bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontogenetic changes in cheliped and uropod morphology of the symbiotic shrimp Stenalpheops anacanthus Miya, 1997 (Decapoda: Caridea: Alpheidae): implications for the taxonomy of the genus
Authors: Aldea Kristian Q , Henmi Yumi , Itani Gyo 
Published: May 2021

Abstract
We investigated collections of the alpheid shrimp Stenalpheops Miya, 1997, symbiotic in the burrows of gebiidean and axiidean shrimps, in Tokyo Bay, Japan to clarify ontogenetic changes in the diagnostic morphology of the cheliped and uropod. The uropod flaps were found only among the largest male shrimp, none among females. The number of articles of the uropod flap ranged from one to five, and uropod length was positively correlated with the length of the carapace. Furthermore, no chelae showing a subcheliped shape were found, while the angle of the propodus-pollex decreased with the development of the carapace. Ontogenetic changes in these characters support the view that the male cheliped is normal in S. anacanthus Miya, 1997 (subcheliped in S. crangonus Anker, Jeng & Chan, 2001), and the uropod flap is found only in the large males of S. anacanthus (in both males and females in S. crangonus).
Finding the missing piece of the puzzle: how NMCPs fit into the plant nuclear lamina
Authors: Graumann Katja 
Published: May 2021

This article comments on:Masuda K, Hikida R, Fujino K. 2021. The plant nuclear lamina proteins NMCP1 and NMCP2 form a filamentous network with lateral filament associations. Journal of Experimental Botany 72, 6190–6204.
Deep conservation of ribosome stall sites across RNA processing genes
Authors: Chyżyńska Katarzyna , Labun Kornel , Jones Carl , Grellscheid Sushma N , Valen Eivind 
Published: May 2021

Abstract
The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be transported, while stalling can serve as quality control and trigger degradation of aberrant mRNA and peptide. Ribosome profiling has allowed for the genome-wide detection of such pauses and stalls, but due to library-specific biases, these predictions are often unreliable. Here, we take advantage of the deep conservation of protein synthesis machinery, hypothesizing that similar conservation could exist for functionally important locations of ribosome slowdown, here collectively called stall sites. We analyze multiple ribosome profiling datasets from phylogenetically diverse eukaryotes: yeast, fruit fly, zebrafish, mouse and human to identify conserved stall sites. We find thousands of stall sites across multiple species, with the enrichment of proline, glycine and negatively charged amino acids around conserved stalling. Many of the sites are found in RNA processing genes, suggesting that stalling might have a conserved role in RNA metabolism. In summary, our results provide a rich resource for the study of conserved stalling and indicate possible roles of stalling in gene regulation.
GeneMark-HM: improving gene prediction in DNA sequences of human microbiome
Authors: Lomsadze Alexandre , Bonny Christophe , Strozzi Francesco , Borodovsky Mark 
Published: May 2021

AbstractComputational reconstruction of nearly complete genomes from metagenomic reads may identify thousands of new uncultured candidate bacterial species. We have shown that reconstructed prokaryotic genomes along with genomes of sequenced microbial isolates can be used to support more accurate gene prediction in novel metagenomic sequences. We have proposed an approach that used three types of gene prediction algorithms and found for all contigs in a metagenome nearly optimal models of protein-coding regions either in libraries of pre-computed models or constructed de novo. The model selection process and gene annotation were done by the new GeneMark-HM pipeline. We have created a database of the species level pan-genomes for the human microbiome. To create a library of models representing each pan-genome we used a self-training algorithm GeneMarkS-2. Genes initially predicted in each contig served as queries for a fast similarity search through the pan-genome database. The best matches led to selection of the model for gene prediction. Contigs not assigned to pan-genomes were analyzed by crude, but still accurate models designed for sequences with particular GC compositions. Tests of GeneMark-HM on simulated metagenomes demonstrated improvement in gene annotation of human metagenomic sequences in comparison with the current state-of-the-art gene prediction tools.
Performance and Operational Evaluation of the Access Bio CareStart Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts
Authors: Pollock Nira R , Tran Kristine , Jacobs Jesica R , Cranston Amber E , Smith Sita , O’Kane Claire Y , Roady Tyler J , Moran Anne , Scarry Alison , Carroll Melissa , Volinsky Leila , Perez Gloria , Patel Pinal , Gabriel Stacey , Lennon Niall J , Madoff Lawrence C , Brown Catherine , Smole Sandra C 
Published: May 2021

