bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrasound Analyses of the Dorsal Hands for Volumetric Rejuvenation
Authors: Hung Yi-Teng , Cheng Chun-Yu , Chen Chun-Bing , Huang Yau-Li
Published: February 2022

Background

Volumetric hand rejuvenation of the dorsal hands is increasingly applied for aged, skeletonized dorsal hand skin, with prominent veins, tendons, and joints due to volumetric loss of subcutaneous fat. However, the aging process of the fatty laminae remains unexplored.

Objectives

The aim of this study was to investigate the impact of aging and potential determinants on the fatty laminae to improve the therapeutic effect of volumetric injection.

Methods

This cross-sectional study enrolled 105 Taiwanese participants aged ≥20 years, divided into 5 decade-based age groups. A single blinded practitioner measured the thicknesses of the dorsal superficial lamina (DSL), dorsal intermediate lamina (DIL), and dorsal deep lamina (DDL) by ultrasonography. The potential determining factors of the laminae thickness (age, sex, BMI, and hand dominance) were analyzed.

Results

The thicknesses of the 3 laminae decreased with age, with the mean decrease in thickness from the 20s to >60 years of the DSL, DIL, and DDL being 0.21 mm (30.0%), 1.38 mm (63.89%), and 0.31 mm (20.95%), respectively. The decrease in DIL thickness was the greatest and most significant in subjects aged >30 years. Multiple linear regression analysis showed age to be the only determinant of thickness for the 3 laminae (all P < 0.001), although the DIL was significantly thicker in men (P < 0.001).

Conclusions

Volumetric fat loss was noted in the 3 fatty laminae of dorsal hands during aging; the DIL showed the greatest progressive fat loss after the age of 30. Volumetric rejuvenation of the 3 laminae may result in the most aesthetic appearance, especially in women.
A review of machine learning approaches for drug synergy prediction in cancer
Authors: Torkamannia Anna , Omidi Yadollah , Ferdousi Reza
Published: February 2022

Combinational pharmacotherapy with the synergistic/additive effect is a powerful treatment strategy for complex diseases such as malignancies. Identifying synergistic combinations with various compounds and structures requires testing a large number of compound combinations. However, in practice, examining different compounds by in vivo and in vitro approaches is costly, infeasible and challenging. In the last decades, significant success has been achieved by expanding computational methods in different pharmacological and bioinformatics domains. As promising tools, computational approaches such as machine learning algorithms (MLAs) are used for prioritizing combinational pharmacotherapies. This review aims to provide the models developed to predict synergistic drug combinations in cancer by MLAs with various information, including gene expression, protein–protein interactions, metabolite interactions, pathways and pharmaceutical information such as chemical structure, molecular descriptor and drug–target interactions.
MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block
Authors: Liu Mengya , Sun Zhan-Li , Zeng Zhigang , Lam Kin-Man
Published: February 2022

DNA N6-methyladenine (6mA) is produced by the N6 position of the adenine being methylated, which occurs at the molecular level, and is involved in numerous vital biological processes in the rice genome. Given the shortcomings of biological experiments, researchers have developed many computational methods to predict 6mA sites and achieved good performance. However, the existing methods do not consider the occurrence mechanism of 6mA to extract features from the molecular structure. In this paper, a novel deep learning method is proposed by devising DNA molecular graph feature and residual block structure for 6mA sites prediction in rice, named MGF6mARice. Firstly, the DNA sequence is changed into a simplified molecular input line entry system (SMILES) format, which reflects chemical molecular structure. Secondly, for the molecular structure data, we construct the DNA molecular graph feature based on the principle of graph convolutional network. Then, the residual block is designed to extract higher level, distinguishable features from molecular graph features. Finally, the prediction module is used to obtain the result of whether it is a 6mA site. By means of 10-fold cross-validation, MGF6mARice outperforms the state-of-the-art approaches. Multiple experiments have shown that the molecular graph feature and residual block can promote the performance of MGF6mARice in 6mA prediction. To the best of our knowledge, it is the first time to derive a feature of DNA sequence by considering the chemical molecular structure. We hope that MGF6mARice will be helpful for researchers to analyze 6mA sites in rice.
Integrated Genome Browser App Store
Authors: Shanbhag Sameer , Patil Riddhi , Zahara Noor , Shetty Chirag , Weidenhammer Rachel , Watharkar Sneha , Tambvekar Pranav , Badzuh Philip P , Dias Chester , Vankayala Narendra , Kulkarni Prutha , Vallapureddy Charan , Kulkarni Shamika , Nikhare Pooja , Freese Nowlan H , Loraine Ann E
Published: February 2022

