bluuebunny/crossref_metadata_2025 huggingface dataset:
A Quality Improvement Initiative to Improve Discharge Timeliness and Documentation
Authors: Larrow Annie , Chong Amy , Robison Treavor , Patel Aarti , Kuelbs Cynthia , Fisher Erin , Hershey Daniel , Pierce Heather
Published: July 2021

Introduction:

Discharge communication is critical for the continuity of patient care. However, discharge summaries are often not available in time for follow-up visits, and the content is inconsistent. We aimed to decrease the average time to discharge summary completion by 25%, reduce deficiencies (information errors) by 50%, and increase discharge summary template use to >80% in 6 months.

Methods:

A pediatric interprofessional team used quality improvement methods to identify barriers and implement interventions, including discharge summary completion time expectation, electronic health record discharge summary template changes addressing gaps, and training. Notable changes to the template included embedded writing tips to guide writers and specific template choices for common diagnoses to standardize content. The primary outcome measure was the mean discharge summary completion time. Secondary measures were the percentage of discharge summaries with deficiencies and the rate of template use.

Results:

After interventions, the mean discharge summary completion time decreased by 70% (from 71.5 to 21.8 hours). Discharge summary deficiencies decreased 44% (from 4.5% to 2.5%), and template use increased from 62% to 97%.

Conclusion:

Quality improvement methods and a newly designed electronic health record-discharge summary template were used to dramatically improve discharge summary timeliness and standardize content to streamline continuity of care.
18F-Fluoroestradiol Tumor Uptake Is Influenced by Structural Components in Breast Cancer
Authors: Takahashi Mizuho , Maeda Hiroyuki , Tsujikawa Tetsuya , Kono Hiroko , Mori Tetsuya , Kiyono Yasushi , Okazawa Hidehiko , Noriki Sakon , Imamura Yoshiaki , Goi Takanori
Published: July 2021

Purpose

Estrogen receptor (ER) is expressed in the majority of invasive breast cancer and is an important prognostic indicator. The tumor stroma also plays an important role in disease progression. This study evaluated the effect of stromal components on 16α-[18F]-fluoro-17β-estradiol (18F-FES) uptake in breast cancer and proposed a partial-volume correction method for 18F-FES PET based on histopathological analyses.

Patients and Methods

Fifteen patients with biopsy-confirmed breast cancer underwent preoperative 18F-FES PET. Estrogen receptor expression in biopsy specimens was assayed by immunohistochemistry, cellular components in surgical specimens were measured using hematoxylin-eosin staining, and nuclear components in surgical and biopsy specimens were measured using Azan-Mallory staining. The relationship between 18F-FES SUV of the primary tumor and histopathological findings including ER expression, the Allred score, ER-positive cellular component ratio, and ER-positive nuclear component ratio (NCR) was examined. The relationship between stroma-free 18F-FES SUV and ER expression was also examined.

Results

18F-FES uptake was not significantly positively correlated with ER expression (r = 0.44, P = 0.10). 18F-FES uptake was significantly correlated with the Allred score, ER-positive cellular component ratio, and ER-positive NCR in surgical specimens (ρ = 0.60, P = 0.02; r = 0.55, P = 0.03; and r = 0.65, P = 0.01, respectively). 18F-FES uptake was predominantly correlated with ER-positive NCR in biopsy specimens (r = 0.84, P < 0.001). Stroma-free 18F-FES SUV was significantly correlated with ER expression (r = 0.78, P < 0.01).

Conclusions

18F-FES PET predominantly demonstrates the level of ER expression in breast cancer cell nucleus. Although tumor 18F-FES uptake is affected by the degree of stromal components, the partial volume effect on the uptake can be corrected by stroma-volume fraction in Azan-Mallory staining.
Bone Marrow Metastases From Gastric Adenocarcinoma on 68Ga-FAPI-04 PET/CT
Authors: Huang Yilin , Cao Jianpeng , Peng Dengsai , Liu Huipan , Chen Yue
Published: July 2021

A 37-year-old woman complained of fatigue and dizziness for 4 days. Bone marrow biopsy findings were suggestive of digestive tract–derived metastases. 18F-FDG PET/CT revealed mild FDG avidity in the stomach and bone marrow, whereas 68Ga-FAPI-04 PET/CT showed strong FAPI uptake in the FDG-avid lesions. The patient was diagnosed with bone marrow metastases from gastric cancer by a bone marrow biopsy.
18F-FDG PET/CT and 68Ga-FAPI-4 PET/CT Findings of Bilateral Knee Osteoarthritis in a Patient With Uveal Malignant Melanoma
Authors: Erol Fenercioğlu Özge , Beyhan Ediz , Ergül Nurhan , Arslan Esra , Çermik Tevfik Fikret
Published: July 2021

