bluuebunny/crossref_metadata_2025_split huggingface dataset:
DAYENU: a simple filter of smooth foregrounds for intensity mapping power spectra
Authors: Ewall-Wice Aaron , Kern Nicholas , Dillon Joshua S , Liu Adrian , Parsons Aaron , Singh Saurabh , Lanman Adam , Plante Paul La , Fagnoni Nicolas , Acedo Eloy de Lera , DeBoer David R , Nunhokee Chuneeta , Bull Philip , Chang Tzu-Ching , Lazio T Joseph W , Aguirre James , Weinberg Sean 
Published: October 2020

ABSTRACT
We introduce DPSS Approximate lazY filtEriNg of foregroUnds (dayenu), a linear, spectral filter for H i intensity mapping that achieves the desirable foreground mitigation and error minimization properties of inverse co-variance weighting with minimal modelling of the underlying data. Beyond 21-cm power-spectrum estimation, our filter is suitable for any analysis where high dynamic-range removal of spectrally smooth foregrounds in irregularly (or regularly) sampled data is required, something required by many other intensity mapping techniques. Our filtering matrix is diagonalized by Discrete Prolate Spheroidal Sequences which are an optimal basis to model band-limited foregrounds in 21-cm intensity mapping experiments in the sense that they maximally concentrate power within a finite region of Fourier space. We show that dayenu enables the access of large-scale line-of-sight modes that are inaccessible to tapered discrete Fourier transform estimators. Since these modes have the largest SNRs,dayenu significantly increases the sensitivity of 21-cm analyses over tapered Fourier transforms. Slight modifications allow us to use dayenu as a linear replacement for iterative delay clean ing (dayenurest). We refer readers to the Code section at the end of this paper for links to examples and code.
AtMAD: Arabidopsis thaliana multi-omics association database
Authors: Lan Yiheng , Sun Ruikun , Ouyang Jian , Ding Wubing , Kim Min-Jun , Wu Jun , Li Yuhua , Shi Tieliu 
Published: October 2020

Abstract
Integration analysis of multi-omics data provides a comprehensive landscape for understanding biological systems and mechanisms. The abundance of high-quality multi-omics data (genomics, transcriptomics, methylomics and phenomics) for the model organism Arabidopsis thaliana enables scientists to study the genetic mechanism of many biological processes. However, no resource is available to provide comprehensive and systematic multi-omics associations for Arabidopsis. Here, we developed an Arabidopsis thaliana Multi-omics Association Database (AtMAD, http://www.megabionet.org/atmad), a public repository for large-scale measurements of associations between genome, transcriptome, methylome, pathway and phenotype in Arabidopsis, designed for facilitating identification of eQTL, emQTL, Pathway-mQTL, Phenotype-pathway, GWAS, TWAS and EWAS. Candidate variants/methylations/genes were identified in AtMAD for specific phenotypes or biological processes, many of them are supported by experimental evidence. Based on the multi-omics association strategy, we have identified 11 796 cis-eQTLs and 10 119 trans-eQTLs. Among them, 68 837 environment-eQTL associations and 149 622 GWAS-eQTL associations were identified and stored in AtMAD. For expression–methylation quantitative trait loci (emQTL), we identified 265 776 emQTLs and 122 344 pathway-mQTLs. For TWAS and EWAS, we obtained 62 754 significant phenotype-gene associations and 3 993 379 significant phenotype-methylation associations, respectively. Overall, the multi-omics associated network in AtMAD will provide new insights into exploring biological mechanisms of plants at multi-omics levels.
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues
Authors: Li Qin , Lai Hongyan , Li Yuchen , Chen Bing , Chen Siyuan , Li Yan , Huang Zhaohui , Meng Zhiqiang , Wang Peng , Hu Zhixiang , Huang Shenglin 
Published: October 2020