Rapid progress in genome science requires equally rapid visualization software development so that researchers can better explore and understand novel datasets. To make developing new visualizations faster and easier, we previously re-factored the Integrated Genome Browser (IGB), a desktop Java application with dozens of features, into a pluggable application framework that can accept new functionality as plug-ins, called IGB Apps. However, developers lacked a centralized location for sharing Apps, making it hard to connect with potential users. To fill this gap, we created an App Store for IGB, a user-friendly Web site for developers to release and document Apps, and for users to find them.

Availability and implementation

The IGB App Store is available from https://bioviz.org.
PCIG: a web-based application to explore immune–genomics interactions across cancer types
Authors: Pedrola Anna , Franch-Expósito Sebastià , Lahoz Sara , Esteban-Fabró Roger , Dienstmann Rodrigo , Bassaganyas Laia , Camps Jordi
Published: February 2022

Motivation

Genomic alterations can modulate the tumor immunophenotype depending on their nature and tissue of origin. Although this immune–genomic interaction may shape disease progression and response to immunotherapy, the factors governing such dynamics and the influence of each tissue-specific context remain poorly understood.

Results

Here, we have developed the PanCancer ImmunoGenomics (PCIG) tool, a web-based resource that provides researchers with the opportunity to mine immunome–genome relationships across several cancer types using data from the Pan-Cancer Analysis of Whole-Genomes (PCAWG) study, which comprises >2,600 samples spanning across 20 different cancer primary sites. PCIG yields an integrative analysis of the crosstalk between somatic genomic alterations and different immune features, thus helping to understand immune response-related processes.

Availability and implementation

PCIG is freely available at https://pcig.vhio.net and is supported by all major web browsers. PCIG was developed with Django, which is a Python-based free and open-source framework, and it uses SQL Server as a relational database management system. The code is freely available for download at GitHub https://github.com/AnnaPG/PCIG and in its online supplementary material.

Supplementary information

Supplementary data are available at Bioinformatics online.
Synergies and Trade-Offs in Reducing Impacts of Unconventional Oil and Gas Development on Wildlife and Human Health
Authors: Deziel Nicole C , Shamasunder Bhavna , Pejchar Liba
Published: February 2022

With growing evidence of widespread health and environmental impacts from oil and gas activity, localities and states are beginning to develop protective measures. Interdisciplinary approaches that integrate across human, wildlife, domesticated animal, and land health are likely to provide more just and comprehensive solutions than would be possible with siloed approaches. However, this is not common practice, and there is little guidance on how to apply such a strategy. In the present article, we summarize the state of knowledge on the impacts of terrestrial unconventional oil and gas development from the fields of ecology and public health. We then discuss synergies and trade-offs regarding impacts and mitigation strategies emerging from these two literatures. Finally, we provide recommendations for research and practice to fill knowledge gaps and better inform integrated decision-making to achieve multiple benefits and minimize impacts on human, wildlife, domesticated animals, and land health from energy development.
Eso-Sponge® for anastomotic leakage after oesophageal resection or perforation: outcomes from a national, prospective multicentre registry
Authors: Richter Florian , Hendricks Alexander , Schniewind Bodo , Hampe Jochen , Heits Nils , von Schönfels Witigo , Reichert Benedikt , Eberle Katrin , Ellrichmann Mark , Baumann Petra , Egberts Jan-Hendrik , Becker Thomas , Schafmayer Clemens
Published: February 2022

Background

Anastomotic leakage (AL) after oesophagectomy and oesophageal perforations are associated with significant morbidity and mortality. Minimally invasive endoscopy is often used as first-line treatment, particularly endoluminal vacuum therapy (EVT). The aim was to assess the performance of the first commercially available endoluminal vacuum device (Eso-Sponge®) in the management of AL and perforation of the upper gastrointestinal tract (GIT).