We present the findings of 68Ga-FAPI-4 PET/CT and 18F-FDG PET/CT of a metastatic malignant melanoma patient with osteoarthritis. A 65-year-old woman with a history of metastatic uveal malignant melanoma was referred to 18F-FDG PET/CT for restaging after enucleation and chemotherapy. 18F-FDG PET/CT imaging showed high radiotracer uptake in liver metastases; additionally mild uptake due to osteoarthritis was observed in both knees. However, although 68Ga-FAPI-4 showed lower uptake in liver lesions, it showed a more prominent uptake in both knee joints compared with 18F-FDG.
Treatment Effects and Lip Profile Changes Following Surgical Mandibular Advancement Versus Premolar Extractions in Class II Div 1 Malocclusion: A Randomized Controlled Trial
Authors: Kochar Gagan Deep , Londhe Sanjay , Chopra Sukhbir Singh , Kohli Sarvraj , Kohli V.S. , Chakranarayan Ashish , Kambojh Ashish , Bhatt Sudarshan
Published: July 2021

No randomized controlled trial has compared the treatment outcome between surgical mandibular advancement and premolar extractions in class II malocclusion. This 2-arm parallel randomized controlled trial evaluated the treatment effects and lip profile changes in skeletal class II adult patients subjected to bilateral sagittal split ramus osteotomy for mandibular advancement and those treated with premolar extractions. Seventy skeletal class II patients were accessed and forty-six subjects who fulfilled inclusion criteria were distributed randomly into Group CG (patients: 23, mean age: 21.28 ± 2.69 years) and Group SG (patients: 23, mean age: 21.15 ± 2.64 years). Group CG was subjected to extraction of maxillary first premolars and mandibular second premolars followed by implant supported space closure and Group SG was managed by surgical mandibular advancement. Skeletal, dental, and soft-tissue changes were analyzed. The study was single-blinded (statistical analyzer). Groups were closely matched for baseline parameters. In the present trial there was no loss to follow-up. Though overjet and overbite were optimized in both the groups but significant improvement was seen in surgical cases. Group CG demonstrated statistically significant point “A” remodeling, dentoalveolar changes, and increase in nasolabial angle. Group SG exhibited significant sagittal and vertical skeletal improvement and lip position change. Surgical mandibular advancement was found to be a better treatment modality compared to premolars extraction for managing skeletal class II div 1 malocclusion as it permits greater improvement of the profile and skeletal relationship.
European Guideline on Craniofacial Microsomia: A Version for Patients and Families
Authors: Renkema Ruben W. , Spivack Olivia K.C.
Published: July 2021

A European guideline on craniofacial microsomia was developed within the European Reference Network for rare and/or complex craniofacial anomalies and ear, nose, and throat disorders and published in 2020. The guideline provides an overview of optimal care provisions for patients with craniofacial microsomia and recommendations for the improvement of care. This document seeks to provide a tailored overview of this guideline for patients and their families.
Midfacial Soft Tissue Changes After Reduction Malarplasty: A Computed Tomographic Study
Authors: Gao Jiaman , Wei Min , Yuan Jie , Yu Zheyuan , Duan Huichuan , Jiang Taoran , Cao Dejun , Xu Liang
Published: July 2021

Background:

The reduction malarplasty has become one of the most popular esthetic surgeries among Asian women to improve facial contour. However, it is still controversial whether midfacial soft tissue changes after surgery, and more studies are needed.

Methods:

This retrospective observational study reviewed 30 patients who underwent L-shaped reduction malarplasty during January 2018 and August 2019. The preoperative and postoperative soft tissue thickness and the angle of nasolabial fold of the midfacial were assessed using photographs, three-dimensional skull computerized tomography images, and the Wrinkle Severity Rating Scale.

Results:

The postoperative average level of nasolabial fold angle was lower than that observed in preoperative conditions, with the difference being statistically significant (t = -10.262, P < 0.001). The postoperative fifth and sixth layers of soft tissue in the midface were significantly higher than those observed in preoperative tissues.

Conclusions:

Although L-shaped reduction malarplasty has evident effects on soft tissue changes of middle face, they are within acceptable ranges and do not affect patient satisfaction.
Evolving Trends in Unilateral Cleft Lip Repair Based on Continuous Certification by the American Board of Plastic Surgery
Authors: Shah Nikhil , Kearney Aaron M. , Zins James , Gosain Arun K.
Published: July 2021

Background:

The American Board of Plastic Surgery (ABPS) began collecting data from unilateral cleft lip (UCL) corrections in 2011 as a component of the continuous certification process. We evaluated these data to understand practice patterns in UCL repair, in the United States, and whether these practice patterns had changed over the past 9 years.

