bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithms for inference in SVARs identified with sign and zero restrictions
Authors: Read Matthew 
Published: February 2022

Summary
I develop algorithms to facilitate Bayesian inference in structural vector autoregressions that are set-identified with sign and zero restrictions by showing that the system of restrictions is equivalent to a system of sign restrictions in a lower-dimensional space. Consequently, algorithms applicable under sign restrictions can be extended to allow for zero restrictions. Specifically, I extend algorithms proposed in Amir-Ahmadi and Drautzburg (2021) to check whether the identified set is nonempty and to sample from the identified set without rejection sampling. I compare the new algorithms to alternatives by applying them to variations of the model considered by Arias et al. (2019a), who estimate the effects of US monetary policy using sign and zero restrictions on the monetary policy reaction function. The new algorithms are particularly useful when a rich set of sign restrictions substantially truncates the identified set given the zero restrictions.
CALL-K score: predicting the need for renal replacement therapy in cardiogenic shock
Authors: Rodenas-Alesina Eduard , Wang Vicki N , Brahmbhatt Darshan H , Scolari Fernando Luis , Mihajlovic Vesna , Fung Nicole L , Otsuki Madison , Billia Filio , Overgaard Christopher B , Luk Adriana 
Published: February 2022

Abstract

Aims
The clinical predictors and outcomes of patients with cardiogenic shock (CS) requiring renal replacement therapy (RRT) have not been studied previously. This study assesses the impact of RRT on mortality in patients with CS and aims to identify clinical factors that contribute to the need of RRT.

Methods and results
Consecutive patients presenting with CS were included from a prospective registry of cardiac intensive care unit admissions at a single institution between 2014 and 2020. Of the 1030 patients admitted with CS, 123 (11.9%) received RRT. RRT was associated with higher 1-year mortality [adjusted hazard ratio = 1.62, 95% confidence interval (CI) 1.02–2.14], and a higher in-hospital incidence of sepsis [risk ratio = 2.76, P &lt; 0.001], and pneumonia (risk ratio = 2.9, P = 0.001). Those who received RRT were less likely to receive guideline-directed medical treatment at time of discharge, undergo heart transplantation (2.4% vs. 11.5%, P = 0.002) or receive a durable left ventricular assist device (0.0% vs. 11.6%, P &lt; 0.001). Five variables at admission best predicted the need for RRT (age, lactate, haemoglobin, use of pre-admission loop diuretics, and admission estimated glomerular filtration rate) and were used to generate the CALL-K 9-point risk score, with better discrimination than creatinine alone (P = 0.008). The score was internally validated (area under the curve = 0.815, 95% CI 0.739–0.835) with good calibration (Hosmer–Lemeshow P = 0.827).

Conclusions
RRT is associated with worse outcomes, including a lower likelihood to receive advanced heart failure therapies in patients with CS. A risk score comprising five variables routinely collected at admission can accurately estimate the risk of needing RRT.
Structure of the Pf12 and Pf41 heterodimeric complex ofPlasmodium falciparum6-cysteine proteins
Authors: Dietrich Melanie H , Chan Li-Jin , Adair Amy , Boulet Coralie , O'Neill Matthew T , Tan Li Lynn , Keremane Sravya , Mok Yee-Foong , Lo Alvin W , Gilson Paul , Tham Wai-Hong 
Published: February 2022

