bluuebunny/crossref_metadata_2025 huggingface dataset:
SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images
Authors: Tu Yanlun , Lei Houchao , Shen Hong-Bin , Yang Yang
Published: December 2021

With the rapid growth of high-resolution microscopy imaging data, revealing the subcellular map of human proteins has become a central task in the spatial proteome. The cell atlas of the Human Protein Atlas (HPA) provides precious resources for recognizing subcellular localization patterns at the cell level, and the large-scale annotated data enable learning via advanced deep neural networks. However, the existing predictors still suffer from the imbalanced class distribution and the lack of labeled data for minor classes. Thus, it is necessary to develop new methods for coping with these issues. We leverage the self-supervised learning protocol to address these problems. Especially, we propose a pre-training scheme to enhance the conventional supervised learning framework called SIFLoc. The pre-training is featured by a hybrid data augmentation method and a modified contrastive loss function, aiming to learn good feature representations from microscopic images. The experiments are performed on a large-scale immunofluorescence microscopic image dataset collected from the HPA database. Using the same deep neural networks as the classifier, the model pre-trained via SIFLoc not only outperforms the model without pre-training by a large margin but also shows advantages over the state-of-the-art self-supervised learning methods. Especially, SIFLoc improves the prediction accuracy for minor organelles significantly.
SPEQ: quality assessment of peptide tandem mass spectra with deep learning
Authors: Gholamizoj Soroosh , Ma Bin
Published: December 2021

Motivation

In proteomics, database search programs are routinely used for peptide identification from tandem mass spectrometry data. However, many low-quality spectra cannot be interpreted by any programs. Meanwhile, certain high-quality spectra may not be identified due to incompleteness of the database or failure of the software. Thus, spectrum quality (SPEQ) assessment tools are helpful programs that can eliminate poor-quality spectra before the database search and highlight the high-quality spectra that are not identified in the initial search. These spectra may be valuable candidates for further analyses.

Results

We propose SPEQ: a spectrum quality assessment tool that uses a deep neural network to classify spectra into high-quality, which are worthy candidates for interpretation, and low-quality, which lack sufficient information for identification. SPEQ was compared with a few other prediction models and demonstrated improved prediction accuracy.

Availability and implementation

Source code and scripts are freely available at github.com/sor8sh/SPEQ, implemented in Python.
Cryptic Plasmodium inui and Plasmodium fieldi Infections Among Symptomatic Malaria Patients in Thailand
Authors: Putaporntip Chaturong , Kuamsab Napaporn , Seethamchai Sunee , Pattanawong Urassaya , Rojrung Rattanaporn , Yanmanee Surasuk , Weng Cheng Chew , Jongwutiwes Somchai
Published: December 2021

Background

Some nonhuman primate Plasmodium species including P. knowlesi and P. cynomolgi can cross-transmit from macaque natural hosts to humans under natural infection. This study aims to retrospectively explore other simian Plasmodium species in the blood samples of symptomatic malaria patients in Thailand.

Methods

A total of 5271 blood samples from acute febrile patients from 5 malaria endemic provinces and 1015 blood samples from long-tailed and pig-tailed macaques from 3 locations were examined for Plasmodium species by microscopy and species-specific polymerase chain reaction. The Plasmodium mitochondrial cytochrome oxidase 1 (COX1) gene was analyzed by amplicon deep sequencing as well as Sanger sequencing from recombinant plasmid clones to reaffirm and characterize P. inui and P. fieldi.

Results

Besides human malaria, P. knowlesi, P. cynomolgi, P. inui and P. fieldi infections were diagnosed in 15, 21, 19, and 3 patients, respectively. Most P. inui and all P. fieldi infected patients had simultaneous infections with other Plasmodium species, and seemed to be responsive to chloroquine or artemisinin-mefloquine. P. inui was the most prevalent species among macaque populations. Phylogenetic analysis of the COX1 sequences from human and macaque isolates reveals the genetic diversity of P. inui and suggests that multiple parasite strains have been incriminated in human infections.

Conclusions

Both P. inui and P. fieldi could establish infection in humans under natural transmission. Despite occurring at a low prevalence and mostly co-existing with other Plasmodium species, P. inui infections in humans have a wide distribution in Thailand.
Evaluation of Sperm DNA Integrity by Mean Number of Sperm DNA Breaks Rather Than Sperm DNA Fragmentation Index
Authors: Yan Bei , Ye Weicong , Wang Juan , Jia Shaotong , Gu Xiuli , Hu Hao , Xiang Wenpei , Wu Tongbo , Xiao Xianjin
Published: December 2021

Background

Sperm DNA integrity is crucial for normal fertilization, implantation, and embryo development. Several assays are available to assess sperm DNA fragmentation but are limited by high price, complicated processes, and low accuracy.