Methods:

Tracer data for UCL correction were reviewed from its inception in October 2011 through 2016 and compared to UCL cases between 2017 and March 2020. Trends in practice patterns were evaluated against literature reviews meant to coincide with the ABPS continuous certification data.

Results:

A total of 520 cases were included from October 2011 to March 2020. Median age of UCL repair was 4 months and 66% of patients were male. Fifty-one percent of cases presented with a complete cleft lip. There was a decrease in postoperative adverse events when data from 2011 to 2016 was compared to 2017 to 2019 (P = 0.020). Revisions were the most common postoperative adverse event (2%). There was a decrease in nasoalveolar molding from 25% to 12% (P < 0.001) and 56% of total cases underwent a concurrent primary cleft rhinoplasty. The rate of gingivoperiosteoplasty at the time of primary cleft lip repair also fell (9% versus 1%; P < 0.001).

Conclusions:

This article reviews tracer data obtained by the ABPS for UCL repair. The American Board of Plastic Surgery tracer data provides a national, cleft lip-specific database with longer follow-up times than other large databases.
Buried Bumper Syndrome
Authors: Ölmez Şehmus , Sarıtaş Bünyamin , Yalçın Mehmet Suat , Öztürk Nevin Akçaer , Taş Adnan , Kara Banu
Published: July 2021

Buried bumper syndrome (BBS) is a rare and serious complication of percutaneous endoscopic gastrostomy (PEG) tube placement. In the literature, BBS is considered to be a late complication of PEG procedure, but it may occur in the early period after PEG tube placement. Early diagnosis and proper treatment are important. Different treatment modalities may be used to treat BBS. The aim of this study was to evaluate patients with BBS. During a time frame between January 2015 and February 2020, a hospital medical database was screened for PEG placement and BBS. Buried bumper syndrome was found in 36 patients. Demographic and clinical characteristics of these patients were retrospectively investigated. Those who developed BBS in the first month were evaluated as early BBS. Those who developed BBS after more than a month were evaluated as late BBS. The median BBS development time was 135.9 ± 208.1 days (9–834 days). In 18 (50%) patients, BBS developed within the first month. Serious complications such as abscess and peritonitis were observed in 8 (22.2%) patients on admission. Thirty-two (88.9%) of 36 patients were treated with external traction and four patients were treated with surgery. No complications were observed in patients who were treated with traction. Five patients died, of whom three of them died because of BBS complications, whereas two of them died from other causes unrelated to BBS. Buried bumper syndrome is a complication that can be seen in the early period after gastrostomy. External traction is a reliable method for treating these patients. Proper education of patients' relatives and caregivers is very important to prevent BBS and related complications.
Design-Based Bone Marrow Biopsy Training
Authors: Brondfield Sam , Harmon Derek , Romero Dylan , Tai Jenny , Hsu Gerald
Published: July 2021

Introduction

Hematology/oncology fellows must achieve bone marrow biopsy proficiency. However, opportunities for fellows to perform bone marrow biopsies on patients are highly dependent on clinical volume. An easily accessible and feasible system to practice these procedures repetitively has not been described. Other specialties use 3-dimensional (3D)–printed models to practice procedures, but hematology/oncology has not yet incorporated this novel medical education tool, which has the potential to provide such an accessible and feasible system for procedural practice.

Methods

We used design thinking to develop and pilot a bone marrow biopsy simulation using 3D-printed pelvis models. We printed and optimized 2 models through iterative prototyping. In July 2019, we conducted a 1-hour session with 9 fellows. After an anatomy review, fellows practiced biopsies using the models with faculty feedback. To evaluate feasibility, we reviewed session evaluations, measured fellow comfort, surveyed supervising attendings, and gathered fellow and attending feedback.

Results

Fellows rated the 3D session highly. Fellow comfort improved after orientation. Supervisors noted no difference between the 2019 fellows and prior years. Fellows praised the opportunity to rehearse mechanics, receive feedback, and internalize anatomy. Fellows suggested incorporating a female pelvis and more soft tissue. Attending feedback on the model aligned with fellow feedback. We implemented the session again in 2020 with adjustments based on feedback.

