bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pregnancy and Pregnancy Outcomes in a National Population Cohort of Patients Treated for Substance Use Disorders
Authors: Bretteville-Jensen Anne Line , Williams Jenny 
Published: December 2024

Objectives
The objectives of this study were to i) provide population-level prevalence rates of pregnancy, birth, elective termination, and miscarriage among females treated for SUDs and their demographic counterparts and ii) examine associations between SUD treatment and pregnancy and elective terminations.

Methods
Data were analyzed from a prospective registry-linkage study of all females (15–45 years) recorded as treated for SUDs in the Norwegian Patient Registry over a 2-year period (n = 6470) and a non-treated frequency-matched cohort of females from the general population (n = 6286). Pregnancy and pregnancy outcomes over a 4-year follow-up were retrieved from the Norwegian Patient Registry. Multivariable logistic regression models tested for associations of SUD treatment with pregnancy and with elective termination among pregnant females.

Results
Annual pregnancy and elective termination rates per 1000 females were significantly higher for the SUD cohort than the non-treated cohort (94.2 vs 71.3 for pregnancy, P < 0.001; 54.7 vs 17.8 for elective termination, P < 0.001), the annual birth rate was lower for the SUD cohort (25.3 vs 41.8, P < 0.001), and the rate of miscarriage did not differ across cohorts. Multivariable analysis showed that SUD treatment was associated with a significant increase in the odds of pregnancy (adjusted Odds Ratio 1.34, Confidence Interval [1.18–1.54]) and the odds of an elective termination, conditional on pregnancy (aOR 2.55, Confidence Interval [1.97–3.29]).

Conclusions
Females treated for SUDs had substantially higher odds of pregnancy and elective terminations than the non-treated cohort. To improve their reproductive health, targeted interventions such as free long-acting contraception and integration of family planning guidance into substance use treatment should be considered.
Increased Wound Prevalence in those Exposed to Xylazine and Fentanyl Compared to Those Exposed to Fentanyl: An Observational Study
Authors: Semancik Carolanne E. 
Published: December 2024

Objectives
The aim of this study is to determine the difference, if any, in prevalence of wounds in individuals who were exposed to xylazine and fentanyl compared to individuals who were exposed to fentanyl and not xylazine.

Methods
A large inpatient substance use disorder specialty hospital provided medical records over an 8-month period from July 2023 to February 2024. Individuals were admitted to an American Society of Addiction Medicine 3.7 level of care where a urine drug screen and skin assessment was conducted on admission. If the urine screen noted a presence of fentanyl, the sample was then tested for xylazine exposure. Patients were considered positive for wounds on admission to treatment if any wound was noted during the skin assessment during the admission process.

Results
A total of 282 medical records were identified. A chi square test of association was completed and revealed a statistically significant association between xylazine exposure and wounds (P = 0.002, odds ratio = 2.420, 95% confidence interval = 1.376–4.254).

Conclusions
This study provides early support for the previously theorized connection between xylazine exposure and wounds.
Comparison of 2 Methods for Measuring Chronotropic Response to Exercise: Heart Rate–Work Rate Slope Versus Percent Change in Heart Rate–Work Rate Slope—A Cross-Sectional Study
Authors: Scott Rachel , Taylor J. David , Allen Melissa , Fletcher James , Mathis Ruth Ann , McGee Margaret , Rainey Jacquie 
Published: December 2024

Purpose:
Chronotropic response to exercise (CRE) is an indicator of cardiovascular health and is evaluated using different methodologies. The purpose of this cross-sectional investigation was to compare 2 methods for measuring CRE: heart rate (HR)–work rate slope versus percent change in HR–work rate slope.

Methods:
Thirty-three participants met the inclusion criteria. Participants completed a two-stage graded exercise protocol. Heart rate and work rate data were recorded at rest (0 watts), the final minute of stage 1, and the final minute of stage 2. Heart rate–work rate slope was defined as the slope of HR increase relative to work rate increase. Percent change in HR–work rate slope was calculated as the percent change in HR–work rate slope between stage 1 and stage 2.

Results:
Spearman correlation coefficient indicated a significant, but relatively low, correlation between the 2 measurements (rs = 0.388, P = .01). The 95% limits of agreement (z-scores) between the 2 measurements were −2.29 to 2.29, suggesting considerable disagreement.