AbstractDuring the different stages of the Plasmodium life cycle, surface-associated proteins establish key interactions with the host and play critical roles in parasite survival. The 6-cysteine (6-cys) protein family is one of the most abundant surface antigens and expressed throughout the Plasmodium falciparum life cycle. This protein family is conserved across Plasmodium species and plays critical roles in parasite transmission, evasion of the host immune response and host cell invasion. Several 6-cys proteins are present on the parasite surface as hetero-complexes but it is not known how two 6-cys proteins interact together. Here, we present a crystal structure of Pf12 bound to Pf41 at 2.85 Å resolution, two P. falciparum proteins usually found on the parasite surface of late schizonts and merozoites. Our structure revealed two critical interfaces required for complex formation with important implications on how different 6-cysteine proteins may interact with each other. Using structure-function analyses, we identified important residues for Pf12-Pf41 complex formation. In addition, we generated 16 nanobodies against Pf12 and Pf41 and showed that several Pf12-specific nanobodies inhibit Pf12-Pf41 complex formation. Using X-ray crystallography, we were able to describe the structural mechanism of an inhibitory nanobody in blocking Pf12-Pf41 complex formation. Future studies using these inhibitory nanobodies will be useful to determine the functional role of these two 6-cys proteins in malaria parasites.
The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont
Authors: Gagalova Kristina K , Whitehill Justin G A , Culibrk Luka , Lin Diana , Lévesque-Tremblay Véronique , Keeling Christopher I , Coombe Lauren , Yuen Macaire M S , Birol Inanç , Bohlmann Jörg , Jones Steven J M 
Published: February 2022

Abstract
The highly diverse insect family of true weevils, Curculionidae, includes many agricultural and forest pests. Pissodes strobi, commonly known as the spruce weevil or white pine weevil, is a major pest of spruce and pine forests in North America. Pissodes strobi larvae feed on the apical shoots of young trees, causing stunted growth and can destroy regenerating spruce or pine forests. Here, we describe the nuclear and mitochondrial Pissodes strobi genomes and their annotations, as well as the genome of an apparent Wolbachia endosymbiont. We report a substantial expansion of the weevil nuclear genome, relative to other Curculionidae species, possibly driven by an abundance of class II DNA transposons. The endosymbiont observed belongs to a group (supergroup A) of Wolbachia species that generally form parasitic relationships with their arthropod host.
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package
Authors: Griffiths Emma J , Timme Ruth E , Mendes Catarina Inês , Page Andrew J , Alikhan Nabil-Fareed , Fornika Dan , Maguire Finlay , Campos Josefina , Park Daniel , Olawoye Idowu B , Oluniyi Paul E , Anderson Dominique , Christoffels Alan , da Silva Anders Gonçalves , Cameron Rhiannon , Dooley Damion , Katz Lee S , Black Allison , Karsch-Mizrachi Ilene , Barrett Tanya , Johnston Anjanette , Connor Thomas R , Nicholls Samuel M , Witney Adam A , Tyson Gregory H , Tausch Simon H , Raphenya Amogelang R , Alcock Brian , Aanensen David M , Hodcroft Emma , Hsiao William W L , Vasconcelos Ana Tereza R , MacCannell Duncan R 
Published: February 2022

Abstract

Background
The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard.

Results
As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories.

Conclusions
Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.
P38 Audit and reaudit of penicillin allergy documentation in patients presenting through the Emergency Department at the Royal Berkshire Hospital
Authors: Shenoy Aniruddh , Malakouti Afsaneh , Iyer Shabnam 
Published: February 2022

Abstract

Background
Penicillin allergy is the commonest reported drug allergy in the UK. However, it is estimated that under 10% are true allergies. Evidence shows that using second-line antibiotics is associated with worse clinical outcomes, greater healthcare costs and increased risk of antimicrobial resistance.

Objectives
To evaluate the completeness of allergy history taking as per Trust guidelines on penicillin allergy classification, for patients with a positive penicillin allergy status presenting through the Emergency Department (ED) at the Royal Berkshire Hospital (RBH).

Methods
In the first audit, 30 consecutive patients prescribed antibiotics in the acute medical unit (AMU) via ED at RBH were selected in April 2021. Electronic patient records were reviewed for the percentage documentation of the causative antibiotic, symptoms, time and management of reaction in those with an active penicillin allergy status. Findings were fed back to the ED team at departmental teaching. Thirty consecutive patients with recorded penicillin allergy presenting to ED were selected for re-audit in June 2021.

Results
A small improvement in penicillin allergy history documentation was seen between the first audit and re-audit (Figure 1). However, 56% of patients' notes still lacked enough information to classify severity. Under 5% of patients' documented allergy history constituted absolute contraindication to penicillin-based antibiotics (Figure 2).