Methods

The Eso-Sponge® registry was designed in 2014 as a prospective, observational, national, multicentre registry. Patients were recruited with either AL or perforation within the upper GIT. Data were collected with a standardized form and transferred into a web-based platform. Twenty hospitals were enrolled at the beginning of the study (registration number NCT02662777; http://www.clinicaltrials.gov). The primary endpoint was successful closure of the oesophageal defect.

Results

Eleven out of 20 centres recruited patients. A total of 102 patients were included in this interim analysis; 69 patients with AL and 33 with a perforation were treated by EVT. In the AL group, a closure of 91 per cent was observed and 76 per cent was observed in the perforation group. The occurrence of mediastinitis (P = 0.002) and the location of the defect (P = 0.008) were identified as significant predictors of defect closure.

Conclusions

The Eso-Sponge® registry offers the opportunity to collate data on EVT with a uniform, commercially available product to improve standardization. Our data show that EVT with the Eso-Sponge® is an option for the management of AL and perforation within the upper GIT.
Algorithms for inference in SVARs identified with sign and zero restrictions
Authors: Read Matthew
Published: February 2022

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

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 < 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 < 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

During 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

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

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

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

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

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

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

In 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 < 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 >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

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

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

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.
Umbilical epidermal inclusion cysts, an unusual cause of umbilical mass following laparoscopic surgery: case report
Authors: Li Christine , Robertson Amanda
Published: February 2022

Umbilical lumps are a common presentation that can represent a diagnostic challenge as the differentials are broad. Epidermal inclusion cysts occur when epidermal cells are implanted in the dermis following trauma, or surgery. Although epidermal inclusion cysts are common, they are rarely cause of umbilical mass, with less than 10 cases described in the literature. Very few cases have been reported following abdominal surgery and none following laparoscopy. These lesions can occur with or without pain, mass, redness or spontaneous discharge and symptoms can persist for years. This paper reports a case of an umbilical epidermal inclusion cyst in a 52-year-old female presenting with a 6-week history of a painful, red umbilical lump on a background of two previous diagnostic laparoscopies. This was successfully treated with complete excision of the lesion.
Malignant epithelioid hemangioendothelioma of the ear
Authors: Senaratne Radha , Casey Máire-Caitlín , Kelly Jack L
Published: February 2022

Skin cancer is the most common cancer in Ireland. Our patient presented for removal of a cutaneous lesion on his ear. The histopathological diagnosis was malignant epithelioid hemangioendothelioma. It is very rare for this to present primarily as a cutaneous lesion. Here, we discuss the management of this patient and the surveillance he required. It is important to consider alternative histological diagnoses in patients presenting with cutaneous lesions and how this affects management and prognosis.
Pancreatic and splenic tuberculosis mimicking a pancreatic cancer with splenic metastases in an immunocompetent adolescent: a case report
Authors: Konlack Mekontso Joel Gabin , Nguefang Tchoukeu Guy Loic , Nwabo Fabrice Leo Tamhouo , Mbessoh Kengne Ulrich Igor , Nana Gwabap Michel Arsène , Notue Yves Alain , Moifo Boniface , Sando Linda Ngueffo , Kabeyene Okono Angèle Clarisse
Published: February 2022

We present a case of pancreatic and splenic tuberculosis (TB) in a 15-year-old human immunodeficiency virus-negative patient who was initially misdiagnosed as suffering from a pancreatic carcinoma with splenic metastases. Pancreatic and splenic TB are extremely rare in young immunocompetent patients, with a nonspecific clinical presentation, making the diagnosis elusive.
A lipid viewpoint on the plant endoplasmic reticulum stress response
Authors: Kanehara Kazue , Cho Yueh , Yu Chao-Yuan
Published: February 2022

Organisms, including humans, seem to be constantly exposed to various changes, which often have undesirable effects, referred to as stress. To keep up with these changes, eukaryotic cells may have evolved a number of relevant cellular processes, such as the endoplasmic reticulum (ER) stress response. Owing to presumably intimate links between human diseases and the ER function, the ER stress response has been extensively investigated in various organisms for a few decades. Based on these studies, we now have a picture of the molecular mechanisms of the ER stress response, one of which, the unfolded protein response (UPR), is highly conserved among yeasts, mammals, higher plants, and green algae. In this review, we attempt to highlight the plant UPR from the perspective of lipids, especially membrane phospholipids. Phosphatidylcholine (PtdCho) and phosphatidylethanolamine (PtdEtn) are the most abundant membrane phospholipids in eukaryotic cells. The ratio of PtdCho to PtdEtn and the unsaturation of fatty acyl tails in both phospholipids may be critical factors for the UPR, but the pathways responsible for PtdCho and PtdEtn biosynthesis are distinct in animals and plants. We discuss the plant UPR in comparison with the system in yeasts and animals in the context of membrane phospholipids.
Erythrocyte Sedimentation Rate in Patients with Renal Insufficiency and Renal Replacement Therapy
Authors: Buckenmayer Anna , Dahmen Lotte , Hoyer Joachim , Kamalanabhaiah Sahana , Haas Christian S
Published: February 2022

