bluuebunny/crossref_metadata_2025 huggingface dataset:
Using existing pediatric cancer data from the Gabriella Miller Kids First Data Resource Program
Authors: Hudson Alexandra , Fournier Marcia , Coulombe James , Daee Danielle
Published: October 2023

Childhood cancer and birth defects are leading causes of childhood mortality, and studies suggest that birth defects increase pediatric cancer risk. The Gabriella Miller Kids First Pediatric Research Program (Kids First) seeks to alleviate these conditions by building an expansive resource of genetic and clinical data from patients with pediatric cancer and birth defects and their families. This article describes the data and support provided by the Kids First Data Resource Center and the Kids First Data Resource Center Data Resource Portal, which enables the public to review Kids First studies and request access to individual data. The Kids First Portal contains data from more than 34 000 participants and connects with CAVATICA (Seven Bridges Genomics, Inc, now part of Velsera), a cloud-based analysis and sharing platform. Researchers have used Kids First data to investigate a variety of cancers and further funding opportunities are available. The Kids First Portal is a unique resource that unites pediatric cancer and birth defects to uncover their genetic etiology and improve patients’ lives.
Administrative Burden in Citizen–State Interactions: A Systematic Literature Review
Authors: Halling Aske , Baekgaard Martin
Published: October 2023

Based on a systematic review of 119 articles and working papers, we provide an overview of how administrative burdens in citizen–state interactions have been studied since the inception of the research agenda in 2012. We develop a new and comprehensive model of how key concepts in the framework are related, assess the evidence of the causal relationships proposed by the model, and discuss where more evidence is needed. Empirical research supports conventional claims that burdens are consequential, distributive, and constructed. However, the literature has moved further by (1) demonstrating that factors such as frontline service delivery and government communication influence experiences of burdens; (2) highlighting how factors beyond ideology influence constructions of burdens; (3) introducing the burden tolerance concept; (4) illustrating that experiences of burden influence policymakers’ and members of the publics’ burden tolerance. Based on the review, we propose an agenda for future administrative burden research. We call for studies linking experiences of burden to outcomes such as democratic behavior and take-up, and for studies connecting policymakers’ burden tolerance to actual state actions. Moreover, we argue that future studies should use qualitative methods to further explore the nature of burdens from the perspective of citizens, rely on experimental methods to establish causal links between state actions and experiences of burden, and compare burdens across contexts. Further, empirical studies should examine the tradeoffs between legitimacy and experiences of burden, and how actors outside the citizen–state interaction may influence experiences of administrative burden.
Genomic Analysis of Group B Streptococcus Carriage Isolates From Botswana Reveals Distinct Local Epidemiology and Identifies Novel Strains
Authors: Hanze Villavicencio Karen L , Job Megan J , Burghard Anne Claire , Taffet Allison , Banda Francis M , Vurayai Moses , Mokomane Margaret , Arscott-Mills Tonya , Mazhani Tiny , Nchingane Seeletso , Thomas Brady , Steenhoff Andrew P , Ratner Adam J
Published: October 2023

In pregnant people colonized with group B Streptococcus (GBS) in Botswana, we report the presence/expansion of sequence types 223 and 109, a low rate of erythromycin resistance, and 3 novel sequence types. These data highlight the importance of local epidemiologic studies of GBS, a significant source of neonatal disease.
Derivation of expressions for interdiffusion and intrinsic diffusion flux in presence of chemical potential gradient in a multicomponent system with composition dependent molar volume
Authors: Kulkarni Kaustubh N
Published: October 2023

It has been generally accepted and often mentioned in the text books that gradient in chemical potential of a species is the fundamental driving force for its diffusion. However, a general derivation of the interrelation between the diffusion flux of a component and chemical potential gradients in a non-ideal solution is lacking. Although there have been various studies in the literature reporting such interrelations for a binary system, they all assume constant molar volume. In a non-ideal system though molar volume changes with composition. Hence, in the present work, kinetic theory is used to derive a relation between diffusion flux and the chemical potential gradients for a multicomponent system with composition dependent molar volume. It is shown that the velocity of the marker as measured in a diffusion couple experiment should consist of the drift velocity (UN) due to change in molar volume accompanied by diffusion as well as the Kirkendall velocity caused by vacancy equilibration process. For the assumption of volume change occurring only in the direction of diffusion, the Kirkendall velocity is same as the marker velocity measured in a diffusion couple. However, if the lattice is allowed to relax in all directions, the contribution of UN to the marker velocity can be significant. This is shown to be as high as 20% for Cu in a Cu-Ni diffusion couple.
Impacts of sample storage time on estimates of phytoplankton abundance: how long is too long?
Authors: Nogueira Patricia , Barbosa Ana B , Domingues Rita B
Published: October 2023