Conclusions

Three-dimensional printing represents an accessible and feasible educational tool. Three-dimensional–printed models provide opportunities for iterative practice, feedback, and anatomy visualization. Future iterations should continue to incorporate user feedback to optimize model utility.
Developing Consensus on Simulation Fellowship Requirements on the Path to Accreditation Council of Graduate Medical Education Accreditation
Authors: Tayeb Baraa , Dobiesz Valerie , Pozner Charles N.
Published: July 2021

Introduction

Nonaccredited simulation fellowships have multiplied resulting in fellowship differences. Standardization of fellowship content and requirements is needed, especially if accreditation is to be achieved. Simulation fellowship criteria were developed using expert consensus and the Accreditation Council for Graduate Medical Education requirements to frame the supporting pillars for accreditation.

Methods

Core curricular components, subelements, and requirements for graduation were derived from a literature review and existing fellowship curricula. A modified Delphi process was performed to establish fellowship program content and requirements. A priori criteria for inclusion or exclusion were used during 3 iterative rounds. Experts could recommend items for inclusion.

Results

Fourteen publications and 71 curricula were reviewed with 7 core curriculum components and 44 subelements identified for subsequent expert panel review. All core components were included by consensus: application of teaching and debriefing, business and leadership, curriculum development, educational theory, operational support, research, and assessment and evaluation. Thirty-eight subelements reached consensus. Graduation requirements included a research or scholarly project and a minimum number of debriefing activities, evaluation activities, original simulation curricula, skill-based teaching activities, scenario-based activities, and interprofessional education activities. The maximum number of clinical hours per week was 16 to 20.

Conclusions

Using a modified Delphi process, experts reached consensus on core curriculum components, subelements, graduation requirements, and maximum number of clinical hours to establish Accreditation Council for Graduate Medical Education accreditation criteria for a simulation standardization of simulation fellowships for physicians. Further work is needed to define other parameters including program infrastructure and assessment.
Assessing Competence With a Task Trainer
Authors: Poeppelman Rachel Stork , Coles Mary T. , Heater Thomas , Vohsing Luke , Von Sadovszky Victoria , Lutmer Jeffrey E. , Maa Tensing
Published: July 2021

Introduction

The purpose of this study was to develop a caregiver and healthcare provider assessment tool to evaluate essential tracheostomy skills using a simulated task trainer.

Methods

Three tracheostomy skill checklists were developed: closed suctioning, open suctioning, and tracheostomy change. Checklist items were developed based on institutional guidelines and a literature review. Items were revised based on iterative expert review and pilot testing. A total of 64 intensive care staff and 24 caregivers were evaluated using the checklists, of which 29 staff members and 4 caregivers were rated simultaneously by 2 raters to estimate interrater reliability. The relationships between checklist performance and staff demographics (experience and discipline) were calculated. A survey examining the selection of automatic fail items and minimum passing score was sent to 660 multidisciplinary staff members.

Results

Intraclass correlations were 0.93 for closed suctioning, 0.93 for open suctioning, and 0.76 for tracheostomy change. Staff performance only correlated with experience for the tracheostomy change checklist and was inconsistently associated with discipline (respiratory therapy vs nursing). A large, multidisciplinary survey with 132 of 660 respondents confirmed the selection of automatic fail items and minimum passing score. A total of 92.9% of the survey respondents agreed with a minimum passing score of 80%.

Conclusions

We developed 3 essential tracheostomy skill checklists with multiple sources of validity evidence to support their use in a simulation-based assessment of tracheostomy skills.
Effectiveness of a Simulation Curriculum on Clinical Application
Authors: Harwayne-Gidansky Ilana , Askin Gulce , Fein Daniel M. , McNamara Courtney , Duncan Ellen , Delaney Kristen , Greenberg Jacob , Mojica Michael , Clapper Timothy , Ching Kevin
Published: July 2021

Introduction

The use of simulation to develop clinical reasoning and medical decision-making skills for common events is poorly established. Validated head trauma rules help identify children at low risk for clinically important traumatic brain injury and guide the need for neuroimaging. We predicted that interns trained using a high-fidelity, immersive simulation would understand and apply these rules better than those trained using a case-based discussion. Our primary outcomes were to determine the effectiveness of a single targeted intervention on an intern's ability to learn and apply the rules.

Methods

This was a prospective randomized controlled trial. Interns were randomized to participate in either a manikin-based simulation or a case discussion. Knowledge and application of the Pediatric Emergency Care Applied Research Network Head Trauma tool were assessed both under testing conditions using standardized vignettes and in clinical encounters. In both settings, interns completed a validated assessment tool to test their knowledge and application of the Pediatric Emergency Care Applied Research Network Head Trauma tool when assessing patients with head injury.