Abstract

Background
To facilitate deployment of point-of-care testing for severe acute respiratory syndrome coronavirus 2, we evaluated the Access Bio CareStart COVID-19 Antigen test in a high-throughput, drive-through, free community testing site using anterior nasal (AN) swab reverse-transcription polymerase chain reaction (RT-PCR) for clinical testing.

Methods
Consenting symptomatic and asymptomatic children (≤18 years) and adults received dual AN swabs. CareStart testing was performed with temperature/humidity monitoring. All tests had 2 independent reads to assess interoperator agreement. Patients with positive CareStart results were called and instructed to isolate pending RT-PCR results. The paired RT-PCR result was the reference for sensitivity and specificity calculations.

Results
Of 1603 participants, 1245 adults and 253 children had paired RT-PCR/CareStart results and complete symptom data. Eighty-three percent of adults and 87% of children were asymptomatic. CareStart sensitivity/specificity were 84.8% (95% confidence interval [CI], 71.1–93.7)/97.2% (95% CI, 92.0–99.4) and 85.7% (95% CI, 42.1–99.6)/89.5% (95% CI, 66.9–98.7) in adults and children, respectively, within 5 days of symptoms. Sensitivity/specificity were 50.0% (95% CI, 41.0–59.0)/99.1% (95% CI, 98.3–99.6) in asymptomatic adults and 51.4% (95% CI, 34.4–68.1)/97.8% (95% CI, 94.5–99.4) in asymptomatic children. Sensitivity in all 234 RT-PCR-positive people was 96.3% with cycle threshold (Ct) ≤25, 79.6% with Ct ≤30, and 61.4% with Ct ≤35. All 21 false-positive CareStart tests had faint but normal bands. Interoperator agreement was 99.5%. Operational challenges included identification of faint test bands and inconsistent swab elution volumes.

Conclusions
CareStart had high sensitivity in people with Ct ≤25 and moderate sensitivity in symptomatic people overall. Specificity was unexpectedly lower in symptomatic versus asymptomatic people. Excellent interoperator agreement was observed, but operational challenges indicate that operator training is warranted.
First Experience Addressing the Prognostic Utility of Novel Urinary Biomarkers in Patients With COVID-19
Authors: Tantry Udaya S , Bliden Kevin P , Cho Alastair , Walia Naval , Dahlen Jeffrey R , Ens Gordon , Traianova Malina , Jerjian Christophe , Usman Abira , Gurbel Paul A 
Published: May 2021

Abstract
Urine 11-dehydro-thromboxane B2 (u11-dh-TxB2), 8-hydroxy-2’-deoxyguanosine (8-OHdG), and liver-type fatty acid binding protein levels (L-FABP) at the time of hospitalization were higher in coronavirus disease 2019 (COVID-19) patients with adverse events vs without events. Higher u11-dh-TxB2 and L-FABP levels were associated with longer hospitalization, more thrombotic events, and greater mortality, providing evidence for potential utility as early prognostic biomarkers for COVID-19.
Linkage Arguments For and Against Rights
Authors: Nickel James 
Published: May 2021

Abstract
This article is about relations of support and conflict within systems of fundamental legal rights—and the arguments for and against rights that those relations make possible. Justificatory linkage arguments defend controversial rights by claiming that they provide very useful support to the realisation of well-accepted rights. This article analyses such arguments in detail and discusses their structures, uses and pitfalls. It then shows that linkage arguments can be used not just to defend rights, but also to attack them. When rights conflict—whether severely or weakly, logically or practically—negative linkage arguments attacking them can be based on the trouble they make for other rights. Many examples of conflicts of rights are provided. Negative linkage arguments provide reasons for rejecting, repealing or trimming the criticised right. Such arguments are already in regular use, but their close relation to justificatory linkage arguments has not been recognised.
AV Dicey and the Making of Common Law Constitutionalism†
Authors: Loughlin Martin 
Published: May 2021