Methods

We developed a secondary amplification detection system based on terminal deoxynucleotidyl transferase and endonuclease IV, which could efficiently measure the number of 3'-OH (equivalent to the number of breakpoints). We applied this detection system in single stranded DNA with standard concentrations to obtain the standard curve. We then broke the double stranded genomic DNA by ultrasound and enzyme digestion and used the detection system to monitor the increase of DNA breakpoints. Finally, we used this method to measure the mean number of sperm DNA breakpoints (MDB) in 80 sperm samples.

Results

We successfully measured the number of 3'-OH in single stranded DNA with standard concentration and obtained the standard curve. The linear range for the number of DNA breakpoints was from 0.1 nM to 15 nM. The detection method was successfully validated on λ DNA and 80 human sperm samples. The results of real clinical samples revealed that the mean number of DNA breakpoints (MDB) had a stronger relevance with the sperm motility and clinical pregnancy outcomes than the commonly used parameter of DNA fragmentation index (DFI).

Conclusion

We have developed a straight-forward method for direct measurement of the mean number of DNA breakpoints in sperms. The method has advantages of short time-consumption, simple operation, high analytical sensitivity, and low requirement for instrumentation, which makes it conducive to clinical application. The proposed new parameter (MDB) could be a more direct, accurate and clinically significant indicator for evaluating the sperm DNA integrity.
Information Operations Increase Civilian Security Cooperation
Authors: Sonin Konstantin , Wright Austin L
Published: December 2021

Information operations are considered a central element of modern warfare and counter-insurgency, yet there remains little systematic evidence of their effectiveness. Using a geographic quasi-experiment conducted during Operation Enduring Freedom in Afghanistan, we demonstrate that civilians exposed to the government’s information campaign resulted in more civilian security cooperation, which in turn increased bomb neutralisations. These results are robust to a number of alternative model specifications that account for troop presence, patrol-based operations, and local military aid allocation. The paper demonstrates that information campaigns can lead to substantive attitudinal and behavioural changes in an adversarial environment and substantially improve battlefield outcomes.
Posterior mediastinal arteriovenous haemangioma
Authors: Feng Qianqian , He Xiaopeng
Published: December 2021

Mediastinal arterio-venous haemangiomas are rare benign vascular tumours. To the best of our knowledge, very few cases of mediastinal arterio-venous haemangiomas have ever been reported. Herein, we report about a 55-year-old woman who presented to our hospital with a mass in the right posterior mediastinum. The tumour was successfully resected via video-assisted thoracoscopic surgery, and further pathological analysis confirmed the mass to be an arterio-venous haemangioma. The patient made a full recovery without any postoperative complications.
A non-cephalometric two-dimensional appraisal of soft tissue changes by functional therapy in Class II patients: a systematic review and meta-analysis
Authors: Luyten Jonathan , Vierendeel Michiel , De Roo Noëmi M C , Temmerman Liesbeth , De Pauw Guy A M
Published: December 2021

Background

Facial attractiveness has social, psychological, and economic repercussions. Class II malocclusions are associated with a retroposition of the mandible, facial convexity, protruded upper lip, retruded lower lip, and pronounced mentolabial fold. Functional appliances (FA) try to increase mandibular length and normalize lip position, thereby decreasing the facial profile convexity and aesthetics.

Objectives

The aim of this review and meta-analysis is to investigate the effects of FA on the soft tissues in a non-cephalometric two-dimensional manner.

Search methods

Medline (via PubMed), Embase (via Ovid), Web of Science, and Cochrane Central were used to identify studies describing the soft tissue results of FA in a non-cephalometric way. The search was conducted up to July 2021.

Selection criteria

Prospective and retrospective studies investigating the effects of FA appliances on the soft tissues, with non-ionizing, two-dimensional imaging, including an attractiveness assessment based on Visual Analogue Scale or Likert scale, were considered eligible.

Data collection and analysis

Data extraction was performed separately by two authors. Risk of bias was assessed using the ROBINS-I tool.

Results

From the eight eligible studies, four were included in the meta-analysis to investigate the influence of assessors on facial attractiveness scores. Age range of the included studies varied from 8 to 21 years old including 313 Caucasian patients whereof 64% females. Six out of eight studies used growing patients as treatment group and only two studies reported follow-up after the end of treatment. Overall facial attractiveness increased after treatment with FA, resulting from a decrease in facial convexity and a normalization of the lip relationship. Orthodontists score higher aesthetic improvements after FA treatment as compared to laypeople.

Conclusions

Current evidence suggests the positive effects of FA on the facial attractiveness in growing and non-growing patients. FA normalize the lip relationship. Furthermore, they tend to decrease facial convexity and advance the chin point. More pleasing results can be expected in growing patients. Orthodontists are more generous when assessing treatment changes as compared to laypeople.

Registration

PROSPERO registration (CRD42021254835).
Burden of cardiovascular diseases attributable to risk factors in Brazil: data from the Global Burden of Disease 2019 study
Authors: Brant L C , Nascimento B R , Veloso G A , Gomes C S , Polanczyk C , Oliveira G M M , Ribeiro A L P , Malta D C
Published: December 2021

Introduction

Cardiovascular diseases (CVD) continue to be the main cause of death in Brazil, a middle-income country. As such, it is essential to understand the trends of risk factors (RFs) for CVDs in order to implement effective and tailored public policies.