Phytoplankton play a key role in marine ecosystems, making the accurate quantification of functional groups/species, using standardized microscopy techniques, essential in many research efforts. In this study we aimed to evaluate the effects of (a) storage time on the abundance of microphytoplankton in samples fixed with acid Lugol’s solution; (b) storage time on the abundance of pico- and nanophytoplankton in frozen microscopy slides; (c) storage time on the abundance of pico- and nanophytoplankton in fixed refrigerated samples and (d) storage protocol (refrigerated versus frozen) on the abundance of pico- and nanophytoplankton. Microphytoplankton were analyzed using inverted microscopy, and pico- and nanophytoplankton using epifluorescence microscopy. Results indicate storage time negatively impacted the abundances of all phytoplankton size classes; however, effects were group-specific. For accurate abundance estimates, we suggest that samples fixed with acid Lugol’s should be analyzed within 30 and 180 days, for dinoflagellates/total microphytoplankton and diatoms, respectively. For picoeukaryotes, glutaraldehyde fixed samples should be kept refrigerated for up to 4 days, and slides should be prepared immediately before observation. It is recommended that authors specify the exact lag times between sample collection, fixation and analysis, to allow the comparability of phytoplankton datasets across different studies and/or monitoring programs.
PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1A redox states alleviate photoinhibition during changes in light intensity
Authors: Chaturvedi Amit Kumar , Dym Orly , Levin Yishai , Fluhr Robert
Published: October 2023

Plants have evolved photosynthetic regulatory mechanisms to maintain homeostasis in response to light changes during diurnal transitions and those caused by passing clouds or by wind. One such adaptation directs photosynthetic electron flow to a cyclic pathway to alleviate excess energy surges. Here, we assign a function to regulatory cysteines of PGR5-like protein 1A (PGRL1A), a constituent of the PROTON GRADIENT REGULATION5 (PGR5)-dependent cyclic electron flow (CEF) pathway. During step increases from darkness to low light intensity in Arabidopsis (Arabidopsis thaliana), the intermolecular disulfide of the PGRL1A 59-kDa complex was reduced transiently within seconds to the 28-kDa form. In contrast, step increases from darkness to high light stimulated a stable, partially reduced redox state in PGRL1A. Mutations of 2 cysteines in PGRL1A, Cys82 and Cys183, resulted in a constitutively pseudo-reduced state. The mutant displayed higher proton motive force (PMF) and nonphotochemical quenching (NPQ) than the wild type (WT) and showed altered donor and acceptor dynamic flow around PSI. These changes were found to correspond with the redox state of PGRL1A. Continuous light regimes did not affect mutant growth compared to the WT. However, under fluctuating regimes of high light, the mutant showed better growth than the WT. In contrast, in fluctuating regimes of low light, the mutant displayed a growth penalty that can be attributed to constant stimulation of CEF under low light. Treatment with photosynthetic inhibitors indicated that PGRL1A redox state control depends on the penultimate Fd redox state. Our results showed that redox state changes in PGRL1A are crucial to optimize photosynthesis.
Social and built neighborhood environments and sleep health: The Hispanic Community Health Study/Study of Latinos Community and Surrounding Areas and Sueño Ancillary Studies
Authors: Savin Kimberly L , Carlson Jordan A , Patel Sanjay R , Jankowska Marta M , Allison Matthew A , Sotres-Alvarez Daniela , Sallis James F , Talavera Gregory A , Roesch Scott C , Malcarne Vanessa L , Larsen Britta , Rutledge Thomas , Gallo Linda C
Published: October 2023

Study Objectives

To test associations between neighborhood social, built, and ambient environment characteristics and multidimensional sleep health in Hispanic/Latino adults.

Methods

Data were from San Diego-based Hispanic/Latino adults mostly of Mexican heritage enrolled in the Hispanic Community Health Study/Study of Latinos (N = 342). Home addresses were geocoded to ascertain neighborhood characteristics of greenness, walkability (density of intersections, retail spaces, and residences), socioeconomic deprivation (e.g. lower income, lower education), social disorder (e.g. vacant buildings, crime), traffic density, and air pollution (PM 2.5) in the Study of Latinos Communities and Surrounding Areas Study. Sleep dimensions of regularity, satisfaction, alertness, timing, efficiency, and duration were measured by self-report or actigraphy approximately 2 years later. Multivariable regression models accounting for study design (stratification and clustering) were used to examine associations of neighborhood variables with individual sleep dimensions and a multidimensional sleep health composite score.

Results

Neighborhood characteristics were not significantly associated with the multidimensional sleep health composite, and there were few significant associations with individual sleep dimensions. Greater levels of air pollution (B = 9.03, 95% CI: 1.16, 16.91) were associated with later sleep midpoint, while greater social disorder (B = −6.90, 95% CI: −13.12, −0.67) was associated with earlier sleep midpoint. Lower walkability was associated with more wake after sleep onset (B = −3.58, 95% CI: −7.07, −0.09).

Conclusions

Living in neighborhoods with lower walkability and greater air pollution was associated with worse sleep health, but otherwise findings were largely null. Future research should test these hypotheses in settings with greater variability and investigate mechanisms of these associations.
Polyphenols as a partial replacement for vitamin E in nursery pig diets
Authors: Rao Zhong-Xing , Tokach Mike D , Woodworth Jason C , DeRouchey Joel M , Goodband Robert D , Shah Apoorva S , Foley Brandon H , Kjeldsen Karsten C , Brunsgaard Grete , Gebhardt Jordan T
Published: October 2023