Abstract
Splicing is an essential step of RNA processing for multi-exon genes, in which introns are removed from a precursor RNA, thereby producing mature RNAs containing splice junctions. Here, we develope the RJunBase (www.RJunBase.org), a web-accessible database of three types of RNA splice junctions (linear, back-splice, and fusion junctions) that are derived from RNA-seq data of non-cancerous and cancerous tissues. The RJunBase aims to integrate and characterize all RNA splice junctions of both healthy or pathological human cells and tissues. This new database facilitates the visualization of the gene-level splicing pattern and the junction-level expression profile, as well as the demonstration of unannotated and tumor-specific junctions. The first release of RJunBase contains 682 017 linear junctions, 225 949 back-splice junctions and 34 733 fusion junctions across 18 084 non-cancerous and 11 540 cancerous samples. RJunBase can aid researchers in discovering new splicing-associated targets and provide insights into the identification and assessment of potential neoepitopes for cancer treatment.
Biophysical analysis ofPseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation
Authors: Niazi Marzia , Florio Tyler J , Yang Ruoyu , Lokareddy Ravi K , Swanson Nicholas A , Gillilan Richard E , Cingolani Gino 
Published: October 2020

AbstractThe genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
Relationship between measured and prescribed dialysate sodium in haemodialysis: a systematic review and meta-analysis
Authors: Ng Jack Kit-Chung , Smyth , Brendan , Marshall , Mark R , Kang , Amy , Pinter , Jule , Bassi , Abhinav , Krishnasamy , Rathika , Rossignol , Patrick , Rocco , Michael V , Li , Zuo , Jha , Vivekanand , Hawley Carmel M , Kerr , Peter G , DI Tanna , Gian Luca , Woodward , Mark , Jardine and Meg ,   The RESOLVE Steering Committee
Published: October 2020

Abstract

Background
Dialysate sodium (DNa) prescription policy differs between haemodialysis (HD) units, and the optimal DNa remains uncertain. We sought to summarize the evidence on the agreement between prescribed and delivered DNa, and whether the relationship varied according to prescribed DNa.

Methods
We searched MEDLINE and PubMed from inception to 26 February 2020 for studies reporting measured and prescribed DNa. We analysed results reported in aggregate with random-effects meta-analysis. We analysed results reported by individual sample, using mixed-effects Bland–Altman analysis and linear regression. Pre-specified subgroup analyses included method of sodium measurement, dialysis machine manufacturer and proportioning method.

Results
Seven studies, representing 908 dialysate samples from 10 HD facilities (range 16–133 samples), were identified. All but one were single-centre studies. Studies were of low to moderate quality. Overall, there was no statistically significant difference between measured and prescribed DNa {mean difference = 0.73 mmol/L [95% confidence interval (CI) −1.12 to 2.58; P = 0.44]} but variability across studies was substantial (I2 = 99.3%). Among individually reported samples (n = 295), measured DNa was higher than prescribed DNa by 1.96 mmol/L (95% CI 0.23–3.69) and the 95% limits of agreement ranged from −3.97 to 7.88 mmol/L. Regression analysis confirmed a strong relationship between prescribed and measured DNa, with a slope close to 1:1 (β = 1.16, 95% CI 1.06–1.27; P &lt; 0.0001).

Conclusions
A limited number of studies suggest that, on average, prescribed and measured DNa are similar. However, between- and within-study differences were large. Further consideration of the precision of delivered DNa is required to inform rational prescribing.
Postacute COVID-19: An Overview and Approach to Classification
Authors: Amenta Eva M , Spallone Amy , Rodriguez-Barradas Maria C , El Sahly Hana M , Atmar Robert L , Kulkarni Prathit A 
Published: October 2020

Abstract
As the coronavirus disease 2019 (COVID-19) pandemic has progressed, a large volume of literature has developed delineating the clinical manifestations of acute infection. Recent reports have also started to describe persistent symptoms extending beyond the period of initial illness or hospitalization. Anecdotes of different signs and symptoms occurring after acute infection have also arisen in the lay press. Here we describe the current existing medical literature on the emerging concept of postacute COVID-19 and suggest an approach to classifying different manifestations of the syndrome. We also review long-term clinical manifestations observed in patients who recovered from infection due to other epidemic coronaviruses and briefly discuss potential mechanisms driving the phenomenon of postacute COVID-19.
Volume of Line Bundles via Valuation Vectors (Different from Okounkov Bodies)
Authors: Braunling O 
Published: October 2020