Conclusions
Penicillin allergy documentation in patients presenting through ED at RBH remained below the standard of Trust guidance despite educating the ED team on the issue. This project has instigated an update in the Trust penicillin allergy classification guidelines and a multidisciplinary quality improvement project to identify and challenge inappropriate penicillin allergy labels.
P48 The limited yield of cultures in the critically ill child
Authors: Clark John , White Deborah , Daubney Esther , Curran Martin , Bousfield Rachel , Gouliouris Theodore , Powell Elizabeth , Palmer Adam , Agrawal Shruti , Inwald David , Kean Iain , Török M. Estée , Baker Stephen , Pathan Nazima 
Published: February 2022

Abstract

Background
Broad-spectrum antimicrobial therapy is a key driver of antimicrobial resistance. Here, we aimed to review indications for antimicrobial therapy, determine the proportion of suspected bacterial infections that are confirmed by culture, and assess the time taken for microbiology test results to become available in the paediatric ICU (PICU).

Methods
A single-centre prospective observational cohort study of 100 consecutive general PICU admissions from 30 October 2019 to 19 February 2020. Data were collected from the hospital medical record and entered into a study database prior to statistical analysis using standard methods.

Results
Of all episodes of suspected infection, 22% of lower respiratory tract infection, 43% of bloodstream and 0% of central nervous system infection were associated with growth on microbiology culture. Ninety percent of children received antimicrobial therapy. Hospital-acquired infection occurred less commonly than primary infection, but an organism was grown in a greater proportion (64%) of cultures. Final laboratory reports for negative cultures were issued at a median of 120.3 h for blood cultures and 55.5 h for endotracheal tube aspirate cultures.

Conclusions
Despite most critically children receiving antimicrobial therapy, infection was often not microbiologically confirmed. Novel molecular diagnostics may improve rationalization of treatment in this population.
Clinician collaboration to improve clinical decision support: the Clickbusters initiative
Authors: McCoy Allison B , Russo Elise M , Johnson Kevin B , Addison Bobby , Patel Neal , Wanderer Jonathan P , Mize Dara E , Jackson Jon G , Reese Thomas J , Littlejohn SyLinda , Patterson Lorraine , French Tina , Preston Debbie , Rosenbury Audra , Valdez Charlie , Nelson Scott D , Aher Chetan V , Alrifai Mhd Wael , Andrews Jennifer , Cobb Cheryl , Horst Sara N , Johnson David P , Knake Lindsey A , Lewis Adam A , Parks Laura , Parr Sharidan K , Patel Pratik , Patterson Barron L , Smith Christine M , Suszter Krystle D , Turer Robert W , Wilcox Lyndy J , Wright Aileen P , Wright Adam 
Published: February 2022

Abstract

Objective
We describe the Clickbusters initiative implemented at Vanderbilt University Medical Center (VUMC), which was designed to improve safety and quality and reduce burnout through the optimization of clinical decision support (CDS) alerts.

Materials and Methods
We developed a 10-step Clickbusting process and implemented a program that included a curriculum, CDS alert inventory, oversight process, and gamification. We carried out two 3-month rounds of the Clickbusters program at VUMC. We completed descriptive analyses of the changes made to alerts during the process, and of alert firing rates before and after the program.

Results
Prior to Clickbusters, VUMC had 419 CDS alerts in production, with 488 425 firings (42 982 interruptive) each week. After 2 rounds, the Clickbusters program resulted in detailed, comprehensive reviews of 84 CDS alerts and reduced the number of weekly alert firings by more than 70 000 (15.43%). In addition to the direct improvements in CDS, the initiative also increased user engagement and involvement in CDS.

Conclusions
At VUMC, the Clickbusters program was successful in optimizing CDS alerts by reducing alert firings and resulting clicks. The program also involved more users in the process of evaluating and improving CDS and helped build a culture of continuous evaluation and improvement of clinical content in the electronic health record.
Development and assessment of a natural language processing model to identify residential instability in electronic health records’ unstructured data: a comparison of 3 integrated healthcare delivery systems
Authors: Hatef Elham , Rouhizadeh Masoud , Nau Claudia , Xie Fagen , Rouillard Christopher , Abu-Nasser Mahmoud , Padilla Ariadna , Lyons Lindsay Joe , Kharrazi Hadi , Weiner Jonathan P , Roblin Douglas 
Published: February 2022

Abstract

Objective
To evaluate whether a natural language processing (NLP) algorithm could be adapted to extract, with acceptable validity, markers of residential instability (ie, homelessness and housing insecurity) from electronic health records (EHRs) of 3 healthcare systems.