A total of 300 pigs (241 × 600; DNA, Columbus, NE; initially 6.0 ± 0.01 kg) were used in a 42-d trial to determine the effects of vitamin E levels and partially replacing vitamin E with a polyphenol (Cabanin CSD, R2 Argo, Denmark) on growth performance, complete blood count, serum thiobarbituric acid reactive substances (TBARS), superoxide dismutase (SOD), and cytokine panel. Sixty pens of pigs were weighed and allotted to one of the five dietary treatments in a completely randomized design with 12 pens per treatment. A control treatment was formulated to provide 15 IU/kg of vitamin E equivalence from vitamin E. This control treatment was then used as a base for three replacement strategy diets to determine the effects of replacing an additional 60 IU/kg of vitamin E with polyphenol in diets containing a basal level of vitamin E requirement estimate (15 IU/kg). First, an additional 60 IU/kg of vitamin E was added for a total of 75 IU/kg of vitamin E equivalence. Second, 50% of the additional vitamin E (30 IU/kg) was replaced with the equivalency of polyphenol. Third, all 60 IU/kg of the additional vitamin E was replaced with the equivalency of polyphenol. To evaluate whether there are negative effects of feeding nursery pigs a high level of polyphenol, a fifth treatment was formulated to provide 575 IU/kg of vitamin E equivalence with 75 IU/kg from vitamin E and 500 IU/kg from polyphenol. Whole blood and serum samples were collected on days 10 and 42, and pig weights and feed disappearance were measured on days 10, 21, 31, 38, and 42. For growth performance, increasing vitamin E equivalence tended to improve (quadratic, P < 0.10) gain-to-feed ratio (G:F) from days 10 to 21, and tended to improve (linear, P < 0.10) G:F from days 21 to 42 and 0 to 42. There was a vitamin E equivalence × day interaction (P = 0.050) for serum SOD activity. Increasing vitamin E equivalence increased (linear, P < 0.05) serum SOD activity on day 42 but not on days 10 (P > 0.10). For serum cytokines, there was no evidence of differences (P > 0.10) between treatments and vitamin E equivalence. Moreover, there was no evidence of differences (P > 0.10) in all response variables between the three replacement strategies throughout the entire periods. In summary, increasing vitamin E equivalence tended to improve G:F, which may be related to the improved SOD activity. Furthermore, polyphenol can effectively replace vitamin E provided above the vitamin E requirement to provide similar benefits from increasing vitamin E equivalence.
The involvement of hepatic cytochrome P450s in the cytotoxicity of lapatinib
Authors: Chen Si , Li Xilin , Li Yuxi , He Xiaobo , Bryant Matthew , Qin Xuan , Li Feng , Seo Ji-Eun , Guo Xiaoqing , Mei Nan , Guo Lei
Published: October 2023

Lapatinib, an oral tyrosine kinase inhibitor used as a first-line treatment for HER2-positive breast cancer, has been reported to be associated with hepatotoxicity; however, the underlying mechanisms remain unclear. In this study, we report that lapatinib causes cytotoxicity in multiple types of hepatic cells, including primary human hepatocytes, HepaRG cells, and HepG2 cells. A 24-h treatment with lapatinib induced cell cycle disturbances, apoptosis, and DNA damage, and decreased the protein levels of topoisomerase in HepG2 cells. We investigated the role of cytochrome P450 (CYP)-mediated metabolism in lapatinib-induced cytotoxicity using our previously established HepG2 cell lines, which express each of 14 CYPs (1A1, 1A2, 1B1, 2A6, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 3A4, 3A5, and 3A7). We demonstrate that lapatinib is metabolized by CYP1A1, 3A4, 3A5, and 3A7. Among these, lapatinib-induced cytotoxicity and DNA damage were attenuated in cells overexpressing CYP3A5 or 3A7. Additionally, we measured the production of three primary metabolites of lapatinib (O-dealkylated lapatinib, N-dealkylated lapatinib, and N-hydroxy lapatinib) in CYP1A1-, 3A4-, 3A5-, and 3A7-overexpressing HepG2 cells. We compared the cytotoxicity of lapatinib and its 3 metabolites in primary human hepatocytes, HepaRG cells, and HepG2 cells and demonstrated that N-dealkylated lapatinib is more toxic than the parent drug and the other metabolites. Taken together, our results indicate that lapatinib-induced cytotoxicity involves multiple mechanisms, such as apoptosis and DNA damage; that N-dealkylated lapatinib is a toxic metabolite contributing to the toxic effect of lapatinib; and that CYP3A5- and 3A7-mediated metabolism plays a role in attenuating the cytotoxicity of lapatinib.
A Preliminary Study of Executive Functioning in Preterm-Born Children
Authors: Gillenson Caroline J. , Bagner Daniel M. , Darcy Mahoney Ashley , Baralt Melissa
Published: October 2023

Background:

Preterm-born children are at increased risk for deficits in executive function (EF). EF is a set of cognitive processes including inhibition, attention, memory, and decision-making, among others. Bilingualism, operationalized as productive capacity in 2 languages (ie, English and Spanish), may enhance EF in children born preterm and in term-born children.

Purpose:

The purpose of this study was to examine the impact of bilingualism on executive functioning in bilingual and monolingual preterm and term-born children using a robust measure of bilingualism.

Methods:

This study examined the impact of bilingualism on EF in 17 monolingual or bilingual preterm-born children, aged 6 to 7. The preterm-born sample was also compared with a normed, term-born sample of 38 monolingual, typically developing 6- to 7-year-olds.

Results:

On the Creature Counting task of EF, bilingual preterm-born children performed with more accuracy and total switches than monolingual preterm-born children. There was no difference in accuracy between the term-born and entire preterm-born samples. The bilingual, preterm-born children performed more accurately than the term-born sample.