AbstractUp to a factor 1/n!, the volume of a big line bundle agrees with the Euclidean volume of its Okounkov body. The latter is the convex hull of top rank valuation vectors of sections, all with respect to a single flag. In this paper, we give a new volume formula, valid in the ample cone. It is also based on top rank valuation vectors, but mixes data coming from several different flags.
Anakinra for colchicine refractory familial Mediterranean fever: a cohort of 44 patients
Authors: Marko Limor , Shemer Asaf , Lidar Merav , Grossman Chagai , Druyan Amit , Livneh Avi , Kivity Shaye 
Published: October 2020

Abstract

Objective
FMF is an autoinflammatory disease of genetic origin. Colchicine is the mainstay of treatment for the prevention of attacks and long-term complications but 5–10% of FMF patients are resistant to colchicine therapy. The aim of our study was to investigate the real-life safety and efficacy of anakinra in a cohort of patients with colchicine-resistant FMF.

Methods
In this retrospective study, patients treated with anakinra for colchicine-resistant FMF between 2010 and 2018 were identified using the computerized database of Sheba Medical Center and enrolled in the study. Data from structured clinical files were analysed to evaluate the efficacy and safety outcomes. To assess efficacy, we used the Global Assessment Score (GAS), a measure comprised of three different domains: number of attacks per month, duration of attacks and number of sites involved in the attacks. Reported adverse events were compiled.

Results
A total of 44 patients (24 female) were treated with anakinra. Of these patients, 75% were homozygous for the M649V mutation. The mean duration of treatment was 18 months. The GAS decreased significantly from 6.6 (IQR 5.3–7.8) before treatment to 2 (IQR 0–4.2) while on treatment (P &lt; 0.001). During anakinra treatment, six hospitalizations were reported (three due to related adverse effects). In addition, 11 patients suffered from injection site reactions (5 ceased treatment). Twelve patients reported mild side effects.

Conclusion
Treatment with anakinra is beneficial for the majority of colchicine-resistant FMF patients and is relatively safe.
A framework for open policy analysis
Authors: Hoces de la Guardia Fernando , Grant Sean , Miguel Edward 
Published: October 2020

Abstract
The evidence-based policy movement promotes the use of empirical evidence to inform policy decision-making. While several social science disciplines are undergoing a ‘credibility revolution’ focused on openness and replication, policy analysis has yet to systematically embrace transparency and reproducibility. We argue that policy analysis should adopt the open research practices increasingly espoused in related disciplines to advance the credibility of evidence-based policy making. We first discuss the importance of evidence-based policy in an era of increasing disagreement about facts, analysis, and expertise. We present a novel framework for ‘open’ policy analysis (OPA) and how to achieve it, focusing on examples of recent policy analyses that have incorporated open research practices such as transparent reporting, open data, and code sharing. We conclude with recommendations on how key stakeholders in evidence-based policy can make OPA the norm and thus safeguard trust in using empirical evidence to inform important public policy decisions.
A multicentric knowledge-attitude-practice survey in the community about antimicrobial use and resistance in India
Authors: Chatterjee Suparna , Hazra Avijit , Chakraverty Raja , Shafiq Nusrat , Pathak Ashish , Trivedi Niyati , Sadasivam Balakrishnan , Kakkar Ashish Kumar , Jhaj Ratinder , Kaul Rajni , Kshirsagar Nilima 
Published: October 2020

Abstract

Background
To address the reasons for inappropriate use of antimicrobials, it is important to understand the knowledge, attitude and practices (KAP) of all pertinent stakeholders. This multicentric survey is aimed at understanding the KAP quotients of the community regarding antimicrobial use and antimicrobial resistance (AMR), as such information is lacking in India.

Methods
A cross-sectional survey was conducted by face-to-face interviews across five centers in India using a validated, field-tested questionnaire incorporating KAP domain questions. Scores were appropriately assigned to the questions.

Results
The mean (SD) age of the respondents was 35.2 (12.61) y and 62% had a graduate or higher level of education. The median (IQR) KAP scores were 10 (8–12), 5 (3–5) and 2 (2–3) out of a maximum of 18, 5 and 6, respectively. Higher educational and socioeconomic levels were associated with better attitude scores, but knowledge levels were comparable. Correlations between KAP scores were poor.