Materials and methods
We included patients 18 years and older who received care at 1 of 3 healthcare systems from 2016 through 2020 and had at least 1 free-text note in the EHR during this period. We conducted the study independently; the NLP algorithm logic and method of validity assessment were identical across sites. The approach to the development of the gold standard for assessment of validity differed across sites. Using the EntityRuler module of spaCy 2.3 Python toolkit, we created a rule-based NLP system made up of expert-developed patterns indicating residential instability at the lead site and enriched the NLP system using insight gained from its application at the other 2 sites. We adapted the algorithm at each site then validated the algorithm using a split-sample approach. We assessed the performance of the algorithm by measures of positive predictive value (precision), sensitivity (recall), and specificity.

Results
The NLP algorithm performed with moderate precision (0.45, 0.73, and 1.0) at 3 sites. The sensitivity and specificity of the NLP algorithm varied across 3 sites (sensitivity: 0.68, 0.85, and 0.96; specificity: 0.69, 0.89, and 1.0).

Discussion
The performance of this NLP algorithm to identify residential instability in 3 different healthcare systems suggests the algorithm is generally valid and applicable in other healthcare systems with similar EHRs.

Conclusion
The NLP approach developed in this project is adaptable and can be modified to extract types of social needs other than residential instability from EHRs across different healthcare systems.
Long-term evaluation of male Florida panther (Puma concolor coryi) reproductive parameters following genetic introgression
Authors: Penfold Linda M , Criffield Marc , Cunningham Mark W , Jansen Deborah , Lotz Mark , Shea Colin , Onorato Dave 
Published: February 2022

AbstractIn 1995, eight female pumas from Texas (Puma concolor stanleyana) were introduced into five areas in South Florida to remediate morphological and biomedical correlates of inbreeding depression that threatened the long-term survival of Florida panthers (P. c. coryi). Initial analysis of the results of this genetic introgression initiative has highlighted its success, including growth of the population, increased genetic heterozygosity, and reduced frequencies of physical traits associated with inbreeding, including cryptorchidism. However, panthers remain isolated from other puma populations and natural gene flow is not currently plausible. Using data collected from 65 panthers in the post-genetic introgression era (1998–2020), we assessed the benefits accrued to male panther reproductive parameters via this management initiative, the effect of genetic variables, and compared results to historic data. Microsatellite data were used to determine individual heterozygosity levels and qualify panther genetic ancestry as admixed (i.e., panthers descended from crosses with female Texas puma) or canonical (i.e., panthers that comprised most of the population prior to genetic introgression). A total of 47 admixed and 10 canonical panthers were identified; mean individual heterozygosity of canonical panthers (0.39) was significantly different from admixed panthers (0.63; t54 = 4.7, P-value &lt; 0.001). Admixed panthers exhibited higher mean values for total testicular volume, structurally normal spermatozoa, and total sperm in comparison to canonical panthers. The progressive improvement of sperm metrics demonstrates that the benefits of genetic introgression continue to have a positive impact on the population &gt;25 years since the release of the Texas pumas. However, the Florida panther population remains small, isolated, and vulnerable to deterministic and stochastic events that warrants continued monitoring to assess when additional genetic introgression initiatives will need to be implemented in the future.
Medication–Associated Phthalate Exposure and Childhood Cancer Incidence
Authors: Ahern Thomas P , Spector Logan G , Damkier Per , Öztürk Esen Buket , Ulrichsen Sinna P , Eriksen Katrine , Lash Timothy L , Sørensen Henrik Toft , Cronin-Fenton Deirdre P 
Published: February 2022

Abstract

Background
Human phthalate exposure is widespread through contact with myriad consumer products. Exposure is particularly high through medications formulated with phthalates. Phthalates disrupt normal endocrine signaling and are associated with reproductive outcomes and incidence of some cancers. We measured associations between gestational and childhood medication-associated phthalate exposures and the incidence of childhood cancers.

