we illustrate in several case studies. We discuss the limitations of current methods, which often have assumptions that are not met due to the peculiarities of microbiome data. We provide practical guidelines for assessing the efficiency of the methods based on visual and numerical outputs and a thorough tutorial to reproduce the analyses conducted in this review.
Mat_peptide: comprehensive annotation of mature peptides from polyproteins in five virus families
Authors: Larsen Christopher N , Sun Guangyu , Li Xiaomei , Zaremba Sam , Zhao Hongtao , He Sherry , Zhou Liwei , Kumar Sanjeev , Desborough Vince , Klem Edward B 
Published: October 2019

Abstract

Motivation
Sequence repositories have few well-annotated virus mature peptide sequences. Therefore post-translational proteolytic processing of polyproteins into mature peptides (MPs) has been performed in silico, with a new computational method, for over 200 species in 5 pathogenic virus families (Caliciviridae, Coronaviridae, Flaviviridae, Picornaviridae and Togaviridae).

Results
Using pairwise alignment with reference sequences, MPs have been annotated and their sequences made available for search, analysis and download. At publication the method had produced 156 216 sequences, a large portion of the protein sequences now available in https://www.viprbrc.org. It represents a new and comprehensive mature peptide collection.

Availability and implementation
The data are available at the Virus Pathogen Resource https://www.viprbrc.org, and the software at https://github.com/VirusBRC/vipr_mat_peptide.
Effectiveness of Private and Public High Schools: Evidence from Finland
Authors: Kortelainen Mika , Manninen Kalle 
Published: October 2019

Abstract
A number of papers have compared the effectiveness of private and public schools in different institutional settings. However, most of these studies are observational and do not utilize experimental or quasi-experimental design to evaluate the value-added or the effectiveness of private schools in comparison to public schools. This study focuses on private and public high schools in Helsinki, the capital city of Finland. We use two different methods to compare private and public schools, value-added estimation and regression discontinuity design (RDD). Although based on somewhat different assumptions, both methods allow us to evaluate the causal effect of private schools on the exit exam results in high school. We find that private schools perform marginally better than public schools, but the difference in performance is very small and statistically insignificant according to both methods. Various robustness and validity checks strengthen our RDD results and the validity of the discontinuity design.
TreeExp2: An Integrated Framework for Phylogenetic Transcriptome Analysis
Authors: Yang Jingwen , Ruan Hang , Xu Wenjie , Gu Xun 
Published: October 2019

AbstractRecent innovations of next-generation sequencing such as RNA-seq have generated an enormous amount of comparative transcriptome data, which have shed lights on our understanding of the complexity of transcriptional regulatory systems. Despite numerous RNA-seq analyses, statistical methods and computational tools designed for phylogenetic transcriptome analysis and evolution have not been well developed. In response to this need, we developed software TreeExp2 specifically for RNA-seq data. The R-package TreeExp2 has implemented a suite of advanced, recently developed methods for transcriptome evolutionary analysis. Its main functions include the ancestral transcriptome inference, estimation of the strength of expression conservation, new expression distance, and the relative expression rate test. TreeExp2 provides an integrated, statistically sound framework for phylogenetic transcriptome analysis. It will considerably enhance our analytical capability for exploring the evolution and selection at the transcriptome level. The current version of TreeExp2 is available under GPLv3 license at the Github developer site https://github.com/jingwyang/TreeExp; last accessed November 12, 2019, and its online tutorial which describes the biological theories in details and fully worked case studies with real data can be found at https://jingwyang.github.io/TreeExp-Tutorial; last accessed November 12, 2019.
Redress for Involuntarily Sterilised Trans People in Sweden against Evolving Human Rights Standards: A Critical Appraisal
Authors: Alaattinoğlu Daniela , Rubio-Marín Ruth 
Published: October 2019

Abstract
Involuntary sterilisation is a long-standing practice that has targeted vulnerable and marginalised groups in different historical and geographical contexts. These include transgender and transsexual people who have often had to undergo sterilisation as a requirement for legal gender recognition. During the last decades, the international community has started to recognise involuntary sterilisation as a violation of human rights, with remedial implications flowing from state responsibility. To date, however, no binding remedial human rights standards have been established with reference to trans people specifically. Importantly, in March 2018, the Swedish Parliament approved legislation to compensate sterilised trans people on an ex gratia basis. This article evaluates the new Swedish legislation against developing human rights remedial standards. While pointing out enduring shortcomings, it welcomes the remedial initiative in the Swedish Compensation Act, highlighting the need for equal and coherent international remedial standards concerning involuntarily sterilised persons regardless of their gender identity.
Implementing a hash-based privacy-preserving record linkage tool in the OneFlorida clinical research network
Authors: Bian Jiang , Loiacono Alexander , Sura Andrei , Mendoza Viramontes Tonatiuh , Lipori Gloria , Guo Yi , Shenkman Elizabeth , Hogan William 
Published: October 2019

Abstract

Objective
To implement an open-source tool that performs deterministic privacy-preserving record linkage (RL) in a real-world setting within a large research network.

Materials and Methods
We learned 2 efficient deterministic linkage rules using publicly available voter registration data. We then validated the 2 rules’ performance with 2 manually curated gold-standard datasets linking electronic health records and claims data from 2 sources. We developed an open-source Python-based tool—OneFL Deduper—that (1) creates seeded hash codes of combinations of patients’ quasi-identifiers using a cryptographic one-way hash function to achieve privacy protection and (2) links and deduplicates patient records using a central broker through matching of hash codes with a high precision and reasonable recall.