Abstract
The work of the mid-Victorian jurist, AV Dicey, has had a remarkable influence on British constitutional thought, not least in establishing the orthodox framework within which modern constitutional lawyers continue to work. That legal positivist framework has, however, recently been challenged by jurists advocating what is generally called common law constitutionalism. Accepting the core of sense in Dicey’s account, their objective has been to revise some of the jurisprudential underpinnings of his framework for the purpose of showing that the dominant characteristic of the British system is not sovereignty but legality. Mark Walters now builds on this revisionary work by offering a new historically informed study of Dicey’s Law of the Constitution, which is designed to show that the orthodox interpretation of Dicey as a legal positivist is itself misconceived. Walters argues that, properly understood, Dicey had a more nuanced appreciation of the relationship between sovereignty and legality than is commonly appreciated. This review article examines Walters’s exercise and assesses its contemporary significance.
A diagnostic challenge in an unresponsive refugee child improving with neurosurgery—a case report
Authors: Makris George , Papageorgiou Nefeli , Panagopoulos Dimitrios , Brubakk Katrin Glatz 
Published: May 2021

ABSTRACT
An unresponsive paediatric patient may present a diagnostic challenge for health professionals, as rapid identification of the cause is needed to provide proper interventions. The following report details a challenging diagnosis of unresponsiveness in a refugee child. In the migratory context, observed unresponsiveness states are frequently attributed to psychologic factors, and overlapping psychiatric classifications (resignation syndrome, functional coma and catatonia) are common. Our patient fell into an unresponsive state for 6 months after witnessing a traumatic event. Diagnostic workup for multiple medical comorbidities led to surgical intervention for tethered cord syndrome. Shortly after that, the patient’s responsiveness improved, putting to question her condition’s underlying cause. This case highlights the need for a biopsychosocial approach in such cases, reflected in thorough clinical examination and diagnostic investigations. A multidisciplinary perspective and expertise proved crucial and may help in the rehabilitation of children in similar situations.
Case of an unreported genetic variant of salt losing 3-β-hydroxysteroid dehydrogenase deficiency
Authors: Alkhatib Einas H , Adams Stacie D , Miller Emily R 
Published: May 2021

ABSTRACT
Salt losing 3-β-hydroxysteroid dehydrogenase deficiency (HSD3B2) is a rare form of congenital adrenal hyperplasia, seen in &lt;0.5% of cases. We present a 7-year-old male diagnosed with HSD3B2 deficiency, not identified by state newborn screen, due to a novel variant identified in the HSD3B2 gene (c.694C &gt; G; p.His232Asp). This patient was referred to pediatric endocrinology and pediatric biochemical genetics following a fourth hospitalization for emesis and electrolyte derangements including hyponatremia, hyperkalemia, ketoacidosis and hypoglycemia. Endocrinology evaluation yielded elevated 17-hydroxyprogesterone (17-OHP), 17-hydroxypregnenolone (17-OHPreg), dehydroepiandrosterone and adrenocorticotropic hormone (ACTH). ACTH stimulation test indicated flat response. Sequencing of the HSD3B2 revealed a pathogenic variant inherited in trans with the novel c.694C &gt; G (p.His232Asp) variant. The patient was started on daily glucocorticoid and mineralocorticoid replacement and has since had no further adrenal crises.
DEPDC5 variant in focal cortical dysplasia: a case report and review of the literature
Authors: Jesus-Ribeiro Joana , Pereira Cristina , Robalo Conceição , Pereira Daniela J , Duro Diana , Ramos Fabiana , Freire António , Melo Joana B 
Published: May 2021