Implications for Practice and Research:

This preliminarily suggests bilingualism confers an advantage to preterm-born children's EF. Further research is needed on bilingual advantage of preterm-born children.
Lateral Pelvic Nodal Management and Patterns of Failure in Patients Receiving Short-Course Radiation for Locally Advanced Rectal Cancer
Authors: Hassanzadeh Comron , Mirza Kasim , Kalaghci Bita , Fallahian Fedra , Chin Re-I , Roy Amit , Stowe Hayley , Low Gregory , Pedersen Katrina , Wise Paul , Glasgow Sean , Roach Michael , Henke Lauren , Badiyan Shahed , Mutch Matthew , Kim Hyun
Published: October 2023

BACKGROUND:

Management of lateral pelvic lymph nodes in locally advanced rectal cancer is controversial, with limited data indicating the optimal approach. Additionally, no data exists regarding treatment of lateral nodes in the setting of short course radiation and nonoperative intent.

OBJECTIVE:

We evaluate a novel approach incorporating simultaneous integrated boost to suspicious lateral nodes.

DESIGN:

This was a retrospective study.

SETTING:

This study was conducted at a large, tertiary referral center.

PATIENTS:

Patients treated with radiation and consolidation chemotherapy were included. All primary tumors were biopsy confirmed and disease-staged with pelvic magnetic resonance imaging.

INTERVENTIONS:

Primary tumors were biopsy proven and staged with pelvic magnetic resonance imaging. A subset of lateral pelvic lymph nodes patients received simultaneous integrated boost to 35 Gy in 5 fractions. Then, chemotherapy was administered with the majority receiving mFOLFOX (modified folinic acid, fluorouracil, and oxaliplatin). Clinical partial response required total mesorectal excision.

MAIN OUTCOME MEASURES:

Patterns of failure and survival analyses by subgroup were assessed. Outcomes based on receipt of radiation were compared across node status.

RESULTS:

Between January 2017 – January 2022, 155 patients were treated with short course and chemotherapy with 121 included in final analysis. Forty-nine percent underwent nonoperative management. Median follow-up was 36 months and median age was 58 years. Thirty-eight patients (26%) had positive lateral pelvic lymph nodes. Comparing lateral node status, progression-free survival was significantly worse for patients with positive disease (p < 0.001) with a trend for worse overall survival. Receipt of nodal boost in patients with lateral nodes resulted in meaningful locoregional control. Nodal boost did not contribute to additional acute or late GI toxicity.

LIMITATIONS:

Limitations included retrospective nature and lack of lateral nodes pathology; however, thorough radiographic review was performed.

CONCLUSIONS:

Lateral node positive rectal cancer is correlated with worse oncologic outcomes and higher locoregional failure. Boost to clinically positive lateral nodes is a safe approach in the setting of short course and in those receiving nonoperative intent.
Sleep disturbances in women with early-onset menopausal transition: a population-based study
Authors: Salin Satu A.E. , Savukoski Susanna M. , Pesonen Paula R.O. , Auvinen Juha P. , Niinimäki Maarit J.
Published: October 2023

Objective

The aim of this study was to investigate sleep disturbances in 46-yr-old women and their association with early-onset menopausal transition.

Methods

The women of this cross-sectional birth cohort study were divided into climacteric (n = 359) and preclimacteric (n = 2,302) groups by their menopausal status, defined by follicle-stimulating hormone levels and menstrual history. Sleep disturbances were evaluated with Athens Insomnia Scale 5. We performed univariable and multivariable logistic regression models in which sleep parameters were dependent variables and climacteric status, hot flashes, smoking, and education level were independent variables. The use of hormone therapy was also evaluated in women suffering from sleeping disturbances.

Results

On the basis of the scale questions, climacteric women experienced significantly delayed sleep induction (12.2% vs 8.7%,P= 0.047), more problems with awakenings during the night (23.4% vs 14.6%,P< 0.001), earlier final awakening (13.8% vs 9.9%,P= 0.039), and more unsatisfying sleep quality (11.9% vs 7.9%,P= 0.023). Climacteric women who were experiencing hot flashes reported unsatisfactory sleep quality more frequently compared with climacteric women who did not experience hot flashes (17.0% vs 9.2%,P= 0.047). In the univariable and multivariable logistic regression models, being climacteric was independently associated with different impaired sleeping parameters. Most climacteric women who had a scale score of 4 or greater were not using hormone therapy, according to their medicine purchases over the past year.

Conclusions

Being climacteric was associated with sleep disturbances in women in their mid-40s. However, this association seemed to be particularly driven by hot flashes. Most climacteric women with clinically significant sleeping disturbances were not using hormone therapy.
Sensitivity and Specificity of Pulse Oximetry for Identification of Peripheral Artery Disease
Authors: Phua Sheryl , Hawke Fiona Ellen , Chuter Vivienne Helaine , Tehan Peta Ellen
Published: October 2023

Background

Lower limb peripheral artery disease (PAD) is associated with poor outcomes including ulceration, gangrene, amputations, and mortality. Clinicians therefore routinely perform point-of-care tests in high-risk populations to identify PAD and subsequently implement cardiovascular management and appropriate interventions. Pulse oximetry has been suggested as a useful adjunct test for identifying PAD.