Methods
We identified all live births in Denmark between 1997 and 2017, including both children and birth mothers. Using drug ingredient data merged with the Danish National Prescription Registry, we measured phthalate exposure through filled prescriptions for mothers during pregnancy (gestational exposure) and for children from birth until age 19 years (childhood exposure). Incident childhood cancers were ascertained from the Danish Cancer Registry, and associations were estimated with Cox regression models.

Results
Among 1 278 685 children, there were 2027 childhood cancer cases diagnosed over 13.1 million person–years of follow-up. Childhood phthalate exposure was strongly associated with incidence of osteosarcoma (hazard ratio [HR] = 2.78, 95% confidence interval [CI] = 1.63 to 4.75). We also observed a positive association with incidence of lymphoma (HR = 2.07, 95% CI = 1.36 to 3.14), driven by associations with Hodgkin and non-Hodgkin lymphoma but not Burkitt lymphoma. Associations were apparent only for exposure to low-molecular phthalates, which have purportedly greater biological activity.

Conclusions
Childhood phthalate exposure was associated with incidence of osteosarcoma and lymphoma before age 19 years. Lingering questions include which specific phthalate(s) are responsible for these associations, by what mechanisms they occur, and to what extent childhood cancer cases could be avoided by reducing or eliminating the phthalate content of medications and other consumer products.
“Honor List” and “Shame Roll”: Quasi-Experimental Evidence of the Effect of Performance Feedback under Political Control
Authors: Wei Wenchi , Wang Chengwei , Zhai Wenkang , Li Wenzhao 
Published: February 2022

Abstract
This article examines how the use of an “honor list” and “shame roll” as a means of performance feedback can influence governments’ future performance improvement, focusing on a prominent performance management reform implemented in Chinese local governments. We draw upon classic behavioral theories of organizations to propose testable hypotheses. The empirical analyses use 3,300 observations based on the 333 grassroots governments of the capital city of China as the unit of analysis. Regression discontinuity design estimations show that entering the honor list reduces governments’ performance improvement in the next period, while entering the shame roll helps governments improve their performance. Moreover, the level of performance improvement is higher at the cutoff for both the honor list and shame roll if governments rely more on the higher authority’s fiscal resources. This study advances a more nuanced understanding of the performance feedback effect under political control and a rigid administrative hierarchy.
Greater soil microbial biomass loss at low frequency of N addition in an Inner Mongolia grassland
Authors: Ning Qiushi , Jiang Liangchao , Wang Ruzhen , Wang Jing , Han Xingguo , Yang Junjie 
Published: February 2022

Abstract
Soil microbial biomass is critical for biogeochemical cycling and serves as precursor for carbon (C) sequestration. The anthropogenic nitrogen (N) input has profoundly changed the pool of soil microbial biomass. However, traditional N deposition simulation experiments have been exclusively conducted through infrequent N addition, which may have caused biased effects on soil microbial biomass compared with those under the natural and continuous N deposition. Convincing data are still scarce about how the different N addition frequencies affect soil microbial biomass. By independently manipulating the frequencies (2 times vs. 12 times N addition yr–1) and the rates (0–50 g N m−2 yr−1) of N addition, our study aimed to examine the response of soil microbial biomass C (MBC) to different N addition frequencies with increasing N addition rates. Soil MBC gradually decreased with increasing N addition rates under both N addition frequencies, while the soil MBC decreased more at low frequency of N addition, suggesting that traditional studies have possibly overestimated the effects of N deposition on soil microbial biomass. The greater soil microbial biomass loss with low N frequency resulted from the intensified soil acidification, higher soil inorganic N, stronger soil C and N imbalance, less net primary production allocated to belowground and lower fungi to bacteria ratio. To reliably predict the effects of atmospheric N deposition on soil microbial functioning and C cycling of grassland ecosystems in future studies, it is necessary to employ both the dosage and the frequency of N addition.