Conclusions:
The findings of this study indicated that HR–work rate slope and percent change in HR–work rate slope were not comparable. The low correlation and lack of agreement between the 2 methods could be explained by the possible measurement of different constructs (cardiorespiratory fitness vs coronary artery disease risk). Because of considerable disagreement, clinicians should not make decisions related to patient care using the 2 methodologies interchangeably. The findings of this investigation support the perspective that a standardized procedure for measuring CRE is warranted.
Early Retinal Detachments Following Open Globe Repair: Incidence and Risk Factors
Authors: Sheth Neil , Chang Arthur Y. , Bharadwaj Arthi , Wu David , Ivakhnitskaia Evguenia , Mieler William F. 
Published: December 2024

Purpose:
Risk factors for the development of rhegmatogenous retinal detachments (RRDs) in the early postoperative period following open globe repair (OGR) are not well understood. RRDs are often diagnosed late after OGIs, which can negatively impact visual prognosis. We assessed the incidence and risk factors that predict the development of this complication.

Methods:
We conducted a retrospective case-control study of all OGIs at a single ocular trauma center from January 2016 to September 2021 where at baseline the retina was attached. Cases were defined as postoperative RRDs that developed within 90 days of OGR.

Results:
Of 96 eyes included, 40 (41.7%) subsequently developed RRD. Univariate analysis revealed initial visual acuity (VA) of light perception (LP) or worse (OR 7.64; 95% CI, 3.03-19.22; p < .01), zone 3 injuries (OR 7.54; 95% CI, 2.64-21.54; p < .01), no view of the lens (OR 4.26; 95% CI, 1.77-10.26; p < .01), and the presence of injuries external to the globe (OR 5.33; 95% CI, 2.09-13.63; p < .01) to be associated with early RRD development. On multivariate analysis, presenting VA of LP (p < .001), the presence of external injuries (p = .001), and zone 3 injuries (p = .037) remained significant. Of the 40 patients with early RD, 34 (85%) remained attached following repair, with variable visual outcomes.

Conclusion:
Presenting VA of LP, zone 3 injuries, and external injuries to the globe confer increased risk of early postoperative RRD after OGR. The majority of RRDs can be successfully repaired.
Decreasing outer retina traumatism of ILM peeling in diabetic eyes with foveal sparing technique
Authors: Caporossi Tomaso , Crincoli Emanuele , Culiersi Carola , Scampoli Alessandra , Governatori Lorenzo , Bernardinelli Patrizio , Baldascino Antonio , Rizzo Stanislao 
Published: December 2024

Purpose:
To evaluate the effect on outer retina integrity of foveal sparing internal limiting membrane (ILM) peeling compared to standard ILM peeling on proliferative diabetic retinopathy (PDR) eyes affected by diabetic macular edema (DME) and epiretinal membrane (ERM).

Materials and methods:
Eyes diagnosed with PDR, DME and ERM eligible for vitrectomy were prospectively recruited and randomly assigned to either foveal sparing (FS) group and no foveal sparing (nFS) group. Ellipsoid zone (EZ) lesion size, EZ reflectivity and external limiting membrane (ELM) integrity and angular sign of Henle Fiber Layer Hyperreflectivity (ASHH) were assessed preoperatively and 1 year postoperatively.

Results:
Twelve (12) eyes and fifteen (15) eyes were included in FS and nFS group respectively. The two groups showed no differences in terms of EZ lesion size (p=0.549), EZ reflectivity (p=0.657) and ELM integrity (0.999) at preoperative examination. A significant increase in EZ lesion size was noted in nFS group between preoperative and postoperative examination (p=0.040) which was not present in FS group (p=0.862). Moreover, nFS group showed a higher prevalence of ASHH and a lower EZ reflectivity at follow up compared to FS group (respectively p=0.047 and p=0.041).

Conclusions:
Vitrectomy with FS ILM peeling may result in a better preservation of the Muller-photoreceptors complex in PDR complicated with DME and ERM.
TNF-α Suppression Attenuates Limbal Stem Cell Damage in Ocular Injury
Authors: Zhou Chengxin , Lei Fengyang , Mittermaier Mirja , Dana Reza , Dohlman Claes H. , Chodosh James , Paschalis Eleftherios I. 
Published: December 2024

Purpose:
Ocular chemical injuries often cause uveal inflammation, upregulation of TNF-α at the limbus, and subsequent limbal stem cell (LSC) damage. In this study, we investigate the protective role of TNF-α suppression in LSC survival.