Results

Under testing conditions, both being in the simulation group and shorter time from training were independently associated with higher score under testing conditions using standardized vignettes (P = 0.038 and P < 0.001), but not with clinical encounters.

Conclusions

Interns exposed to manikin-based simulation training demonstrated performance competencies that are better than those in the case discussion group under testing conditions using standardized vignettes, but not in real clinical encounters. This study suggests that information delivery and comprehension may be improved through a single targeted simulation-based education.
A comparative analysis of parechovirus protein structures with other picornaviruses
Authors: Domanska Aušra , Guryanov Sergey , Butcher Sarah J.
Published: July 2021

Parechoviruses belong to the genus
Parechovirus
within the family
Picornaviridae
and are non-enveloped icosahedral viruses with a single-stranded RNA genome. Parechoviruses include human and animal pathogens classified into six species. Those that infect humans belong to the
Parechovirus A
species and can cause infections ranging from mild gastrointestinal or respiratory illness to severe neonatal sepsis. There are no approved antivirals available to treat parechovirus (nor any other picornavirus) infections. In this parechovirus review, we focus on the cleaved protein products resulting from the polyprotein processing after translation comparing and contrasting their known or predicted structures and functions to those of other picornaviruses. The review also includes our original analysis from sequence and structure prediction. This review highlights significant structural differences between parechoviral and other picornaviral proteins, suggesting that parechovirus drug development should specifically be directed to parechoviral targets.
Appendage regeneration is context dependent at the cellular level
Authors: Aztekin Can
Published: July 2021

Species that can regrow their lost appendages have been studied with the ultimate aim of developing methods to enable human limb regeneration. These examinations highlight that appendage regeneration progresses through shared tissue stages and gene activities, leading to the assumption that appendage regeneration paradigms (e.g. tails and limbs) are the same or similar. However, recent research suggests these paradigms operate differently at the cellular level, despite sharing tissue descriptions and gene expressions. Here, collecting the findings from disparate studies, I argue appendage regeneration is context dependent at the cellular level; nonetheless, it requires (i) signalling centres, (ii) stem/progenitor cell types and (iii) a regeneration-permissive environment, and these three common cellular principles could be more suitable for cross-species/paradigm/age comparisons.
On the impact of publicly available news and information transfer to financial markets
Authors: Jazbec Metod , Pàsztor Barna , Faltings Felix , Antulov-Fantulin Nino , Kolm Petter N.
Published: July 2021

We quantify the propagation and absorption of large-scale publicly available news articles from the World Wide Web to financial markets. To extract publicly available information, we use the news archives from the Common Crawl, a non-profit organization that crawls a large part of the web. We develop a processing pipeline to identify news articles associated with the constituent companies in the S&P 500 index, an equity market index that measures the stock performance of US companies. Using machine learning techniques, we extract sentiment scores from the Common Crawl News data and employ tools from information theory to quantify the information transfer from public news articles to the US stock market. Furthermore, we analyse and quantify the economic significance of the news-based information with a simple sentiment-based portfolio trading strategy. Our findings provide support for that information in publicly available news on the World Wide Web has a statistically and economically significant impact on events in financial markets.
Principled network extraction from images
Authors: Baptista Diego , De Bacco Caterina
Published: July 2021

Images of natural systems may represent patterns of network-like structure, which could reveal important information about the topological properties of the underlying subject. However, the image itself does not automatically provide a formal definition of a network in terms of sets of nodes and edges. Instead, this information should be suitably extracted from the raw image data. Motivated by this, we present a principled model to extract network topologies from images that is scalable and efficient. We map this goal into solving a routing optimization problem where the solution is a network that minimizes an energy function which can be interpreted in terms of an operational and infrastructural cost. Our method relies on recent results from optimal transport theory and is a principled alternative to standard image-processing techniques that are based on heuristics. We test our model on real images of the retinal vascular system, slime mould and river networks and compare with routines combining image-processing techniques. Results are tested in terms of a similarity measure related to the amount of information preserved in the extraction. We find that our model finds networks from retina vascular network images that are more similar to hand-labelled ones, while also giving high performance in extracting networks from images of rivers and slime mould for which there is no ground truth available. While there is no unique method that fits all the images the best, our approach performs consistently across datasets, its algorithmic implementation is efficient and can be fully automatized to be run on several datasets with little supervision.
Numerical method for parameter inference of systems of nonlinear ordinary differential equations with partial observations
Authors: Chen Yu , Cheng Jin , Gupta Arvind , Huang Huaxiong , Xu Shixin
Published: July 2021