Background

Determination of the erythrocyte sedimentation rate (ESR) is a simple diagnostic tool for estimating systemic inflammation. It remains unclear whether ESR is influenced by renal disease or renal replacement therapy (RRT).

Objective

To report the incidence and extent of ESR elevations in patients with chronic kidney disease (CKD) and the possible impact of RRT.

Methods

We performed a single-center, retrospective study in inpatients with or without renal disease and in those with RRT, comparing ESR levels and other laboratory and clinical information.

Results

A total of 203 patients were included. On average, ESR was elevated (mean [SD], 51.7 [34.6] mm/h), with no statistically significant difference between the patient groups. Only those receiving PD showed significantly higher ESR (78.3 [33.1] mm/h; P < .001).

Conclusions

ESR testing can be used without restriction in patients with CKD and in patients undergoing hemodialysis and who have received kidney transplantation; however, this measurement should be monitored carefully in patients with PD.
One-dimensional fragment over words and trees
Authors: Kieroński Emanuel , Kuusisto Antti
Published: February 2022

One-dimensional fragment of first-order logic is obtained by restricting quantification to blocks of existential (universal) quantifiers that leave at most one variable free. We investigate this fragment over words and trees, presenting a complete classification of the complexity of its satisfiability problem for various navigational signatures and comparing its expressive power with other important formalisms. These include the two-variable fragment with counting and the unary negation fragment.
Engaging an infrastructure of time production with international law
Authors: Gordon Geoff
Published: February 2022

This article explores international legal entanglements with the infrastructure of Coordinated Universal Time (UTC), a socio-technical construction that comprises the globally definitive measure of seconds, minutes and hours working in lockstep around the world. UTC is produced and maintained with international law, through international administration with social, political, material and technical dimensions. In analysing mutual entanglements of international law with infrastructural relations organized around UTC, the article assesses their imbrication in globalized governance routines and distributive patterns, instantiated here with reference to the field of finance. The article further considers ways to engage legal-infrastructural relations for material change in patterns of governance.
Survey for Distant Solar Twins (SDST) – I. epic method for stellar parameter measurement
Authors: Lehmann Christian , Murphy Michael T , Liu Fan , Flynn Chris , Berke Daniel A
Published: February 2022

Solar twins are stars of key importance to the field of astronomy and offer a multitude of science applications. Only a small number (≲200) of solar twins are known today, all of which are relatively close to our Sun (${\lesssim}{800}\, {\rm pc}$). The goal of our Survey for Distant Solar Twins (SDST) is to identify many more solar twin and solar analogue stars out to much larger distances (${\sim}{4}\, {\rm kpc}$). In this paper, we present a new method to identify solar twins using relatively low S/N, medium resolving power ($R\sim 28\, 000$) spectra that will be typical of such distant targets observed with HERMES on the ${3.9}\, {\rm m}$ Anglo-Australian Telescope (AAT). We developed a novel approach, namely epic, to measure stellar parameters (SPs) which we use to identify stars similar to our Sun. epic determines the stellar atmospheric parameters (effective temperature Teff, surface gravity log g, and metallicity [Fe/H]) using differential equivalent width (EW) measurements of selected spectroscopic absorption features and a simple model, trained on previously analysed spectra, that connects these EWs to the SPs. The reference for the EW measurements is a high S/N solar spectrum which is used to minimize several systematic effects. epic is fast, optimized for Sun-like stars and yields SP measurements with small enough uncertainties to enable spectroscopic identification of solar twin and analogue stars up to ${\sim}{4}\, {\rm kpc}$ away using AAT/HERMES, i.e. $\sigma \left(T_{\mathrm{eff}}, \log g, \textrm {[Fe/H]}\right) = \left({50}\, {\rm K}, {0.08}\, {\rm dex}, {0.03}\, {\rm dex}\right)$ on average at S/N = 25.
Search for X/Z-shaped radio sources from TGSS ADR 1
Authors: Bhukta Netai , Pal Sabyasachi , Mondal Sushanta K
Published: February 2022