Purpose

The present study sought to analyze the trend of RF for CVD and the disease burden attributable to these from 1990 to 2019, in Brazil and its states, based on estimates from the Global Burden of Disease Study 2019 (2019 GBD).

Methods

To estimate RF exposure, the Summary Exposure Value (SEV) (risk-weighted prevalence) was used, whereas for disease burden attributed to RFs, mortality and Disability-adjusted life-years (DALY) by CVD were used. For comparisons over time and between states, the age-standardized rates were considered. The sociodemographic index (SDI) was used as a marker of socioeconomic conditions.

Results

In 2019, 82% of CVD mortality in Brazil was attributable to RFs. For SEV, there was a reduction in smoking and environmental RFs, as well as an increase in metabolic RFs. High systolic blood pressure and dietary risks continue to be the main RFs for CVD mortality and DALY (Figure 1). While there was a decline in age-standardized mortality rates attributable to the evaluated RFs, there was also a stability or increase in crude mortality rates, with the exception of smoking. It is important to highlight the increase in the risk of death attributable to a high body mass index (BMI) (35 to 46/100,000 in habitants in 1990 and 2019). Regarding the analysis per state, SEVs and mortality attributable to RF were higher in those states with lower SDIs.

Conclusion

Despite the reduction in CVD mortality and DALY rates attributable to RF, the stability or increase in crude rates attributable to metabolic RFs is worrisome, requiring investments and a renewal of health policies.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Health Surveillance Secretariat, Brazilian Ministry of Health Figure 1
Carbon Accumulation and Partitioning Above and Belowground under Coppiced and Replanted Eucalypt Plantations
Authors: Pegoraro Rodinei F , Silva Ivo R , Souza Ivan F , Novais Roberto F , Barros Nairam F , Fonseca Sebastião
Published: December 2021

The extent to which the C sink strength of eucalypt plantations can be affected by coppicing or replanting remains unclear. To address this issue, we evaluated variations in C stocks under coppiced or replanted eucalypt stands formed by clones or seedlings. For each field assessment (0 [T0], 2.5, 3.5, 4.5, 5.5 and 7.0 years [at harvest]), tree biomass, litterfall, and soil C stocks (0–120 cm depth) were determined. At harvest, debarked stemwood productivity was similar under coppice or replanting, about 50.0 Mg C ha–1. Generally, coppiced stands favored subsoil C storage (40–100 cm), whereas replanted stands favored soil C accrual in topsoil (0–20 cm), depending on the genetic material. Relative to T0, soil C increased about 2.14, 1.91, and 1.84 Mg C ha–1 yr–1 under coppice, replanting with seedlings and clones, respectively. Coarse root biomass under these stands were about 17.3, 13.4, and 9.5 Mg C ha–1, respectively, equivalent to 50% of total harvest residues. Hence, inputs from coarse roots could represent a large contribution to soil C over multiple rotations under coppiced or replanted stands. Otherwise, short-term C losses can be high where stumps and coarse roots are harvested, especially following successive coppice cycles.

Study Implications: Our findings have important implications for forest managers growing eucalypt plantations aiming to maximize C accumulation. Both coppiced and replanted stands can fix up to 50 Mg C ha−1 only in debarked stemwood over 7 years, with a comparatively higher C storage in coarse roots under coppice. Despite the increasing demand for forest residues in bioenergy production, harvesting stumps and coarse roots should be avoided, especially upon replanting eucalypt stands after successive coppice cycles.
Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature
Authors: Lange Matthias , Alako Blaise T F , Cochrane Guy , Ghaffar Mehmood , Mascher Martin , Habekost Pia-Katharina , Hillebrand Upneet , Scholz Uwe , Schorch Florian , Freitag Jens , Scholz Amber Hartman
Published: December 2021

Background

Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.

Findings

We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics.

Conclusions

The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.
Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season
Authors: Harris Zachary N , Awale Mani , Bhakta Niyati , Chitwood Daniel H , Fennell Anne , Frawley Emma , Klein Laura L , Kovacs Laszlo G , Kwasniewski Misha , Londo Jason P , Ma Qin , Migicovsky Zoë , Swift Joel F , Miller Allison J
Published: December 2021

Background

Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown.

Results

Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season.