Parameter inference of dynamical systems is a challenging task faced by many researchers and practitioners across various fields. In many applications, it is common that only limited variables are observable. In this paper, we propose a method for parameter inference of a system of nonlinear coupled ordinary differential equations with partial observations. Our method combines fast Gaussian process-based gradient matching and deterministic optimization algorithms. By using initial values obtained by Bayesian steps with low sampling numbers, our deterministic optimization algorithm is both accurate, robust and efficient with partial observations and large noise.
Domestic egg-laying hens,Gallus gallus domesticus, do not modulate flapping flight performance in response to wing condition
Authors: León Brianna M. , Tobalske Bret W. , Sassi Neila Ben , Garant Renée , Powers Donald R. , Harlander-Matauschek Alexandra
Published: July 2021

Wild birds modulate wing and whole-body kinematics to adjust their flight patterns and trajectories when wing loading increases flight power requirements. Domestic chickens (Gallus gallus domesticus) in backyards and farms exhibit feather loss, naturally high wing loading, and limited flight capabilities. Yet, housing chickens in aviaries requires birds to navigate three-dimensional spaces to access resources. To understand the impact of feather loss on laying hens' flight capabilities, we symmetrically clipped the primary and secondary feathers before measuring wing and whole-body kinematics during descent from a 1.5 m platform. We expected birds to compensate for increased wing loading by increasing wingbeat frequency, amplitude and angular velocity. Otherwise, we expected to observe an increase in descent velocity and angle and an increase in vertical acceleration. Feather clipping had a significant effect on descent velocity, descent angle and horizontal acceleration. Half-clipped hens had lower descent velocity and angle than full-clipped hens, and unclipped hens had the highest horizontal acceleration. All hens landed with a velocity two to three times greater than in bird species that are adept fliers. Our results suggest that intact laying hens operate at the maximal power output supported by their anatomy and are at the limit of their ability to control flight trajectory.
The risk for a new COVID-19 wave and how it depends on
R
0
, the current immunity level and current restrictions
Authors: Britton Tom , Trapman Pieter , Ball Frank
Published: July 2021

The COVID-19 pandemic has hit different regions differently. The current disease-induced immunity level
î
in a region approximately equals the cumulative fraction infected, which primarily depends on two factors: (i) the initial potential for COVID-19 in the region (
R
0
), and (ii) the preventive measures put in place. Using a mathematical model including heterogeneities owing to age, social activity and susceptibility, and allowing for time-varying preventive measures, the risk for a new epidemic wave and its doubling time are investigated. Focus lies on quantifying the minimal overall effect of preventive measures
p
Min
needed to prevent a future outbreak. It is shown that
î
plays a more influential roll than when immunity is obtained from vaccination. Secondly, by comparing regions with different
R
0
and
î
it is shown that regions with lower
R
0
and low
î
may need higher preventive measures (
p
Min
) compared with regions having higher
R
0
but also higher
î
, even when such immunity levels are far from herd immunity. Our results are illustrated on different regions but these comparisons contain lots of uncertainty due to simplistic model assumptions and insufficient data fitting, and should accordingly be interpreted with caution.
Monitoring moisture content and evaporation kinetics from mine slurries through albedo measurements to help predict and prevent dust emissions
Authors: Maurais Josée , Orban Frédéric , Dauphinais Emrik , Ayotte Patrick
Published: July 2021

The prediction and prevention of fugitive dust emissions from mine tailings surfaces depend largely on our ability to monitor and monitor and predict the evolution of tailings moisture content (TMC). Albedo measurements are demonstrated here to be valuable tools to quantify TMC in bauxite residue samples under controlled conditions in the laboratory. The difference in albedo between 1.30 and 1.55 µm obtained through the infrared integrating sphere method shows good correlations with those acquired with a field spectroradiometer while both are strongly correlated with TMC. Additionally, continuous spectroscopic characterization of evaporating residues is shown to reveal the evolution in their surface drying rates. These optical methods could help predict surface drying state, thereby improving the accuracy of dust emissions risk assessment protocols that support mining industries intervention and mitigation strategies.
Forensic characteristics and population construction of two major minorities from southwest China revealed by a novel 37 Y-STR loci system
Authors: Luo Li , Yao Lilan , Chai Siyu , Zhang Hao , Li Min , Yu Jian , Hu Xijie , Li Chengtao , Bian Yingnan , Chen Pengyu
Published: July 2021