A small subclass of radio galaxies, exhibiting a pair of secondary low-surface-brightness radio lobes oriented at an angle to the primary high-surface-brightness lobes, is the group known as X-shaped radio galaxies (XRGs). In some cases, it is seen that less luminous secondary lobes emerge from the edges of the primary high-brightness lobes, giving a Z-symmetric morphology. These objects are known as Z-shaped radio galaxies (ZRGs). From the Tata Institute of Fundamental Research (TIFR) Giant Metrewave Radio Telescope (GMRT) Sky Survey at 150 MHz, we present systematic search results for XRGs and ZRGs. We identified a total of 58 radio sources, out of which 40 are XRGs and 18 are ZRGs. Taking advantage of the large sample size of XRGs and ZRGs reported in the current work, different properties of XRGs and ZRGs are studied. Out of 58 XRGs and ZRGs presented here, 19 (32 per cent) are FR I and 33 (57 per cent) are FR II radio galaxies. For four XRGs and three ZRGs, the morphology is so complex that they could not be classified. We have estimated the radio luminosity and spectral index of newly discovered winged radio galaxies and made a comparative study with previously detected XRGs and ZRGs. Most of the XRGs show a steep spectral index between 150 and 1400 MHz and only 14 per cent of the sources show a flat spectrum, but for ZRGs a good proportion of the sources (36 per cent) show a flat spectrum.
H ii regions in CALIFA survey: II. The relation between their physical properties and galaxy evolution
Authors: Espinosa-Ponce C , Sánchez S F , Morisset C , Barrera-Ballesteros J K , Galbany L , García-Benito R , Lacerda E A D , Mast D
Published: February 2022

We present here the exploration of the physical properties of the sample of H ii regions and aggregations of the last H ii regions catalogue of the Calar Alto Legacy Integral Field Area (CALIFA) survey. This sample comprises the optical spectroscopic properties of more than ∼26 000 ionized regions corresponding to 924 galaxies from the Integral Field Spectroscopy data, including the flux intensity and equivalent widths and the properties of their underlying stellar population. In the current study, we derive a set of physical quantities for all these regions based on those properties, including (i) the fraction of young stars; (ii) the ionization strength (using six different estimations); (iii) the oxygen abundance (using 25 different calibrators); (iv) the nitrogen and nitrogen-to-oxygen abundance; (v) the dust extinction; and (vi) the electron density. Using this data set, we explore how the loci in the classical diagnostic diagrams are connected with those quantities, the radial distributions of these parameters, and the interrelations between themselves and with the properties of the underlying stellar populations. We conclude that many properties of the H ii regions are tightly related to the galactic stellar evolution at the location where those regions are observed. Those properties are modulated only as a second-order effect by the properties of the ionizing stars and the ionized nebulae that do not depend on the astrophysical context in which they are formed. Our results highlight the importance of H ii regions to explore the chemical evolution in galaxies, clarifying which of their properties can be used as proxies of that evolution.
Skyrmions-based logic gates in one single nanotrack completely reconstructed via chirality barrier
Authors: Yu Dongxing , Yang Hongxin , Chshiev Mairbek , Fert Albert
Published: February 2022

Logic gates based on magnetic elements are promising candidates for logic-in-memory applications with non-volatile data retention, near-zero leakage and scalability. In such spin-based logic devices, however, the multi-strip structure and fewer functions are obstacles to improving integration and reducing energy consumption. Here we propose a skyrmions-based single-nanotrack logic family including AND, OR, NOT, NAND, NOR, XOR and XNOR that can be implemented and reconstructed by building and switching the Dzyaloshinskii–Moriya interaction (DMI) chirality barrier on a racetrack memory. Besides the pinning effect of the DMI chirality barrier on skyrmions, the annihilation, fusion and shunting of two skyrmions with opposite chirality are also achieved and demonstrated via local reversal of the DMI, which are necessary for the design of an engineer programmable logic nanotrack, transistor and complementary racetrack memory.