Results
We deployed the OneFl Deduper (https://github.com/ufbmi/onefl-deduper) in the OneFlorida, a state-based clinical research network as part of the national Patient-Centered Clinical Research Network (PCORnet). Using the gold-standard datasets, we achieved a precision of 97.25∼99.7% and a recall of 75.5%. With the tool, we deduplicated ∼3.5 million (out of ∼15 million) records down to 1.7 million unique patients across 6 health care partners and the Florida Medicaid program. We demonstrated the benefits of RL through examining different disease profiles of the linked cohorts.

Conclusions
Many factors including privacy risk considerations, policies and regulations, data availability and quality, and computing resources, can impact how a RL solution is constructed in a real-world setting. Nevertheless, RL is a significant task in improving the data quality in a network so that we can draw reliable scientific discoveries from these massive data resources.
Development of optimal genetic evaluations for teat and udder structure in Canadian Angus cattle
Authors: Devani Kajal , Valente Tiago S , Crowley John J , Orsel Karin 
Published: October 2019

AbstractDespite their heritability and influence on female productivity, there are currently no genetic evaluations for teat and udder structure in Canadian Angus cattle. The objective of this study was to develop optimal genetic evaluations for these traits in the Canadian Angus population. Guidelines recommended by Beef Improvement Federation (BIF) were used to score teat and udder structure in 1,735 Canadian Angus cows from 10 representative herds. Cows scored ranged in parity from 1 to 13; however, >70% of cows were parity ≤4. Scores ranged from 1 (large, bottle shaped) to 9 (very small) for teats and from 1 (very pendulous) to 9 (very tight) for udders. Consistent with parity distribution, >70% of teat and udder scores were ≥6. Teat and udder scores (TS9 and US9, respectively) were modeled using a multiple trait animal model with random effects of contemporary group (herd-year-season) and additive genetic effect, and fixed effects of breed, parity group, and days between calving and scoring. To test good versus poor structure, a binary classification of 1 or 2 (TS2, US2) [comprised of scores 1 to 5 = 1 (poor structure) and scores 6 to 9 = 2 (good structure)] was created. Further, to assess the impact of grouping less frequently observed poor scores, a 1 to 7 scale (TS7, US7) was created by combining teat and udder scores 1 to 3. Analyses for teat and udder scores on scales TS9, US9, TS7, US7, and TS2, US2 were compared. In addition, both threshold and linear animal models were used to estimate variance components for the traits. Data treatment and models were evaluated based on correlation of resulting estimated breeding value (EBV) with corrected phenotypes, Spearman’s rank correlation coefficient, average EBV accuracies (r), and deviance information criteria (DIC). TS9, US9 scales for teat and udder scores and linear models performed best. Estimates of heritability (SE) for teat and udder score were 0.32 (0.06) and 0.15 (0.04), respectively, indicating these traits were moderately heritable and that genetic improvement for teat and udder scores was possible. Estimates of phenotypic and genotypic correlations for teat and udder score were 0.46 (0.02) and 0.71 (0.09), respectively. Estimates of genotypic correlations with birth weight (BW), weaning weight (WW), and yearling weight (YW), ranged from −0.04 (0.10) to −0.20 (0.12), verifying the importance of selecting for improved teat and udder score as individual traits, alongside performance traits.
Utility of index lesion volume assessed by multiparametric MRI combined with Gleason grade for assessment of lymph node involvement in patients with high-risk prostate cancer
Authors: Hatano Koji , Tanaka Junichiro , Nakai Yasutomo , Nakayama Masashi , Kakimoto Ken-ichi , Nakanishi Katsuyuki , Nishimura Kazuo 
Published: October 2019

Abstract

Purpose
We examined the potential predictors of lymph node involvement and evaluated whether index lesion volume assessed using multiparametric magnetic resonance imaging is associated with lymph node involvement among patients with high-risk prostate cancer.

Methods
Extended pelvic lymph node dissection was used to evaluate patients with lymph node involvement. We retrospectively analyzed consecutive 102 patients with high-risk prostate cancer who underwent extended pelvic lymph node dissection at our institution between 2011 and 2017. To evaluate the index lesion volume at multiparametric magnetic resonance imaging (mrV), lesions were manually contoured on each T2-weighted axial slice in combination with diffusion-weighted and dynamic contrast-enhanced magnetic resonance imaging and integrated using image analysis software. Logistic regression analysis was performed to identify predictors of lymph node involvement.

Results
The median mrV was 1.4 ml (range 0–30.1 ml), and the median number of resected lymph nodes was 14 (range 7–38). Among 102 patients, 28 (28%) had lymph node involvement. Multivariate analysis identified significant predictors of lymph node involvement as follows: biopsy Gleason-grade group 5 (odds ratio = 17.2; 95% confidence interval, 2.1–299.0; P = 0.005), preoperative mrV (odds ratio = 1.14; 95% confidence interval, 1.02–1.30; P = 0.025) and percentage of positive cores with highest Gleason-grade group (odds ratio = 1.05; 95% confidence interval, 1.01–1.10; P = 0.005). Lymph node involvement was prevalent (69%) among tumors with Gleason-grade group 5 and mrV ≥3.4 ml, but was infrequently (10%) present among tumors with Gleason-grade group ≤4 and mrV &lt;3.4 ml.

Conclusions
The combination of biopsy Gleason-grade and mrV may serve as a useful tool to stratify patients according to their risk of nodal metastases.