Objective

The aim of this systematic review was to determine the sensitivity and specificity of pulse oximetry in the lower limb for identifying PAD.

Methods

MEDLINE, EMBASE, and CINAHL were searched up until January 10, 2023, to identify studies of sensitivity and specificity of pulse oximetry that used criterion standard diagnostic imaging as a reference standard. Two authors screened articles for inclusion and appraised quality of included studies using the Quality Appraisal for Diagnostic Accuracy Studies, version 2.

Results

A total of 6371 records were screened, and 4 were included. The included studies had a total of 471 participants, with an age range of 41 to 80.6 years. All studies were cross-sectional and conducted in hospital settings. Sensitivity values for pulse oximetry compared with diagnostic imaging in identifying PAD ranged from 44% to 76%, and specificity values ranged from 85% to 96%. There was no consensus regarding measurement techniques and diagnostic thresholds for pulse oximetry, which precluded meta-analysis.

Conclusions

There is currently inadequate evidence to support the use of pulse oximetry for identifying PAD. Current evidence suggests that pulse oximetry has low levels of sensitivity and is therefore likely to miss PAD when it is present.
Outcomes of living donor liver transplant recipients receiving grafts with the graft-to-recipient weight ratio less than 0.6%: A matched pair analysis
Authors: Matsushima Hajime , Soyama Akihiko , Hara Takanobu , Maruya Yasuhiro , Fujita Takuro , Imamura Hajime , Adachi Tomohiko , Hidaka Masaaki , Eguchi Susumu
Published: October 2023

We sometimes experience living donor liver transplantation (LDLT) involving very small grafts with graft-to-recipient weight ratio (GRWR) < 0.6% when the actual graft size is smaller than predicted. The outcomes in this situation have not been fully investigated. The present study aimed to determine the graft outcomes of LDLT with GRWR < 0.6%. We retrospectively reviewed 280 cases of adult LDLT performed at our institution between January 2000 and March 2021. In our institution, the lower limit for graft volume/standard liver volume ratio was 30%. The patients were divided into 2 groups according to the cutoff value of 0.6% for actual GRWR. Graft survival and surgical outcomes, including small-for-size syndrome (SFSS), were compared between the groups using propensity score matching analysis. Risk factors associated with SFSS in recipients with GRWR < 0.6% were also evaluated. Fifty-nine patients received grafts with GRWR < 0.6%. After propensity score matching, similar graft survival rates were observed for GRWR < 0.6% (n = 53) and GRWR ≥ 0.6% (n = 53) (p = 0.98). However, patients with GRWR < 0.6% had a significantly worse 3-month graft survival rate (86.8% vs. 98.1%, p = 0.03) and higher incidence of SFSS (p < 0.001) than patients with GRWR ≥0.6%. On multivariate analysis, Model for End-Stage Liver Disease score and donor age were associated with SFSS in patients with GRWR < 0.6%. The same factors were also associated with graft survival. In conclusion, although similar overall graft survival rates were observed for LDLT with GRWR < 0.6% and GRWR ≥ 0.6%, GRWR < 0.6% was associated with an increased risk of SFSS. Appropriate donor and recipient selection is important for successful LDLT with very small grafts.
The Recent Rise of Eutylone Intoxications in Onondaga County and Surrounding Counties
Authors: Tawil Michel , El Marj Nicole , Monday Katrina , Gitto Lorenzo
Published: October 2023

Eutylone is an emerging synthetic stimulant that is quickly gaining popularity due to its affordability and wide availability. A recent surge has been observed in Upstate New York. This study presents a retrospective review of deaths in which eutylone was identified in postmortem samples from January 2018 to December 2021 in the electronic database of the Onondaga County medical examiner's office in Syracuse, NY. Of the 176 subjects who met the study criteria, 128 (73%) were male and 48 (27%) were female, with a mean age of 37.6 years. Most of the subjects were listed as White (89%), followed by African American (9%). Most of the cases had multiple medical comorbidities (89%), with anxiety and hypertension being the most common illnesses. Chromatography/mass spectrometry was used to perform a qualitative analysis of femoral blood and urine samples to detect multiple drugs, including eutylone. Substance abuse disorder was present in 135 (77%) cases, with opiates and cocaine being the most common additional drugs detected. The most common cause and manner of death were drug toxicity and accident, in 137 (78%) and 143 (81%) cases, respectively. Overall, the study suggests that eutylone is a growing concern in Upstate New York, and its use is increasing in prevalence. Policymakers and health care providers should take steps to address this emerging issue and prevent further harm to individuals and communities affected by drug overdose.
Preventing Community-Acquired Pressure Injuries in Spinal Cord Injury
Authors: Burkhart Elizabeth , Zurek Stacey , Desmond Mary E. , Aguina Keith , Cabigon Ralph D. , Smith Autumn , Bates-Jensen Barbara
Published: October 2023

Purpose

The aim of this study was to develop and pilot an educational curriculum for healthcare providers to better understand community-acquired pressure injury (CAPrI) prevention in veterans living with spinal cord injury (SCI).

