bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

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

Abstract
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

Abstract

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.
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

AbstractThe 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 SignificanceSodium-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

ABSTRACTBrain 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

ABSTRACTBackgroundIn 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.MethodsAs 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.ResultsWe 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.ConclusionsThe 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

AbstractFar-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

AbstractNanobodies, 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 repositoryhttps://github.com/WangLabforComputationalBiology/NanoBERTa-ASP
Rare variant analyses validate known ALS genes in a multi-ethnic population and identifiesANTXR2as a candidate in PLS
Authors: Pottinger Tess D. , Motelow Joshua E. , Povysil Gundula , Moreno Cristiane A. Martins , Ren Zhong , Phatnani Hemali ,   The New York Genome Center ALS Sequencing Consortium, Aitman Timothy J. , Santoyo-Lopez Javier ,   Scottish Genomes Partnership, Mitsumoto Hiroshi ,   ALS COSMOS Study Group,   PLS COSMOS Study Group,   GTAC Investigators, Goldstein David B. , Harms Matthew B. 
Published: October 2023

ABSTRACTBackgroundAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 30,000 people in the United States. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms, such as antisense oligonucleotides, continue to develop, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible due to an increase in power. These analyses could highlight novel pathways in disease manifestation.MethodsBuilding on our previous discoveries using rare variant association analyses, we conducted rare variant burden testing on a substantially larger cohort of 6,970 ALS patients from a large multi-ethnic cohort as well as 166 PLS patients, and 22,524 controls. We used intolerant domain percentiles based on sub-region Residual Variation Intolerance Score (subRVIS) that have been described previously in conjunction with gene based collapsing approaches to conduct burden testing to identify genes that associate with ALS and PLS.ResultsA gene based collapsing model showed significant associations withSOD1,TARDBP, andTBK1(OR=19.18, p = 3.67 × 10−39; OR=4.73, p = 2 × 10−10; OR=2.3, p = 7.49 × 10−9, respectively). These genes have been previously associated with ALS. Additionally, a significant novel control enriched gene,ALKBH3(p = 4.88 × 10−7), was protective for ALS in this model. An intolerant domain based collapsing model showed a significant improvement in identifying regions inTARDBPthat associated with ALS (OR=10.08, p = 3.62 × 10−16). Our PLS protein truncating variant collapsing analysis demonstrated significant case enrichment inANTXR2(p=8.38 × 10−6).ConclusionsIn a large multi-ethnic cohort of 6,970 ALS patients, rare variant burden testing validated known ALS genes and identified a novel potentially protective gene,ALKBH3. A first-ever analysis in 166 patients with PLS found a candidate association with loss-of-function mutations inANTXR2.
Scaling use of the rust fungusPuccinia punctiformisfor biological control of Canada thistle (Cirsium arvense(L.) Scop.): First report on a U.S. statewide effort
Authors: Bean Dan W. , Gladem Kristi , Rosen Karen , Blake Alexander , Clark Robert E. , Henderson Caitlin , Kaltenbach John , Price Joel , Smallwood Emily L. , Berner Dana K. , Young Stephen L. , Schaeffer Robert N. 
Published: October 2023

AbstractCanada thistle (Cirsium arvense(L.) Scop., CT) is one of the worst weeds threatening temperate regions of the world. A host-specific rust fungus,Puccinia punctiformis(F. Strauss) Rohl., is known to cause systemic disease of CT, ultimately killing individuals and reducing stand densities. In 2013, it was demonstrated that fall inoculation of rosettes with coarsely ground leaves bearingP. punctiformistelia can successfully initiate epiphytotics. In the same year, a cooperative project between the Colorado Department of Agriculture and United States Department of Agriculture was initiated, in which CT patches across the state of Colorado (USA) were inoculated and tracked over subsequent years for changes in stem density. Here, we report our findings from 8 years (2014-2021) of monitoring effort. At most sites (N= 87), CT stem densities declined, from a mean (± SE) of 87.9 (± 6.5) stems to 44.7 (± 4.2). These declines however were spatially-autocorrelated, and likely attributable to local growing conditions, as mean annual daily maximum temperature and standard deviation of elevation, as well as climatic conditions around the times of both treatment and monitoring, were found to be important predictors of CT decline. Further, we observed that the amount of inoculum deployed, timing since last release, and method in which it was spread locally at a site were also associated with the magnitude of CT stem decline. These results are indicative of the value ofP. punctiformisas a CT biological control agent. The nameCirsium arvensedieback (CADB) is proposed herein to describe the agriculturally important decline in CT stem densities attributable to this previously un-named systemic disease.