Y-chromosome short tandem repeats (Y-STRs) have become important supplementary evidence in forensic science. Nowadays, the Y-chromosome STR haplotype reference database (YHRD) contains abundant Y-STR haplotype data from all over the world, while haplotype data of Guizhou Miao and Tujia are scarce. Hence, genetic polymorphisms of 37 Y-STRs were investigated in 446 unrelated males (206 Miao males and 246 Tujia males) residing in Guizhou Province. A total of 206 and 242 unique haplotypes with the highest diversity value of 0.9665 and 0.9470 were obtained. The heatmap, multidimensional scaling (MDS), the unweighted pair-group method with arithmetic means (UPGMA) tree and principal component analysis (PCA) based on the genetic distance (Rst) value within our studied populations and other 26 populations indicated that population structures follow the boundary of the continent. Guizhou Miao and Guizhou Tujia populations have intimate relationships with East Asian populations, especially the geographically close, similar history and the same language family populations.
Modelling disease transmission from touchscreen user interfaces
Authors: Di Battista Andrew , Nicolaides Christos , Georgiou Orestis
Published: July 2021

The extensive use of touchscreens for all manner of human–computer interactions has made them plausible instruments of touch-mediated disease transmission. To that end, we employ stochastic simulations to model human–fomite interaction with a distinct focus on touchscreen interfaces. The timings and frequency of interactions from within a closed population of infectious and susceptible individuals was modelled using a queuing network. A pseudo-reproductive number
R
was used to compare outcomes under various parameter conditions. We then apply the simulation to a specific real-world scenario; namely that of airport self-check-in and baggage drop. A counterintuitive result was that
R
decreased
with
increased
touch rates required for touchscreen interaction. Additionally, as one of few parameters to be controlled, the rate of cleaning/disinfecting screens plays an essential role in mitigating
R
, though alternative technological strategies could prove more effective. The simulation model developed provides a foundation for future advances in more sophisticated fomite disease-transmission modelling.
Impacts of additional noise on the social interactions of a cooperatively breeding fish
Authors: Braga Goncalves Ines , Richmond Emily , Harding Harry R. , Radford Andrew N.
Published: July 2021

Anthropogenic noise is a global pollutant known to affect the behaviour of individual animals in all taxa studied. However, there has been relatively little experimental testing of the effects of additional noise on social interactions between conspecifics, despite these forming a crucial aspect of daily life for most species. Here, we use established paradigms to investigate how white-noise playback affects both group defensive actions against an intruder and associated within-group behaviours in a model fish species, the cooperatively breeding cichlidNeolamprologus pulcher. Additional noise did not alter defensive behaviour, but did result in changes to within-group behaviour. Both dominant and subordinate females, but not the dominant male, exhibited less affiliation and showed a tendency to produce more submissive displays to groupmates when there was additional noise compared with control conditions. Thus, our experimental results indicate the potential for anthropogenic noise to affect social interactions between conspecifics and emphasize the possibility of intraspecific variation in the impacts of this global pollutant.
Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution
Authors: Kratochvíl Lukáš , Stöck Matthias , Rovatsos Michail , Bullejos Mónica , Herpin Amaury , Jeffries Daniel L. , Peichel Catherine L. , Perrin Nicolas , Valenzuela Nicole , Pokorná Martina Johnson
Published: July 2021

Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue ofPhil. Trans. R. Soc. B.We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
Whole-chromosome fusions in the karyotype evolution ofSceloporus(Iguania, Reptilia) are more frequent in sex chromosomes than autosomes
Authors: Lisachov Artem P. , Tishakova Katerina V. , Romanenko Svetlana A. , Molodtseva Anna S. , Prokopov Dmitry Yu. , Pereira Jorge C. , Ferguson-Smith Malcolm A. , Borodin Pavel M. , Trifonov Vladimir A.
Published: July 2021

Whole-chromosome fusions play a major role in the karyotypic evolution of reptiles. It has been suggested that certain chromosomes tend to fuse with sex chromosomes more frequently than others. However, the comparative genomic synteny data are too scarce to draw strong conclusions. We obtained and sequenced chromosome-specific DNA pools ofSceloporus malachiticus, an iguanian species which has experienced many chromosome fusions. We found that four of seven lineage-specific fusions involved sex chromosomes, and that certain syntenic blocks which constitute the sex chromosomes, such as the homologues of theAnolis carolinensischromosomes 11 and 16, are repeatedly involved in sex chromosome formation in different squamate species. To test the hypothesis that the karyotypic shift could be associated with changes in recombination patterns, we performed a synaptonemal complex analysis in this species and inSceloporus variabilis(2n= 34). It revealed that the sex chromosomes inS. malachiticushad two distal pseudoautosomal regions and a medial differentiated region. We found that multiple fusions little affected the recombination rate inS. malachiticus. Our data confirm more frequent involvement of certain chromosomes in sex chromosome formation, but do not reveal a connection between the gonosome–autosome fusions and the evolution of recombination rate.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?
Authors: Kratochvíl Lukáš , Gamble Tony , Rovatsos Michail
Published: July 2021

Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
Actinoplanes lichenicola sp. nov. and Actinoplanes ovalisporus sp. nov., isolated from lichen in Thailand
Authors: Saeng-in Patcharin , Kanchanasin Pawina , Yuki Masahiro , Kudo Takuji , Ohkuma Moriya , Phongsopitanun Wongsakorn , Tanasupawat Somboon
Published: July 2021

Two actinobacteria, designated as strain LDG1-01T and LDG1-06T, were isolated from lichen samples collected in Thailand. Results of morphological characterization, chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains were members of the genus

Actinoplanes

. MK-9(H4) was found as the major menaquinone. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were observed as the polar lipids, but differences in minor unidentified polar lipids were found between the strains. Results of comparative genome analysis based on average nucleotide identity and digital DNA–DNA hybridization calculations revealed that both strains showed values below 95 and 70 %, respectively, from each other and closely related

Actinoplanes

type strains. Based on data from this polyphasic study, strains LDG1-01T and LDG1-06T represent novel species of the genus

Actinoplanes

. The names proposed are Actinoplanes lichenicola sp. nov. (type strain, LDG1-01T (=JCM 33066T=TISTR 2982T) and Actinoplanes ovalisporus sp. nov. (type strain, LDG1-06T=JCM 33067T=TISTR 2983T).
Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces
Authors: Niemhom Nantawan , Suriyachadkun Chanwit , Kittiwongwattana Chokchai
Published: July 2021

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus

Chitinophaga

. Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with

Chitinophaga eiseniae

YC6729T,

Chitinophaga qingshengii

JN246T,

Chitinophaga varians

10-7 W-9003T and

Chitinophaga fulva

G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1
 ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
 ω7c/C16 : 1
 ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus

Chitinophaga

, for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).
Fluoroquinolone resistance in non-typhoidal Salmonella enterica isolated from slaughtered pigs in Thailand
Authors: Poomchuchit Suleepon , Kerdsin Anusak , Chopjitt Peechanika , Boueroy Parichart , Hatrongjit Rujirat , Akeda Yukihiro , Tomono Kazunori , Nuanualsuwan Suphachai , Hamada Shigeyuki
Published: July 2021

Introduction. The emergence and spread of non-typhoidal

Salmonella enterica

(NTS) serovars resistant to fluoroquinolones and third- and higher-generation cephalosporins is a matter of great concern. Antimicrobial-resistant NTS is increasingly being discovered in humans, animals, food animals, food products, and agricultural environments. Pigs are considered a major reservoir of antimicrobial-resistant

Salmonella

spp.

Hypothesis/Gap Statement. Fluoroquinolone-resistant

Salmonella

spp. warrant further surveillance and characterization for a better understanding of the bacteria isolated from animals.

Aim. NTS isolated from pork from slaughterhouses across Thailand were characterized in terms of their serovars; resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems; and antimicrobial resistance genes.

Methodology. A total of 387 NTS isolates, collected from slaughtered pigs in ten provinces across Thailand between 2014 and 2015, were characterized based on their serovars, antimicrobial resistance genes, and susceptibility to fluoroquinolones, third-generation cephalosporins, and carbapenems.

Results. Among all NTS isolates,

S. enterica

serovar Rissen was predominant. Antimicrobial resistance was exhibited in 93/387 isolates (24 %). Although 24 (6.2 %) isolates were susceptible to all the tested antimicrobials, they were found to possess β-lactamase genes, such as bla
TEM, bla
SHV, or bla
CTX-M. Mobilized colistin-resistant genes (mcr) and resistance to colistin were not observed in any tested isolate. Carbapenem resistance was detected in ten isolates (10.7 %); however, bla
KPC, bla
NDM, bla
OXA-48-like, and bla
IMP were not present. Among the 93 antimicrobial-resistant isolates, 87.1 % showed fluoroquinolone resistance with the quinolone resistance gene (qnrS) combined with topoisomerase genes parC (T57S) or gyrA (S83E/Y and D124E/G) substitutions, or topoisomerase gene substitutions alone.

Conclusion. We found high fluoroquinolone resistance rates among the NTS isolates from pigs from slaughterhouses. The fluoroquinolone resistance mechanism in NTS was associated with the combination of qnrS and substitutions in gyrA, parC, or both. To prevent the transmission of antimicrobial-resistant NTS between animals and humans, continuous monitoring, surveillance, and regulation of

Salmonella

in the pork supply chain are pivotal.