Conclusions

These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.
Modeling Culinary Value
Authors: Engisch Patrik
Published: December 2021

Culinary products have culinary value. That is, they have value qua culinary products. However, what is the nature of culinary value and what elements determine it? In the light of the central and universal role that culinary products play in our lives, offering a philosophical analysis of culinary value is a matter of interest. This article attempts to do just this. It develops three different possible models of culinary value, two rather restricted ones and a third more encompassing one, rejects the first two, and defends the third one.
Effects of physical or fenceline boar exposure and exogenous gonadotropins on puberty induction and subsequent fertility in gilts
Authors: Knox Robert V , Arend Lidia S , Buerkley Ashley L , Patterson Jennifer L , Foxcroft George R
Published: December 2021

The present study was part of a larger experiment that evaluated litter of origin effects on gilt production. The objectives of this study were to determine the effect of physical or fenceline boar exposure and exogenous gonadotropins on puberty induction and subsequent fertility in a commercial farm environment. The experiment was performed in three replicates. Prepubertal gilts were assigned by pen (13/pen) to receive 15 min of daily Fenceline (FBE, n = 153) or Physical (PBE, n = 154) Boar Exposure (BE) for 3 weeks starting at 184 d of age in a purpose-designed Boar Exposure Area (BEAR). At the start of week 3, prepubertal gilts were randomly assigned to receive PG600 or none (Control). From weeks 4 to 6, estrus was checked using only FBE. During weeks 1 to 3, measures of reproductive status were obtained weekly or until expression of estrus. Upon detection of first estrus, gilts were relocated into stalls and inseminated at second estrus. PBE reduced age (P = 0.001) and days to puberty (P = 0.002), increased the proportion of gilts in estrus (P = 0.04) in week 1 (38.3 vs. 27.5%), and tended (P = 0.08) to improve estrus in week 2 (37.6 vs. 26.1%) compared to FBE, respectively. In week 3, more prepubertal gilts receiving PBE-PG600 exhibited estrus (P = 0.04; 81.8%) compared to PBE-Control (40.3%), FBE-PG600 (56.4%), and FBE-Control (47.8%). Overall, expression of estrus through week 6 tended (P = 0.08) to be greater for PBE than FBE (91.5 vs. 85.0%). PBE increased (P ≤ 0.05) or tended to increase (P > 0.05 and ≤0.10) service and farrowing rates in parities 1 through 4, but within parity, there were no effects (P > 0.10) on pig production or wean to service interval. Analyses also indicated that weeks from start of boar exposure to puberty, litter of origin traits, and follicle measures at puberty were related to the subsequent fertility. The results of this study confirm the advantages of using increased intensity of boar exposure, combined with PG600 treatment, for effective induction of pubertal estrus in a commercial setting.
Effect of bupivacaine liposome suspension administered as a local anesthetic block on indicators of pain and distress during and after surgical castration in dairy calves
Authors: Martin Miriam S , Kleinhenz Michael D , Viscardi Abbie V , Curtis Andrew K , Johnson Blaine T , Montgomery Shawnee R , Lou Maria E , Coetzee Johann F
Published: December 2021

Castration is a routine procedure performed on beef and dairy operations in the United States. All methods of castration cause behavioral, physiologic, and neuroendocrine changes associated with pain. The American Veterinary Medical Association and the American Association of Bovine Practitioners recommend that anesthesia and analgesia be administered during castration. The objective of this study was to evaluate the effectiveness of bupivacaine liposome suspension, a novel, long-acting, local anesthetic formulation administered as a nerve block at castration. The authors chose to investigate this novel formulation as an alternative to the current industry standards using lidocaine nerve blocks alone or in combination with meloxicam. Thirty male Holstein calves, 16 to 20 wk of age, were enrolled and randomly assigned to one of the four treatment groups prior to surgical castration: 1) bupivacaine liposome suspension block + oral placebo (BUP), 2) lidocaine block + oral placebo (LID), 3) lidocaine block + oral meloxicam (1 mg/kg) (LID + MEL), and 4) saline block + oral placebo (CON). Biomarkers were collected at −24 h and from 0 to 120 h post-castration and included infrared thermography, pressure mat gait analysis, chute defense and behavior scoring (pain and activity), and blood sampling for serum cortisol and prostaglandin E2 metabolites (PGEMs). Responses were analyzed using repeated measures, with calf nested in treatment as a random effect, and treatment, time, and their interaction designated as fixed effects. The results from pressure mat gait analysis show that the CON had a shorter front limb stance time from baseline (−8.73%; 95% confidence interval [CI]: −24.84% to 7.37%) compared with BUP and LID + MEL (>5.70%; 95% CI: −22.91% to 23.79%) (P < 0.03). The CON tended to have an increase in front limb force from baseline (6.31%; 95% CI: −1.79% to 14.41%) compared with BUP, LID, and LID + MEL (<−5.06%; 95% CI: −14.22% to 0.95%) (P < 0.04). The CON displayed higher counts of hunched standing (2.00; 95% CI: 1.68 to 2.32) compared with LID + MEL (1.43; 95% CI: 1.13 to 1.72) (P = 0.05). The CON had higher cortisol concentrations at 24 h (7.70 ng/mL; 95% CI: 1.52 to 13.87 ng/mL) relative to BUP (3.11 ng/mL; 95% CI: −2.56 to 8.79 ng/mL) (P = 0.002). At 4 and 24 h, LID + MEL had lower PGEM concentrations from baseline (−32.42% and −47.84%; 95% CI: −78.45% to −1.80%) compared with CON (27.86% and 47.63%; 95% CI: 7.49% to 82.98%) (P < 0.02). The administration of bupivacaine liposome suspension as a local anesthetic block at the time of castration was as effective at controlling pain as a multimodal approach of lidocaine and meloxicam.
Ever-expanding NGLY1 biology
Authors: Suzuki Tadashi , Yoshida Yukiko
Published: December 2021