Methods:
Corneal alkali injuries were performed using NaOH as previously described by our group. Anterior chamber pH elevation in the absence of corneal alkali exposure was achieved by cannulation. A CX3CR1+/EGFP::CCR2+/RFP bone marrow chimera was used to study the role of innate immune cells in LSC damage, which was assessed by TUNEL assay, ABCB5, cytokeratin 12 and 13 staining, flow cytometry, in situ hybridization, and qPCR. Corneal neovascularization and conjunctivalization were evaluated by light microscopy. Intraperitoneal injection of 6.25 mg/kg infliximab was administered after irrigation. A TNFR1/2 knockout mouse was used to confirm the findings by a second method.

Results:
Systemic administration of 6.25 mg/kg infliximab suppressed uveal inflammation after anterior chamber pH elevation or corneal alkali injury and led to reduction of TNF-α secreting CCR2+ and CX3CR1+ monocytes in the basal limbal tissue. In turn, this led to LSC survival (P < 0.01) and allowed reestablishment of K12+ epithelium (P < 0.05) on the injured cornea. Moreover, it led to less corneal neovascularization, conjunctivalization, and scarring, as compared with untreated animals. The protective effect of TNF-α suppression was confirmed in TNFR1/2 knockout mice.

Conclusions:
Prompt systemic administration of TNF-α inhibitor prevents LSC deficiency and facilitates corneal reepithelialization after alkali burn. TNF-α suppression may benefit the outcomes of other ocular injuries that cause LSC deficiency.
Radiation of pain: psychophysical evidence for a population coding mechanism in humans
Authors: Adamczyk Wacław M. , Ramu Vishwanath , Jackson Catherine , Schulze Geraldine , Goldschneider Kenneth R. , Kashikar-Zuck Susmita , King Christopher D. , Coghill Robert C. 
Published: December 2024

Abstract
The spread of pain across body locations remains poorly understood but may provide important insights into the encoding of sensory features of noxious stimuli by populations of neurons. In this psychophysical experiment, we hypothesized that more intense noxious stimuli would lead to spread of pain, but more intense light stimuli would not produce perceptual radiation. Fifty healthy volunteers (27 females, 23 males, ages 14-44 years) participated in this study wherein noxious stimuli (43, 45, 47, and 49°C) were applied to glabrous (hand) and hairy skin (forearm) skin with 5-second and 10-second durations. Also, visual stimuli displayed on the target bodily area were used as a control. Participants provided pain (and light) spatial extent ratings as well as pain (and light) intensity ratings. In the extent rating procedure, participants adjusted the extent of the square displayed on the screen with the extent of pain (or light) that they experienced. Pain extent ratings showed statistically significant radiation of pain indicated by 12.42× greater spatial spread of pain (pain extent) than the area of the stimulation with 49°C (P < 0.001), in contrast to visual ratings, which closely approximated the size of the stimulus (1.22×). Pain radiation was more pronounced in hairy than glabrous skin (P < 0.05) and was more pronounced with longer stimulus duration (P < 0.001). Pain intensity explained only 14% of the pain radiation variability. The relative independence of the pain radiation from pain intensity indicates that distinct components of population coding mechanisms may be involved in the spatial representation of pain vs intensity coding.
Decisional Control Preferences in Managing Intraductal Papillary Mucinous Neoplasms of the Pancreas
Authors: England Bryce , Habib Joseph R. , Sharma Acacia R. , Hewitt D. Brock , Bridges John F.P. , Javed Ammar A. , Wolfgang Christopher L. , Braithwaite R. Scott , Sacks Greg D. 
Published: December 2024

Abstract

Objectives
To evaluate patient preferences for decision-making role in the management of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas and to identify individual characteristics associated with those preferences.

Background
Management of IPMNs is rooted in uncertainty with current guidelines failing to incorporate patients’ preferences and values.

Methods
A representative sample of participants aged 40-70 were recruited to evaluate a clinical vignette where they were given the option to undergo surveillance or surgical resection of their IPMN. Their preferred role in the decision-making process for the vignette was evaluated using the Control Preference Scale. The relationship between control preference and variables including cancer anxiety, health literacy, and education level was analyzed.