Methods

The Thomas six-step process model guided curricular development and evaluation. Curriculum development followed six steps: (1) problem identification and general needs assessment from a literature review and qualitative research triangulating provider and veteran perspectives of CAPrI prevention in SCI, (2) target needs assessment using a focus group with 14 experienced practicing interprofessional SCI providers, (3) creation of module goals and objectives with content review from experts (n = 8), (4) development of curriculum content and educational strategies, (5) implementation of a pilot (n = 4), and (6) evaluation of satisfaction and curriculum content via survey and focus group.

Results

A five-module online curriculum was evaluated positively and is available publicly. Modules include (1) CAPrI Prevention Clinical Guidelines for the Provider, (2) CAPrI Prevention from the Veteran Perspective, (3) Building Collaborative Relationships, (4) Accessing Resources, and (5) Team Approach. Pilot participants stated objectives were met; they were satisfied with the module. The participants did recommend some changes.

Clinical Relevance

Understanding CAPrI prevention can inform rehabilitation nursing care.

Conclusions

An asynchronous educational curriculum can support nurses in integrating preventive care in community-dwelling veterans living with SCI.
What's the rumpus? Resident temperate forest birds approach an unfamiliar neotropical alarm call across three continents
Authors: Dominguez Jonah S. , Rakovic Marko , Li Donglai , Pollock Henry S. , Lawson Shelby , Novcic Ivana , Su Xiangting , Zeng Qisha , Al-Dhufari Roqaya , Johnson-Cadle Shanelle , Boldrick Julia , Chamberlain Mac , Hauber Mark E.
Published: October 2023

Alarm signals have evolved to communicate pertinent threats to conspecifics, but heterospecifics may also use alarm calls to obtain social information. In birds, mixed-species flocks are often structured around focal sentinel species, which produce reliable alarm calls that inform eavesdropping heterospecifics about predation risk. Prior research has shown that Neotropical species innately recognize the alarm calls of a Nearctic sentinel species, but it remains unclear how generalizable or consistent such innate signal recognition of alarm-calling species is. We tested for the responses to the alarm calls of a Neotropical sentinel forest bird species, the dusky-throated antshrike (
Thamnomanes ardesiacus
), by naive resident temperate forest birds across three continents during the winter season. At all three sites, we found that approaches to the Neotropical antshrike alarm calls were similarly frequent to the alarm calls of a local parid sentinel species (positive control), while approaches to the antshrike's songs and to non-threatening columbid calls (negative controls) occurred significantly less often. Although we only tested one sentinel species, our findings indicate that temperate forest birds can recognize and adaptively respond globally to a foreign and unfamiliar tropical alarm call, and suggest that some avian alarm calls transcend phylogenetic histories and individual ecological experiences.
How to make an inclusive-fitness model
Authors: Scott Thomas W. , Wild Geoff
Published: October 2023

Social behaviours are typically modelled using neighbour-modulated fitness, which focuses on individuals having their fitness altered by neighbours. However, these models are either interpreted using inclusive fitness, which focuses on individuals altering the fitness of neighbours, or not interpreted at all. This disconnect leads to interpretational mistakes and obscures the adaptive significance of behaviour. We bridge this gap by presenting a systematic methodology for constructing inclusive-fitness models. We find a behaviour’s ‘inclusive-fitness effect’ by summing primary and secondary deviations in reproductive value. Primary deviations are the immediate result of a social interaction; for example, the cost and benefit of an altruistic act. Secondary deviations are compensatory effects that arise because the total reproductive value of the population is fixed; for example, the increased competition that follows an altruistic act. Compared to neighbour-modulated fitness methodologies, our approach is often simpler and reveals the model’s inclusive-fitness narrative clearly. We implement our methodology first in a homogeneous population, with supplementary examples of help under synergy, help in a viscous population and Creel’s paradox. We then implement our methodology in a class-structured population, where the advantages of our approach are most evident, with supplementary examples of altruism between age classes, and sex-ratio evolution.
Amygdalobacter indicium gen. nov., sp. nov., and Amygdalobacter nucleatus sp. nov., gen. nov.: novel bacteria from the family Oscillospiraceae isolated from the female genital tract
Authors: Srinivasan Sujatha , Austin Michele N. , Fiedler Tina L. , Strenk Susan M. , Agnew Kathy J. , Gowda G. A. Nagana , Raftery Daniel , Beamer May A. , Achilles Sharon L. , Wiesenfeld Harold C. , Fredricks David N. , Hillier Sharon L.
Published: October 2023

Four obligately anaerobic Gram-positive bacteria representing one novel genus and two novel species were isolated from the female genital tract. Both novel species, designated UPII 610-JT and KA00274T, and an additional isolate of each species were characterized utilizing biochemical, genotypic and phylogenetic analyses. All strains were non-motile and non-spore forming, asaccharolytic, non-cellulolytic and indole-negative coccobacilli. Fatty acid methyl ester analysis for UPII 610-JT and KA00274T and additional isolates revealed C16 : 0, C18 : 0, C18:1ω9c and C18:2ω6,9c to be the major fatty acids for both species. UPII 610-JT had a 16S rRNA gene sequence similarity of 99.4 % to an uncultured clone sequence (AY724740) designated as Bacterial Vaginosis Associated Bacterium 2 (BVAB2). KA00274T had a 16S rRNA gene sequence similarity of 96.5 % to UPII 610-JT. Whole genomic DNA mol% G+C content was 42.2 and 39.3 % for UPII 610-JT and KA00274T, respectively. Phylogenetic analyses indicate these isolates represent a novel genus and two novel species within the Oscillospiraceae family. We propose the names Amygdalobacter indicium gen. nov., sp. nov., for UPII 610-JT representing the type strain of this species (=DSM 112989T, =ATCC TSD-274T) and Amygdalobacter nucleatus gen. nov., sp. nov., for KA00274T representing the type strain of this species (=DSM 112988T, =ATCC TSD-275T).
A molecular switch in RCK2 triggers sodium-dependent activation of KNa1.1 (KCNT1) potassium channels
Authors: Cole Bethan A. , Kalli Antreas C. , Pilati Nadia , Muench Stephen P. , Lippiat Jonathan D.
Published: October 2023