The cytosolic peptide:N-glycanase (PNGase; NGLY1 in humans) is a deglycosylating enzyme that is widely conserved in eukaryotes. This enzyme is involved in the degradation of misfolded N-glycoproteins that are destined for proteasomal degradation in the cytosol, a process that is called endoplasmic reticulum-associated degradation. Although the physiological significance of NGLY1 remained unknown until recently, the discovery of NGLY1 deficiency, a human genetic disorder bearing mutations in the NGLY1 gene, has led to explosive research progress regarding the functional characterization of this enzyme. For example, it is now known that NGLY1 can also act as an ‘editing enzyme’ to convert N-glycosylated asparagine residues to aspartate residues, thus introducing negative charges into a core peptide and modulating the function of the target molecule. Diverse biological processes have also been found to be affected by compromised NGLY1 activity. In this special issue, recent research progress on the functional characterization of NGLY1 and its orthologues in worm/fly/rodents, assay methods/biomarkers useful for the development of therapeutics and the comprehensive transcriptome/proteome of NGLY1-KO cells as well as patient-derived cells are discussed.
Factors Influencing the Efficacy of Novel Attract-and-Kill (ACTTRA SWD) Formulations Against Drosophila suzukii
Authors: Babu Arun , Rodriguez-Saona Cesar , Sial Ashfaq A
Published: December 2021

In the continental United States, the invasive spotted-wing drosophila (SWD), Drosophila suzukii Matsumura, has become a primary pest of multiple stone and soft-skinned fruits. A new innovative adjuvant formulation, ACTTRA SWD, mixed with a suitable insecticide, constitutes a novel attract-and-kill tactic to manage D. suzukii in fruit crops. We hypothesized that background odors present in crop fields, particularly odors from host fruits, negatively affect the effectiveness of this attract-and-kill formulation, as odors from these sources can compete for insect attraction. Additionally, we evaluated the influence of adult D. suzukii sex and physiological status (age and mating status), and fruit ripeness on its response to the ACTTRA SWD formulation. For this, we used two-choice bioassays to test the response of adult D. suzukii to three ACTTRA SWD formulations (named OR1, TD, and HOOK SWD) in the presence and absence of host fruits (blueberries, raspberries, blackberries, and strawberries). Odors from raspberries were significantly more attractive than those from the TD formulation mixed with spinosad (Entrust). For the HOOK SWD formulation and OR1+Entrust formulation, odors from all the fruit types tested were significantly more attractive than the adjuvants. Compared with females, male D. suzukii were more attracted to the TD formulation over the blueberry fruits. Additionally, age and female mating status but not fruit ripeness influenced D. suzukii attraction to both OR1 and TD formulations. The results from this study indicate that D. suzukii physiological status and host fruit availability impact the efficacy of new attract-and-kill adjuvants such as ACTTRA SWD.
Evaluation of Pharmacogenomics Testing of Cytochrome P450 Enzymes in the Military Health System From 2015 to 2020
Authors: Por Elaine D , Selig Daniel J , Chin Geoffrey C , DeLuca Jesse P , Oliver Thomas G , Livezey Jeffrey R
Published: December 2021

Pharmacogenomics (PGx) plays a fundamental role in personalized medicine, providing an evidence-based treatment approach centered on the relationship between genomic variations and their effect on drug metabolism. Cytochrome P450 (CYP450) enzymes are responsible for the metabolism of most clinically prescribed drugs and a major source of variability in drug pharmacokinetics and pharmacodynamics. To assess the prevalence of PGx testing within the Military Health System (MHS), testing of specific CYP450 enzymes was evaluated. Data were retrospectively obtained from the Military Health System Management Analysis and Reporting Tool (M2) database. Patient demographics were identified for each test, along with TRICARE status, military treatment facility, clinic, and National Provider Identifier. A total of 929 patients received 1,833 PGx tests, predominantly composed of active duty/guard service members (N = 460; 49.5%), with highest testing rates in the army (51.5%). An even distribution in testing was observed among gender, with the highest rates in Caucasians (41.7%). Of the CYP enzymes assessed, CYP2C19 and CYP2D6 accounted for 87.8% of all PGx CYP testing. The majority of patients were tested in psychiatry clinics (N = 496; 53.4%) and primary care clinics (N = 233; 25.1%), accounting for 56.4% and 24.8% of all tests, respectively. Testing was found to be provider driven, suggesting a lack of a standardized approach to PGx and its application in patient care within the MHS. We initially recommend targeted education and revising testing labels to be more uniform and informative. Long-term recommendations include establishing pharmacy-driven protocols and point-of-care PGx testing to optimize patient outcomes.
Applying Pharmacogenomic Guidelines to Combat Medical Care
Authors: DeLuca Jesse , Oliver Thomas , Hulsopple Chad , Selig Daniel , Por Elaine , Turner Clesson , Hellwig Lydia , Livezey Jeffrey
Published: December 2021