ABSTRACT
Germline and 2-hit brain somatic variants in DEPDC5 gene, a negative regulator of the mammalian target of rapamycin (mTOR) pathway, are increasingly recognized in patients with focal cortical dysplasia (FCD). Next-generation targeted sequencing identified a heterozygous germline variant in DEPDC5 gene (c.3241A&gt;C, p.Thr1081Pro), classified as of unknown significance, in a patient with clinical features compatible with DEPDC5 phenotype (FCD, focal epilepsy, attention-deficit/hyperactivity disorder and borderline intellectual functioning). This missense variant has previously been reported in two other epileptic patients. Although interpretation of missense variants remains a challenge, DEPDC5 variants in patients with FCD and epilepsy cannot be neglected. Null variants were the most frequently reported in FCD patients, but missense variants have been described as well. The recognition of DEPDC5 phenotype and the appropriate interpretation of the detected variants are essential, since it may have important treatment implications in the near future, namely the use of mTOR inhibitors.
Boosting automated sleep staging performance in big datasets using population subgrouping
Authors: Nasiri Samaneh , Clifford Gari D 
Published: May 2021

AbstractCurrent approaches to automated sleep staging from the electroencephalogram (EEG) rely on constructing a large labeled training and test corpora by aggregating data from different individuals. However, many of the subjects in the training set may exhibit changes in the EEG that are very different from the subjects in the test set. Training an algorithm on such data without accounting for this diversity can cause underperformance. Moreover, test data may have unexpected sensor misplacement or different instrument noise and spectral responses. This work proposes a novel method to learn relevant individuals based on their similarities effectively. The proposed method embeds all training patients into a shared and robust feature space. Individuals who share strong statistical relationships and are similar based on their EEG signals are clustered in this feature space before being passed to a deep learning framework for classification. Using 994 patient EEGs from the 2018 Physionet Challenge (≈6,561 h of recording), we demonstrate that the clustering approach significantly boosts performance compared to state-of-the-art deep learning approaches. The proposed method improves, on average, a precision score from 0.72 to 0.81, a sensitivity score from 0.74 to 0.82, and a Cohen’s Kappa coefficient from 0.64 to 0.75 under 10-fold cross-validation.
Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions
Authors: Piantham Chayada , Ito Kimihito 
Published: May 2021

AbstractIn 2009, a new strain of H1N1 influenza A virus caused a pandemic, and its descendant strains are causing seasonal epidemics worldwide. Given the high mutation rate of influenza viruses, variant strains having different amino acids on hemagglutinin (HA) continuously emerge. To prepare vaccine strains for the next influenza seasons, it is an urgent task to predict which variants will be selected in the viral population. An analysis of 24,681 pairs of an amino acid sequence of HA of H1N1pdm2009 viruses and its patient age showed that the empirical fixation probability of new amino acids on HA significantly differed depending on their frequencies in the population, patient age distributions, and epitope flags. The selective advantage of a variant strain having a new amino acid was modeled by linear combinations of patients age distributions and epitope flags, and then the fixation probability of the new amino acid was modeled using Kimura’s formula for advantageous selection. The parameters of models were estimated from the sequence data and models were tested with four-fold cross validations. The frequency of new amino acids alone can achieve high sensitivity, specificity, and precision in predicting the fixation of a new amino acid of which frequency is more than 0.11. The estimated parameter suggested that viruses with a new amino acid having a frequency in the population higher than 0.11 have a significantly higher selective advantage compared to viruses with the old amino acid at the same position. The model considering the Z-value of patient age rank-sums of new amino acids predicted amino acid substitutions on HA with a sensitivity of 0.78, specificity of 0.86, and precision of 0.83, showing significant improvement compared to the constant selective advantage model, which used only the frequency of the amino acid. These results suggested that H1N1 viruses tend to be selected in the adult population, and frequency of viruses having new amino acids and their patient ages are useful to predict amino acid substitutions on HA.
Systemness Taps the Power of Interdependence in Healthcare
Authors: Stokes Charles D. , Brace Rod 
Published: May 2021