The Na+-activated K+channel KNa1.1, encoded by theKCNT1gene, is an important regulator of neuronal excitability. How intracellular Na+ions bind and increase channel activity is not well understood. Analysis of KNa1.1 channel structures indicate that there is a large twisting of the βN-αQ loop in the intracellular RCK2 domain between the inactive and Na+-activated conformations, with a lysine (K885, human subunit numbering) close enough to form a salt bridge with aspartate (D839) in the Na+-activated state. Concurrently, an aspartate (D884) adjacent in the same loop adopts a position within 4 Å of several acidic or polar residues. In carrying out mutagenesis and electrophysiology with human KNa1.1, we found alanine substitution of each of these residues resulted in almost negligible currents in the presence of up to 40 mM intracellular Na+. The exception was D884A, which resulted in constitutively active channels in both the presence and absence of intracellular Na+. Further mutagenesis of this site revealed an amino acid size-dependent effect. Substitutions at this site by an amino acid smaller than aspartate (D884V) also yielded constitutively active KNa1.1, D884I had Na+- dependence similar to wild-type KNa1.1, whilst increasing the side chain size larger than aspartate (D884E or D884F) yielded channels that could not be activated by up to 40 mM intracellular Na+. We conclude that Na+binding results in a conformational change that accommodates D884 in the acid-rich pocket, which triggers further conformational changes in the RCK domains and channel activation.

Statement of Significance

Sodium-activated potassium channels regulate neuronal excitability, and their dysfunction causes severe childhood disorders. Here, we identify a structural determinant in the intracellular domains that is responsible for triggering channel activation in response to sodium ion binding. An increase in the size of a particular amino acid renders the channel sodium-insensitive, whilst a decrease in size enables the channel to activate in the absence of sodium. This enhances our understanding of how this subclass of potassium channels respond to changes in the intracellular ionic environment. Furthermore, this may also further our understanding of the basis of human neurological disorders and their treatment.
Attention and microsaccades: do attention shifts trigger new microsaccades or only bias ongoing microsaccades?
Authors: Liu Baiwei , Alexopoulou Zampeta-Sofia , van Ede Freek
Published: October 2023

Brain circuitry that controls where we look also contributes to attentional focusing of visual contents outside of current fixation or contents held within the spatial layout of working memory. A behavioural manifestation of the contribution of oculomotor brain circuitry to selective attention comes from modulations in microsaccade direction that accompany attention shifts. Here, we address whether such modulations come about because attention itself triggers new microsaccades or whether, instead, shifts in attention only bias the direction of ongoing microsaccades – i.e., naturally occurring microsaccades that would have been made whether or not attention was also shifted. We utilised an internal-selective-attention task that has recently been shown to yield clear spatial microsaccade modulations and compared microsaccade rates following colour retrocues that were matched for sensory input, but differed in whether they invited an attention shift or not. If shifts in attention trigger new microsaccades then we would expect more microsaccades following attention-directing cues than following neutral cues. In contrast, we found no evidence for an increase in overall microsaccade rate following attention-directing cues, despite observing robust modulations in microsaccade direction. This implies that shifting attention biases the direction of ongoing microsaccades without changing the probability that a microsaccade will occur. These findings provide relevant context for complementary and future work delineating the links between attention, microsaccades, and upstream oculomotor brain circuitry, such as by helping to explain why microsaccades and attention shifts are often correlated but not obligatorily linked.
Dynamic Contact Networks of Residents of an Urban Jail in the Era of SARS-CoV-2
Authors: Jenness Samuel M. , Wallrafen-Sam Karina , Schneider Isaac , Kennedy Shanika , Akiyama Matthew J. , Spaulding Anne C.
Published: October 2023

Background

In custodial settings such as jails and prisons, infectious disease transmission is heightened by factors such as overcrowding and limited healthcare access. Specific features of social contact networks within these settings have not been sufficiently characterized, especially in the context of a large-scale respiratory infectious disease outbreak. The study aims to quantify contact network dynamics within the Fulton County Jail in Atlanta, Georgia, to improve our understanding respiratory disease spread to informs public health interventions.

Methods

As part of the Surveillance by Wastewater and Nasal Self-collection of Specimens (SWANSS) study, jail roster data were utilized to construct social contact networks. Rosters included resident details, cell locations, and demographic information. This analysis involved 6,702 residents over 140,901 person days. Network statistics, including degree, mixing, and turnover rates, were assessed across age groups, race/ethnicities, and jail floors. We compared outcomes for two distinct periods (January 2022 and April 2022) to understand potential responses in network structures during and after the SARS-CoV-2 Omicron variant peak.