Pharmacogenomics is a pillar of personalized medicine that has the potential to deliver optimized treatment in many medical settings. Military medicine in the deployed setting is unique and therefore warrants separate assessment pertaining to its potential capabilities and impact. Pharmacogenomics for United States Active Duty Service Members medical care in the deployed setting has not, to our knowledge, been previously reviewed. We present potential applications of pharmacogenomics to forward medical care through two comprehensive references for deployed medical care, the Tactical Combat Casualty Care Guidelines (TCCC) and Emergency War Surgery (EWS) fifth edition. All drugs within the deployment manuals, TCCC guidelines and EWS book, were identified and the list was cross-referenced to the Clinical Pharmacogenetics Implementation Consortium guidelines and genes–drugs interactions list as well as the Food and Drug Administration Table of Pharmacogenomics Biomarkers in Drug Labeling. Ten pharmacologic categories were identified, consisting of 15 drugs, along with the classes, aminogylcosides, beta-blockers, and volatile anesthetics. Drugs and pharmacogenomics liabilities were tabulated. Eight specific drugs or classes are expounded upon given the belief of the authors of their potential for impacting future treatment on the battlefield in the setting of prolonged field care. This review outlines several genes with liabilities in the prolonged field care setting and areas that may produce improved care with further study.
Prescription Patterns and Relationship to Pharmacogenomics Testing in the Military Health System
Authors: Selig Daniel J , Livezey Jeffrey R , Chin Geoffrey C , DeLuca Jesse P , Guillory II Walter O , Kress Adrian T , Oliver Thomas O , Por Elaine D
Published: December 2021

Introduction

Clinical utilization of pharmacogenomics (PGx) testing is highly institutionally dependent, and little information is known about provider practices of PGx testing in the Military Health System (MHS). In this study, we aimed to characterize Clinical Pharmacogenetics Implementation Consortium (CPIC) actionable prescription (Rx) patterns and their temporal relationship with PGx testing in the MHS.

Methods

Using data from the Military Health System Management Analysis and Reporting Tool (M2) database, this retrospective cohort study included all patients receiving at least one PGx test and at least one CPIC actionable Rx from January 2015 to August 2020 (845 patients, 1,471 PGx, 7,725 index CPIC actionable Rxs). Rx patterns and temporal relationships with PGx testing were characterized via descriptive statistics. Binomial regression was used to determine which patient and provider characteristics were associated with a patient receiving a PGx test within 30 days of an index Rx.

Results

Patients had a median of 9 index CPIC actionable Rx’s (range 1–26). Pain medications were most commonly prescribed (N = 794, 94% patients with at least 1 Rx). However, pain medication had the lowest Rx–PGx match rate (40%) compared to an average of 62% Rx–PGx match rate for all CPIC drugs. Antidepressants were also commonly prescribed (N = 668, 79.1% patients with at least 1 Rx), and antidepressants had the highest Rx–PGx match rate of 86.7%. A minority of providers (20%, N = 249) ordered the majority of PGx tests (86.1%, N = 1,266) and only 8.3% of PGx tests (N = 398) matched to a CPIC actionable drug within 30 days of the test (defined by Rxs ordered within 30 days before or after the PGx test). However, approximately 39.8% of patients (N = 317) had at least one drug match to a PGx test within 30 days. The largest predictor of whether a patient received a PGx test within 30 days of any index Rx was whether or not a specific psychiatry provider ordered the PGx test (odds ratio; OR 3.7, 95% CI 2.13–6.54, P < 0.001). Neither the CPIC level of evidence nor FDA PGx actionable or informative labels had a significant effect on PGx test timing.

Conclusions

PGx testing was generally limited to high Rx-drug users and was found to be an under-utilized resource. PGx testing did not typically follow CPIC guidelines. Implementing PGx testing protocols, simplifying PGx test-ordering by incorporating at minimum CYP2D6, CYP2C19, and CYP2C9 into PGx-testing panels, and unifying providers’ PGx knowledgebase in the MHS are feasible and would improve the clinical utilization of PGx tests in the MHS.
Rapid Bedside Ultrasound Evaluation of a Ruptured Abdominal Aortic Aneurysm With a Prior Repair
Authors: Corcillo Juliet , Stierwalt Joshua , Kaelin Andrea , Murray Brian
Published: December 2021

Ruptured aortic aneurysms carry a high risk of morbidity and mortality, particularly if not rapidly identified. We present an 87-year-old male, with a history of hypertension and prior endovascular aortic repair, who presented to the Emergency Department (ED) with several days of epigastric abdominal pain radiating to his back and flanks. The patient acutely deteriorated in the ED, and point-of-care ultrasound rapidly identified active extravasation from an abdominal aortic aneurysm with visualization of prior endograft. Point-of-care ultrasound in this patient expedited the diagnosis, resuscitation, and transfer to the operating room with definitive repair by vascular surgery. The patient recovered and was discharged in stable condition.
Be, V, and Cu in the halo star CS 31082-001 from near-UV spectroscopy
Authors: Ernandes H , Barbuy B , Friaça A , Hill V , Spite M , Spite F , Castilho B V , Evans C J
Published: December 2021