SUMMARY
While the term systemness has been used in the healthcare sector for decades, its definition varies from organization to organization. Still, the goals are consistent: to improve patient experience, lower costs, reduce risk, and provide insights into a wide range of care and management issues. Most health systems face similar challenges, such as margin enhancement, quality improvement, increased access, and fending off disruptive competition. Systemness is a way to address these challenges while improving the overall interdependence of the organization. Although embraced by and advantageous to healthcare organizations, systemness efforts often fail. The obstacles are surmountable when organizations thoroughly analyze the achievable scale of systemness, community resources, and current mindset regarding the good of the whole. Leaders must play a vital role in promoting systemness by providing education and a routine review of day-to-day organizational activities. Sometimes, systemness requires a change in leadership or an updating of leadership skills.
Organizations must recognize and assess their culture as it relates to principles of independence versus interdependence, and refocus clinical standardization through best-practice protocols and policies as COVID-19 affects the already-fractured healthcare sector. Fortunately, current and developing artificial intelligence, wearables, at-home testing, and improved technologies promise to provide a needed break for a contracting physician field and fatigued front line, and they present an opportunity for those organizations poised to meet the systemness challenge.
Critical issues in alliances between management partners and accountable care organizations
Authors: Murray Genevra F. , D'Aunno Thomas , Lewis Valerie A. 
Published: May 2021

Background
Despite widespread engagement of accountable care organizations (ACOs) with management partners, little empirical evidence on these alliances exists to inform policymakers or payers. Management partners may be providing a valuable service in facilitating the transition to population health management. Alternately, in some cases, partners may be receiving high fees relative to the value of services provided.

Purpose
The aim of this study was to use qualitative data to identify motivations for and critical issues in alliances between ACOs and management partners.

Methodology/Approach
We used qualitative data collected from seven ACOs (193 semistructured interviews and observational data from 12 site visits) to characterize the alliances between management partners and providers in ACOs.

Results
We found that ACOs sought partners to provide financing, technical expertise, and risk bearing. Tensions in partnerships arose around resources (e.g., delivery on promised resources), control (e.g., who holds decision making authority), and values (e.g., commitment to safety net mission). Some partnerships persisted, whereas others dissolved. We found that there are two different underlying models of ACO–management partner alliances in our sample: (1) short-term partnerships aimed at organizational learning and (2) long-term partnerships based on complementarity.

Conclusion
Our results demonstrate how ACO alliances with management partners have unfolded as a kind of natural experiment in value-based payment reform. We expect that there is wide variation in quality, expertise, and delivery by management partners. Now multiple years into many of these alliances, we may address their value, strengths, and weaknesses from the perspective of providers as well as policy makers and payers.

Practice Implications
Accountable care organization providers must determine whether a management partner is the best solution to the challenges they face and, if so, which alliance model to pursue. Policymakers and payers should consider short- and long-term implications of ACO–management partner alliances, including considering changing the regulatory environment.
Could Dispositional Optimism Impair Panic Disorder and Depression Outcomes?
Authors: Rodrigues Michele F. , Vianna Ruan , Galdino Melyssa K. , Nardi Antonio Egídio , Appolinário José Carlos , Levitan Michelle N. 
Published: May 2021

Abstract
The objective of this study was to investigate potential correlates of dispositional optimism and quality of life in patients with depression and panic disorder. The study used a cross-sectional design. The analyzed sample consisted of 77 participants with panic disorder and 75 participants with depression attending two outpatient clinics at the Psychiatry Institute of the Federal University of Rio de Janeiro. Both groups presented similar impairments in optimism and quality of life. In the panic disorder group, optimism scores were significantly correlated with a decrease in anxiety and depression scores (r = 0.26 and r = 0.37, respectively); in the depression group, increases in optimism scores were significantly correlated with decreases in anxiety and depression scores (r = 0.23 and r = 0.3, respectively). The present study showed that high anxiety and depression are correlated with poor optimism and quality of life scores in panic disorder and depression groups. Thus, psychological treatments that can address these topics, besides acute symptoms, are crucial to the absolute recovery of patients.