Conclusions
This study reveals that laypeople have appropriate knowledge and attitude regarding antibiotic use and AMR to some degree but there are important lacunae and practices are often wanting. These issues need to be addressed in sustained public awareness and motivation campaigns to improve the rational use of antibiotics in India.
Recognizing and treating autosomal dominant polycystic kidney disease
Authors: Uko Chigozie G. 
Published: October 2020

Abstract:
Autosomal dominant polycystic kidney disease causes chronic kidney disease and end-stage renal disease. Mechanisms include cyst production, multiplication, and enlargement leading to increased kidney size, and ultimately kidney failure. Although there is no known cure, NPs are uniquely positioned to help patients manage their symptoms and delay onset of kidney failure and need for dialysis.
A 3-way Cross-over Study of Pregabalin, Placebo, and the Histamine 3 Receptor Inverse Agonist AZD5213 in Combination With Pregabalin in Patients With Painful Diabetic Neuropathy and Good Pain-reporting Ability
Authors: Alexander Robert C. , Raudibaugh Karen , Spierings Egilius L.H. , Katz Nathaniel 
Published: October 2020

Objectives:
In this study, patients with painful diabetic neuropathy were trained using an experimental pain paradigm in an attempt to enroll a subset of patients who are “pain connoisseurs” and therefore more able to discriminate between active and placebo treatments.

Methods:
AZD5213, a novel histamine H3 receptor inverse agonist+pregabalin, pregabalin, and placebo were then tested in a 3-period cross-over.

Results:
The study did not provide any evidence of clinical efficacy for AZD5213 when combined with pregabalin in the treatment of painful diabetic neuropathy.

Discussion:
The training of study patients in pain reporting and subsequent enrichment with good pain reporters also did not enable the robust detection of the efficacy of pregabalin relative to placebo in a small sample size. Further work is required before recommending the use of “connoisseur” patients in future neuropathic pain studies.
Comparison of the anterior and posterior approach in treating four-level cervical spondylotic myelopathy
Authors: Zhai Ji-Liang , Guo Shi-Gong , Nie Li , Hu Jian-Hua 
Published: October 2020

Abstract

Background:
The optimal surgical approach for four-level cervical spondylotic myelopathy remains controversial. The purpose of this study was to compare clinical and radiological outcomes and complications between the anterior and posterior approaches for four-level cervical spondylotic myelopathy.

Methods:
A total of 19 patients underwent anterior decompression and fusion and 25 patients underwent posterior laminoplasty and instrumentation in this study. Perioperative information, intraoperative blood loss, clinical and radiological outcomes, and complications were recorded. Japanese Orthopedic Association (JOA) score, 36-item short form survey (SF-36) score and cervical alignment were assessed.

Results:
There were no significant differences in JOA scores between the anterior and posterior group preoperatively (11.6 ± 1.6 vs. 12.1 ± 1.5), immediately postoperatively (14.4 ± 1.1 vs. 13.8 ± 1.3), or at the last follow-up (14.6 ± 1.0 vs. 14.2 ± 1.1) (P > 0.05). The JOA scores significantly improved immediately postoperatively and at the last follow-up in both groups compared with their preoperative values. The recovery rate was significantly higher in the anterior group both immediately postoperatively and at the last follow-up. The SF-36 score was significantly higher in the anterior group at the last follow-up compared with the preoperative value (69.4 vs. 61.7). Imaging revealed that there was no significant difference in the Cobb angle at C2–C7 between the two groups preoperatively (−2.0° ± 7.3° vs. −1.4° ± 7.5°). The Cobb angle significantly improved immediately postoperatively (12.3° ± 4.2° vs. 9.2° ± 3.6°) and at the last follow-up (12.4° ± 3.5° vs. 9.0° ± 2.6°) in both groups compared with their preoperative values (P = 0.00). Three patients had temporary dysphagia in the anterior group and four patients had persistent axial symptoms in the posterior group.