The ‘First Stars’ programme revealed the metal-poor halo star CS 31082-001 to be r-process and actinide rich, including the first measurement of a uranium abundance for an old star. To better characterize and understand such rare objects, we present the first abundance estimates of three elements (Be, V, Cu) for CS 31082-001 from analysis of its near-ultraviolet spectrum. Beryllium is rarely measured in giant stars, and we confirm that its abundance in this star is low due to the rather cool effective temperature that causes destruction of both Be and Li in its atmosphere. Vanadium and copper are iron-peak elements that are starting to be used as chemical-tagging indicators to investigate the origin of stellar populations. We find V and Cu abundances for CS 31082-001 that are comparable to other metal-poor stars, and present new chemical evolution models to investigate our results. In the case of V, extra nucleosynthesis due to interaction of neutrinos with matter is included in the models to be able to reproduce the measured abundance. Given the availability of high-quality spectroscopy of CS 31082-001, we also explore other atomic lines in the near-ultraviolet as a template for future studies of metal-poor stars with the planned CUBES instrument in development for the Very Large Telescope.
Immortalization and functional screening of natively paired human T cell receptor repertoires
Authors: Fahad Ahmed S , Chung Cheng-Yu , Lopez Acevedo Sheila N , Boyle Nicoleen , Madan Bharat , Gutiérrez-González Matias F , Matus-Nicodemos Rodrigo , Laflin Amy D , Ladi Rukmini R , Zhou John , Wolfe Jacy , Llewellyn-Lacey Sian , Koup Richard A , Douek Daniel C , Balfour Jr Henry H , Price David A , DeKosky Brandon J
Published: December 2021

Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. We developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale, and to exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen-specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of disease-relevant antigen interactions with human TCRs.
LOCAL DIAGNOSTIC REFERENCE LEVELS FOR PEDIATRIC RETROGRADE WEDGE PORTOGRAPHY INTERVENTIONAL PROCEDURES USING A DOSE MONITORING SOFTWARE AT A TRANSPLANTATION INSTITUTE
Authors: Gerasia R , Cannataci C , Gallo G S , Tafaro C , Maruzzelli L , Cortis K , Miraglia R
Published: December 2021

The aim of this work was to establish local diagnostic reference levels (DRLs) for retrograde wedge portography (RWP) performed on pediatric patients assessing the usefulness of radiation dose monitoring software in the establishing process. Between September 2016 and April 2020, 66 consecutive RWP were performed at a transplantation institute and were included in our study. Patients were divided in three groups according to age: n = 25 infants, n = 20 middle childhood and n = 21 early adolescence. The third quartile of both Air Kerma at the reference point (Ka,r) and air kerma-area product (PKA) were evaluated to establish local DRLs (lDRLs). In addition, to control high Ka,r levels during procedures, the software notified to operators if Ka,r exceeded the dose ‘alert’ threshold set at 2 Gy. lDRLs were established for all three groups using PKA and Ka,r: infant group: 5.6 Gy.cm 2 and 0.034 Gy; middle childhood: 6.4 Gy.cm2 and 0.018 Gy and early adolescence: 12.8 Gy.cm2 and 0.059 Gy. The dose threshold ‘alert’ was never encountered (alert quota: 0%). The dose monitoring system supports the feasibility of accurate and easier lDRLs’ establishment.
Managing Stubborn Oomycete Plant Pathogens
Authors: Kousik Chandrasekar S. , Quesada-Ocampo Lina M. , Keinath Anthony , Hausbeck Mary , Granke Leah , Naegele Rachel , Ji Pingsheng
Published: December 2021

Diseases caused by oomycete plant pathogens result in devastating losses to agriculture and native forests, despite the significant research efforts that have advanced our understanding of these organisms. Limiting these pathogens has been challenging to plant pathologists and plant health practitioners. In this first focus issue , titled Managing Stubborn Oomycete Plant Pathogens, Plant Health Progress has assembled an array of manuscripts on the biology and management of Phytophthora, Pythium, Pseudoperonospora, Peronospora, and Aphanomyces spp. This focus issue has 28 peer-reviewed papers including three diagnostic guides, three mini-reviews, three briefs, two surveys, and 17 research papers. Of the 28 papers, 20 are on diseases caused by Phytophthora, four on Pythium, three on downy mildews, and one on Aphanomyces. All advance our understanding of these stubborn oomycete pathogens.
Application of the Nursing Process Using Moulage as a Problem-Based Approach to Teaching Dermatologic Content
Authors: Taylor Tracy , Kolcun Kaitlyn , Tornwall Joni
Published: December 2021