Results

We found high cross-sectional network degree at both cell and block levels, indicative of substantial daily contacts. While mean degree increased with age, older residents exhibited lower degree during the Omicron peak, suggesting potential quarantine measures. Block-level networks demonstrated higher mean degrees than cell-level networks. Cumulative degree distributions for both levels increased from January to April, indicating heightened contacts after the outbreak. Assortative age mixing was strong, especially for residents aged 20–29. Dynamic network statistics illustrated increased degrees over time, emphasizing the potential for disease spread, albeit with a lower growth rate during the Omicron peak.

Conclusions

The contact networks within the Fulton County Jail presented ideal conditions for infectious disease transmission. Despite some reduction in network characteristics during the Omicron peak, the potential for disease spread remained high. Age-specific mixing patterns suggested unintentional age segregation, potentially limiting disease spread to older residents. The study underscores the need for ongoing monitoring of contact networks in carceral settings and provides valuable insights for epidemic modeling and intervention strategies, including quarantine, depopulation, and vaccination. This network analysis offers a foundation for understanding disease dynamics in carceral environments.
Ozone and ultra-fine particle concentrations in a hotel quarantine facility during 222 nm far-UVC air disinfection
Authors: Kalliomäki Petri , Sobhani Hamed , Stratton Phillip , Coleman Kristen K. , Srikakulapu Aditya , Salawitch Ross , Dickerson Russell R. , Zhu Shengwei , Srebric Jelena , Milton Donald K.
Published: October 2023

Far-UVC (222 nm UV-C light) is a promising tool to mitigate aerosol transmission of pathogens indoors. However, recent studies have raised concerns related to ozone (O3) production and secondary chemistry. In this study, we measured indoor O3and ultra-fine particle (UFP, 17.5-289 nm) concentrations with and without 222 nm far-UVC (average fluence rate 1.7-1.8 µW/cm2) in a hotel quarantine facility in Baltimore (MD, USA). We obtained nearby outdoor O3concentrations from the Environmental Protection Agency (EPA) website. In a sealed empty guest room, the average O3concentrations were 3 ppb (UV off, 0.1-0.5 ACH), 16 ppb (UV on, 0.1 ACH) and 9 ppb (UV on, 0.5 ACH). In a standard guest room, the average O3concentrations were 12 ppb (UV off, 1.4 ACH) and 14 ppb (UV on, 1.4 ACH), and correlated with outdoor concentrations (ρ= 0.65 – 0.74, p = 2*10−12– 2*10−29). A linear regression model, adjusted for outdoor O3, estimated that use of far-UVC lamps increased the O3concentration by 5.7 ppb (95% confidence interval (CI) 4.9 – 6.5 ppb) in the standard hotel room. Indoor O3concentrations increased with far-UVC usage, however, the concentrations remained 6-12 ppb lower, on average, than outdoors and well below EPA ambient limits. We did not find a clear relationship between indoor UFP concentrations and UV usage. Although our study was limited by absence of direct outdoor measurements of local O3and UFPs, our findings do not support a major impact of far-UVC on UFP concentrations in the real-world environment that we studied.
NanoBERTa-ASP: Predicting Nanobody Binding Epitopes Based on a Pretrained RoBERTa Model
Authors: Li Shangru , Meng Xiangpeng , Li Rui , Huang Bingding , Wang Xin
Published: October 2023

Nanobodies, also known as VHH or single-domain antibodies, are a unique class of antibodies that consist only of heavy chains and lack light chains. Nanobodies possess the advantages of both small molecule drugs and conventional antibodies, making them a promising class of therapeutic biopharmaceuticals. Studying the characteristics of nanobody sequences can aid the development and design of nanobodies. An important challenge in this field is accurately predicting the binding sites between nanobodies and antigens. The binding site is the region where the nanobody interacts with the antigen. The precise prediction of these binding sites is crucial for comprehending the interaction mechanism between the nanobody and the antigen, facilitating the design of effective nanobodies, as well as gaining valuable insights into the properties of nanobodies.

Nanobodies typically have smaller and more flexible binding sites than traditional antibodies, however predictive models trained on traditional antibodies may not be suitable for nanobodies. Moreover, the limited availability of antibodyderived nanobody datasets for deep learning poses challenges in constructing highly accurate predictive models that can generalize well to unseen data.

To address these challenges, we propose a novel nanobody prediction model, named NanoBERTa-ASP (Antibody Specificity Prediction), which is specifically designed for predicting nanobody-antigen binding sites. The model adopts a training strategy more suitable for nanobodies by leveraging an advanced natural language processing (NLP) model called BERT (Bidirectional Encoder Representations from Transformers). The model also utilizes a masked language modeling approach to learn the contextual information of the nanobody sequence and predict its binding site.

The results obtained from training NanoBERTa-ASP on nanobodies highlight its exceptional performance in Precision and AUC, underscoring its proficiency in capturing sequence information specific to nanobodies and accurately predicting their binding sites. Furthermore, our model can provide insights into the interaction mechanisms between nanobodies and antigens, contributing to a better understanding of nanobodies, as well as accelerating the development and design of nanobodies with potential therapeutic applications. To the best of our knowledge, NanoBERTa-ASP is the first nanobody language model that achieved high accuracy in predicting the binding sites.

Github repository

https://github.com/WangLabforComputationalBiology/NanoBERTa-ASP