Results
Of the 520 participants in the study, most preferred an active role (65%), followed by shared (29%), and passive roles (6%) in the decision-making process. Lower health literacy was significantly associated with a more passive control preference (p = 0.003). Non-active preference was significantly associated with Latino race compared to White race (odds ratio = 0.52, p = 0.009) in multivariate analysis. We found no significant association between control preference and education level or cancer anxiety.

Conclusions
Most patients preferred an active role in IPMN treatment decisions. Lower health literacy and Latino race were associated with a preference for non-active decision roles. Clinicians should strive to align patient involvement in IPMN treatment decisions with their patient’s preferred role.
Perceptions and Needs for a Technology-Based Dyadic Intervention on Symptom Management Among Patients With Colorectal Cancer and Their Caregivers: A Qualitative Study
Authors: Epari Amruta , Kim Kevin , Xiao Canhua , Porter Laura S. , Alese Olatunji B. , Northouse Laurel , Liu Darren , Graetz Ilana , Lin Yufen 
Published: December 2024

Background
Colorectal cancer (CRC) patients and their caregivers often experience multiple co-occurring symptoms (eg, fatigue, depression, anxiety, and sleep disturbance). There is a noticeable gap in research regarding symptom management for patient-caregiver dyads, particularly using technology-based tools.

Objective
This study aimed to describe the needs and perceptions of patient-caregiver dyads regarding a technology-based tool to manage their multiple symptoms.

Methods
This study utilized a qualitative descriptive design with purposive sampling. Semistructured interviews were conducted with CRC patients undergoing chemotherapy and their caregivers. Thematic analysis was performed to identify key themes.

Results
The study included 11 patients and 8 caregivers (8 patient-caregiver dyads and 3 patients without dyads). Four main themes emerged: (1) high symptom burden experienced by CRC patients and their caregivers; (2) symptom self-management strategies, including information seeking and self-education, family and social support, and coping strategies; (3) input and suggestions for technology use, covering aspects such as content, format, and specific technology features; and (4) concerns about barriers to healthcare access, including technological literacy, geographical distance, and time constraints.

Conclusions
Our findings provide novel insights into experiences, needs, and suggestions of CRC patient-caregiver dyads for managing multiple symptoms. Participants emphasized the importance of developing a tailored, technology-based tool that includes personalized, evidence-based content; accessible and intuitive design features; and interactive social support capabilities.

Implications for Practice
Leveraging these findings, we aim to develop a technology-based dyadic intervention tool that addresses the psychosocial needs of CRC patient-caregiver dyads. This approach can also enhance health equity by making care more accessible.
Kinetic patterns of single cell gene expression discriminate between the murine cellular responses to live attenuated and inactivated Yellow Fever vaccines
Authors: Chatterjee Budha , Boughter Christopher T. , Gorga Katrina , Ohta Yuko , Blair Carly , Hill Elizabeth M. , Fasana Zachary , Atuheirwe Maxine , Adebamowo Adedola , Ammar Farah , Ayithan Natarajan , Courneya JP , Kosik Ivan , Murugan Vel , Chen Wilbur H. , Pasetti Marcela F. , Meier-Schellersheim Martin , Singh Nevil J 
Published: December 2024

AbstractThe success of the live attenuated Yellow Fever vaccine (YF17D) that elicits immunity lasting over thirty years has made it a widely used model to understand the generation of durable protection. We compare the early single-cell level transcriptional response in mice to YF17D and an adjuvanted-inactivated, but less effective version (InYF). Within the first week, we identify 70 kinetic patterns in 45 cellular clusters, majority of which discriminate between the two formulations, some in a tissue and sex-specific manner. Intriguingly, differential transcripts fall into two categories, one whose association with YF17D or InYF is maintained even when decoupled from their cell-type of expression and the other where such cell-plus-gene pairing is critical to maintain differential marker status. We demonstrate applications of this resource, by identifying B cells with varied interferon and antigen responsiveness in relation to each vaccine. This high-resolution dataset is amenable to further biomarker discovery and hypothesis generation.
Quantifying Pathological Progression from Single-Cell Data
Authors: Khan Samin Rahman , Rahman M. Sohel , Samee Md. Abul Hassan 
Published: December 2024