Teaching dermatologic conditions can be challenging in lecture-style format. A class activity was implemented in a prelicensure nursing course to enhance learning of dermatologic conditions while emphasizing the nursing process, evidence-based treatments, transmission-based precautions, and teamwork. Students worked in teams to identify moulage-based dermatologic conditions and follow the nursing process to develop a plan of care. Students presented their findings to faculty and peers. Positive student feedback on the activity included enhanced teamwork, application of the nursing process, visual emphasis on content, and understanding of holistic care. This activity is an innovative alternative to traditional lecture format.
Beyond Traditional RN-BSN Programs
Authors: Prosser Regina , Gravens Kathleen A.
Published: December 2021

Seamless academic programs are essential to support key national recommendations to increase the number of baccalaureate-prepared nurses (BSN). Associate degree nursing programs graduate approximately 50 percent of the registered nurse workforce. Graduates need a quality RN-BSN in nursing pathway to advance their education. This article discusses a seamless dual admission program in northeast Ohio, a cost-effective partnership between one associate degree nursing program and one BSN program that reduced barriers for students and had positive student outcomes.
Utilizing an Online Communication Module With Baccalaureate Nursing Students to Teach Leadership in Team Meetings
Authors: Wittenberg Elaine , Johnson Renee R. , Tayyeb Ali R.
Published: December 2021

This article presents an online communication module for teaching nurse leadership in team meetings. Baccalaureate students (n = 64) participated in a one-hour online module as part of a leadership course. The module included a quantitative pre-post assessment and qualitative open-ended responses to video-based scenarios of team meetings. Student responses to scenarios revealed high levels of content mastery and ability to apply module content (range, 89 percent to 90 percent across two scenarios). The module was effective in increasing the knowledge, attitude, and behaviors of students and is effective for facilitating student understanding of nurse leadership in team meetings.
Social Presence and Satisfaction in Asynchronous Text-Based Communications in Online Nursing Education: A Comparison With Synchronous Video Communications
Authors: Grech Joseph
Published: December 2021

Asynchronous online nursing education has been associated with poor levels of student interaction. This study investigated perceived social presence, a construct used to understand online interactions, and satisfaction during asynchronous text-based communications with a sample of 33 first-year and second-year nursing students. Participants were also experiencing synchronous video communications for their online education. Although social presence in asynchronous text-based communications correlated positively with satisfaction, most students identified a higher degree of social presence and satisfaction with video communications. Consideration of social presence within online education using synchronous video communications is thus recommended.
Promoting System Thinking and Professionalism Through Simulated Hospital Experiences for Nursing and Clinical Laboratory Science Students
Authors: Stewart MaryAnne , McQuillen Elizabeth P. , Carter Erik V.
Published: December 2021

A simulation laboratory was developed for prelicensure nursing and undergraduate clinical laboratory science students using scripted patient cases with laboratory test results. The experience was guided by TeamSTEPPS (Team Strategies and Tools to Enhance Performance and Patient Safety). Participants (n = 66) completed the modified Interprofessional Professionalism Assessment pre- and postsimulation. Journal reflections provided qualitative data. All aspects of interprofessional professionalism increased after the simulation; the most significant gain was confidence in working with other health care professionals. Analysis of journal themes indicated the students perceived increased communication and collaboration skills concerning patient care and safety.
An Investigation of Program Factors Affecting Clinical Failure by Nursing Students
Authors: Potter Kara
Published: December 2021

Nursing student failure affects the number of nurses prepared to enter practice. Currently, there is a dearth of literature examining program factors that influence clinical failure. This survey of nursing directors used multiple linear regression to determine if the percentage of adjunct faculty, the number of simulation hours, and the number of clinical hours affect clinical failure rates. The results of the study showed a positive correlation between each of the independent variables and the percentage of student clinical failures.
An Innovative Experiential Approach to Learning About Quality Improvement Processes
Authors: Gaffney Mary K.
Published: December 2021

Baccalaureate nursing students receive education to develop quality and safety competencies. Approaches vary due to time constraints and availability of clinical sites. In this innovative, semester-long activity, student groups applied quality improvement resources from the Institute for Healthcare Improvement, addressing problems such as stethoscope hygiene practices and weekly screen time. Students’ evaluation of the experience indicated a growth in knowledge, skills, and positive attitudes toward quality improvement. Experiential nonclinical practices are an innovative and effective way to prepare baccalaureate students for participation in quality improvement activities.
Leveraging Innovation to Design a Psychiatric Mental Health Simulation for Undergraduate Nursing Students During the COVID-19 Global Pandemic
Authors: Hudgins Tracy , Camp-Spivey Logan , Lee Shirleatha
Published: December 2021

Undergraduate nursing students experience challenges integrating didactic knowledge into the clinical care of clients living with psychiatric mental illness. Simulation can be a successful teaching strategy to mitigate some of these challenges. The aim of this pilot simulation experience was to understand how academic technology and telehealth competencies could be leveraged to support the success of standardized patient simulations for nursing students during the COVID-19 pandemic. Data from debriefings found that students had greater confidence in their technical skills than their ability to manage their emotional responses to simulation scenarios.