Conclusions:
Both the anterior and posterior approaches were effective in treating four-level cervical spondylotic myelopathy in terms of neurological clinical outcomes and radiological features. However, the JOA score recovery rate and SF-36 score in the anterior group were significantly higher. Persistent axial pain could be a major concern when undertaking the posterior approach.
Physical Therapy Student Reports of Blood Pressure Guidelines Learned in the Classroom, and Observed and Practiced in Clinical Experiences
Authors: Marks Ted , Berg Sarah Leah , Granek Batsheva , Rybakov Peter , Taranenko Irina , Yee Dana , Garcia Ralph 
Published: October 2020

Purpose:
The purposes of this study were (1) to investigate discrepancies between what physical therapy students report learning in the classroom regarding blood pressure (BP) guidelines and what physical therapy students report observing and practicing in clinical settings and (2) to establish whether students felt discomfort when discrepancies were encountered.

Methods:
This was a prospective descriptive survey study generated using a sample of convenience employing a survey developed by the researchers. Face and content validity were established through expert review. An email was sent to 21 New York State Physical Therapy Programs asking each program to share the survey with students in their programs who had completed clinical experiences. The responses were analyzed descriptively using frequency counts, percentages, and cross tabulations.

Results:
Responses were received from 206 students attending 13 different programs, or 61.9% of the programs contacted. More than half the students (53.4%) reported there were differences between what they learned during classroom instruction regarding BP assessment and what they saw and practiced in the clinic; 24.8% of students expressed discomfort related to discrepancies between what they learned in school and what they saw and practiced in the clinic. Inpatient and outpatient experiences were compared. Statistical differences were found indicating patients had their BP assessed less often in outpatient settings. In addition, students were less likely to discuss BP assessment with their clinical instructors (CIs) in outpatient settings and students were more likely to express increased competence taking BP after inpatient clinical experiences. Across all settings, 20.4% of students reported that neither they nor their CI ever measured BP during their most recent clinical experience.

Conclusions:
Across all settings, the BP assessment practices that students encounter in clinic differ from what students report learning is best practice during their physical therapy education. Students are more likely to encounter discrepancies in outpatient settings. For many students, encountering discrepancies gives rise to feelings of discomfort.
Sutured Custom Foldable Silicone Artificial Iris Implantation Combined With Intraocular Lens Implantation and Penetrating Keratoplasty: Safety and Efficacy Outcomes
Authors: Bonnet Clemence , Vazirnia Parsia , Deng Sophie X. , Aldave Anthony J. , Miller Kevin M. 
Published: October 2020

Purpose:
To assess safety and efficacy outcomes of sutured custom silicone artificial iris and intraocular lens implantation combined with penetrating keratoplasty (triple procedure).

Methods:
Prospective consecutive surgical case series of patients who underwent the triple procedure between 2010 and 2019 at Stein Eye Institute, UCLA, followed up for 1 year minimum. Safety outcomes were changes from preoperative to last follow-up in corrected distance visual acuity (CDVA), endothelial cell count, intraocular pressure (IOP), and postoperative complications. Efficacy outcomes included changes in subjective glare (none to severe), cosmetic appearance (worse to very much improved), and visual function as assessed by the Visual Function Questionnaire-25 at 1-year follow-up.

Results:
Among 82 eyes implanted with an artificial iris, 14 eyes (17.1%) underwent the triple procedure. The median follow-up was 18.1 months (range 12.0–54.9 months). The median CDVA improved from 2.0 log of minimum angle of resolution (logMAR) (range 0.9–2.3 logMAR) to 0.7 logMAR (range 0.2–2.6 logMAR) (P = 0.02). Average endothelial cell count decreased 57.6% (P < 0.01). Six eyes (42.9%) experienced IOP elevations, 13 eyes (92.3%) developed iritis, and 11 eyes (78.6%) underwent secondary surgery. Graft rejection or secondary graft failure occurred in 7 eyes each (50.0%). Cosmesis improved in 12 eyes (85.7%; P < 0.01). The Visual Function Questionnaire-25 score improved from 72 to 77 (P < 0.01). Glare symptoms did not change significantly.

Conclusions:
The triple procedure was effective at improving CDVA, cosmesis, and quality of life; however, it was associated with frequent postoperative complications, of which iritis, IOP elevation, and secondary graft failure were the most common.