AbstractThe surge in single-cell datasets and reference atlases has enabled the comparison of cell states across conditions, yet a gap persists in quantifying pathological shifts from healthy cell states. To address this gap, we introduce single-cell Pathological Shift Scoring (scPSS) which provides a statistical measure for how much a “query” cell from a diseased sample has been shifted away from a reference group of healthy cells. In scPSS, The distance of a query cell to itsk-th nearest reference cell is considered as its pathological shift score. Euclidean distances in the topnprincipal component space of the gene expressions are used to measure distances between cells. The p-value of a query pathological shift score belonging to the null distribution of intra-reference cell shift scores provides a statistical significance measure of the query cell being in the reference cell group. This makes our method both simple and statistically rigorous. Comparative evaluations against a state-of-the-art contrastive variational inference model, modified for shift scores, demonstrate our method’s accuracy and efficiency. Additionally, we have also shown that the aggregation of cell-level pathological scores from scPSS can be used to predict health conditions at the individual level.
MAAPE: A Modular Approach to Evolutionary Analysis of Protein Embeddings
Authors: Wang Xiaoyu , Zhang Heqian , Huang Jiaquan , Qin Zhiwei 
Published: December 2024

AbstractWe present MAPPE, a novel algorithm integrating a k-nearest neighbor (KNN) similarity network with co-occurrence matrix analysis to extract evolutionary insights from protein language model (PLM) embeddings. The KNN network captures diverse evolutionary relationships and events, while the co-occurrence matrix identifies directional evolutionary paths and potential signals of gene transfer. MAPPE overcomes the limitations of traditional sequence alignment methods in detecting structural homology and functional associations in low-similarity protein sequences. By employing sliding windows of varying sizes, it analyzes embeddings to uncover both local and global evolutionary signals encoded by PLMs. We have benchmarked MAAPE approach on two well-characterized protein family datasets: the Als regulatory system (AlsS/AlsR) and the Rad DNA repair protein families. In both cases, MAAPE successfully reconstructed evolutionary networks that align with established phylogenetic relationships. This approach offers a deeper understanding of evolutionary relationships and holds significant potential for applications in protein evolution research, functional prediction, and the rational design of novel proteins.
Neutrophils drive sexual dimorphism in experimental periodontitis
Authors: Martin Kelsey , Mianecki Maxwell , Maglaras Victoria , Sheikh Asfandyar , Saleh Muhammad H. A. , Decker Ann M. , Decker Joseph T. 
Published: December 2024

AbstractThe motivating premise of this study is to improve the treatment of periodontal disease by elucidating sex-specific mechanisms of periodontal disease progression. Men and women experience inflammation in fundamentally different ways and understanding the sex-specific biology leading to inflammation and bone loss in the periodontium will inevitably improve patient outcomes. We therefore examined clinical and immunological differences in the progression of periodontal disease using the ligature-induced periodontitis model. Periodontitis was induced in male and female C57BL/6j mice by tying a 5-0 silk suture around the left maxillary second molar. The ligature was left on for 7 or 21 days at which point maxillae were characterized for bone loss by μCT or immune infiltrate by flow cytometry. Neutrophil depletion was accomplished through systemic administration of a Ly6G antibody. Conditions were compared using two-way ANOVA with Tukey’s multiple comparison correction from n≥5 animals. Ligature-induced periodontitis led to alveolar bone loss at both 7 and 21 days in both female and male mice. Males and females had approximately the same amount of linear bone loss 7 days post-ligature placement, while male mice had significantly more linear bone loss by day 21. Male mice had significantly more immune cells in their maxillae 7 days post ligature placement compared to female mice. Both male and female mice showed a shift in immune populations towards neutrophils, with no significant difference between males and females. Neutrophil counts were significantly elevated in male mice on day 7 but not day 21, while female mice did not have any statistically significant changes in neutrophil counts. Neutrophil depletion using a Ly6G antibody limited bone loss in male but not female mice relative to isotype antibody-treated controls. Analysis of single-cell sequencing data from human patients with periodontitis showed differences in neutrophil phenotypes that were also observed in a mouse model of periodontitis. Together, these data suggest a mechanistic role for neutrophil inflammation in sexual dimorphism in periodontitis.