bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of proximity loggers to record proximity events among beef bulls
Authors: Camargo Vinicius A , Pajor Edmond A , Pearson Jennifer M
Published: January 2025

Social behavior in cattle can be measured by how often and for how long they interact with each other. This information can be used to guide management decisions, identify sick animals, or model the spread of diseases. However, visual observation of proximity events is time-demanding and challenging, especially for rangeland cattle spread over a large area. Although proximity loggers can potentially overcome these challenges remotely, it is unknown how accurate these devices are in recording proximity events among beef bulls. The objectives of this study were: 1) to determine the accuracy of Lotek LiteTrack LR collars with built-in proximity loggers to identify proximity events among bulls and 2) to determine the accuracy of Lotek LiteTrack LR collars to identify proximity events between bulls wearing collars and bulls wearing the Lotek V7E 154D ear tag proximity transmitter. Collars were deployed in 12 bulls in 2021 (Experiment 1), and 10 bulls (5 collars and 5 ear tags) in 2023 (Experiment 2). Videos were recorded of bull behavior in both years to compare proximity observed to proximity recorded by the loggers. Sensitivity (Se), specificity (Sp), precision (Pr), and accuracy (Ac) were calculated after computing true positives (TP), false positives (FP), false negatives (FN), and true negatives (TN). The interquartile range method was used to detect outliers. As collars work as both a transmitter and receiver in Exp. 1, reciprocity was assessed by the Concordance Correlation Coefficient (CCC) as an indirect measure of reliability. In Exp. 1, most observations were TN (95.13%), followed by FN (4.11%), TP (0.70%), and FP (0.06%). A high Sp (median = 1.0; 95% CI = 1.0 to 1.0), Pr (1.00; 0.72 to 1.0), and Ac (0.96; 0.95 to 0.97), and low Se (0.10; 0.06 to 0.21) were observed. A high reciprocity agreement (0.93; 0.89 to 0.96) was also observed. Likewise, in Exp. 2 most observations were TN (85.05%), followed by FN (9.94%), TP (4.36%), and FP (0.65%), while high Sp (0.99; 0.99 to 1.0), Pr (0.89; 0.80 to 0.92), and Ac (0.95; 0.81 to 0.95), and low Se (0.35; 0.24 to 0.61) was observed. The Pr of two loggers in Exp. 1 and Pr and Ac of one logger in Exp. 2 were considered outliers. In conclusion, both proximity loggers demonstrated high precision, specificity, and accuracy but low sensitivity in recording proximity among beef bulls. Therefore, these characteristics should be considered when deciding whether to use these devices or not.
Efficacy of Selected Fungicides for Control of Downy Mildew of Basil in Central Illinois, 2024
Authors: Babadoost Mohammad , Redhu Sahil , Pandey Krishna Raj
Published: January 2025

This study was conducted to evaluate the efficacy of selected fungicides for control of downy mildew of basil, caused by Peronospora belbahrii. Seven fungicides in 11 treatments were tested on ‘Plenty’ basil at the University of Illinois Vegetable Research Farm in Champaign, IL in 2024. Plants were infected by natural inoculum. Downy mildew on plants was first observed on 21 July. Six applications of fungicides, at 7-day interval, began on 22 July and ended on 26 August. Fungicides were applied with a backpack sprayer using 50 gal of water per acre. Severity of downy mildew symptoms in untreated plots was significantly (P = 0.05) higher than treated plots. Severity of the disease in plots treated with Revus plus ProPhyt, alternated with Quadris plus ProPhyt, and alternated with Ranman plus ProPhyt. was significantly (P = 0.05) lower than untreated plots and plots treated with other compounds. No phytotoxicity was observed in any of the plants.
The State of the Science on Mitigating Cancer Inequities Through Measuring and Addressing Social Determinants of Health
Authors: Lee Youran , Gonzalez-Guarda Rosa
Published: January 2025

Cancer is the second-leading cause of death in the US, with disparities in outcomes shaped by social determinants of health. The purpose of this paper is to explore the state of the science on cancer inequities, examine the role of multi-level of social determinants of health in these disparities, and offer guidance to nurse scientists on measuring and addressing social determinants of health in cancer care. Nurse scientists are encouraged to advance research, policy, and community engagement to enhance structural competency, improve support systems, and promote advocacy, ultimately improving cancer care and survivorship outcomes for disadvantaged populations.
Use of Electronic Health Records to Identify Factors Related to Skin Changes in Terminal Patients
Authors: Chan Chia-Jung , Chuang Yeu-Hui , Huang Tsai-Wei , Gautama Made Satya Nugraha
Published: January 2025

OBJECTIVE

To investigate the incidence of skin changes at life’s end (SCALE) among hospice patients and identify associated factors.

METHODS

The authors conducted a retrospective chart review of demographic data, medical history, Braden Scale assessment scores, Charlson Comorbidity Index, symptom records, and medical treatments of patients admitted to a local teaching hospital’s hospice unit between May 2019 and April 2021.

RESULTS

Most (79%) of the 300 hospice patients included in the study had cancer. Of the 181 patients who died, 49 (60.3%) had SCALE. Logistic regression analysis revealed that greater variations in Braden Scale scores from admission to predeath (odds ratio, 1.188; 95% CI, 1.014–1.392; P = .033), higher Eastern Cooperative Oncology Group grades (odds ratio, 1.965; 95% CI, 1.241–3.109; P = .004), and elevated Charlson Comorbidity Index scores (odds ratio, 1.514; 95% CI, 1.237–1.854; P < .001) significantly increased the likelihood of developing SCALE.

CONCLUSIONS

The findings suggest that the occurrence of SCALE may serve as a valuable clinical indicator for healthcare professionals to recognize that a patient is approaching the end of life. Consequently, the care approach should prioritize pain relief and promote comfort rather than wound healing in this patient population. These results provide evidence to support the integration of SCALE-related training programs for hospice care, which can increase healthcare professionals’ awareness and understanding of SCALE. Ultimately, the implementation of such training programs may lead to more appropriate care for hospice patients with SCALE, enhancing their quality of life at the end of life.
Spectrum of Dermatoses Affecting the Lower Leg and Foot in an Outpatient Clinic at a Tertiary Care Hospital
Authors: Passi Shanta , Uikey Deepika , Kumar Manoj
Published: January 2025

BACKGROUND

Infective and noninfective dermatoses of the lower leg and foot can be attributed to factors such as infections, blood stagnation, chemical contact, and abnormal mechanics. These factors make the lower leg and foot more susceptible to microbial infections, contact dermatitis, stasis eczema, ulcers, corns, and calluses.

OBJECTIVE

To identify the patterns of infective and noninfective dermatoses on the lower leg and foot.

METHODS

This study took place between September 2020 and August 2021 at an outpatient dermatology clinic. All patients with lower leg and foot dermatoses were included in the study, irrespective of age, sex, or occupation. Patients with generalized lesions all over the body were excluded.

RESULTS

Of the 42,527 patients who presented to the outpatient dermatology clinic during the study period, 424 patients (1%) had lower leg and foot dermatoses. The ratio of male to female patients was 2.3:1. Patients ranged in age from 4 to 76 (mean, 44.8 ± 15) years. A total of 152 patients had infective dermatoses, and 272 patients had noninfective dermatoses. Fungal infection (21.7%) was most common among patients with infective dermatoses, followed by bacterial infections (8.25%) and viral infections (7.07%). Lichen simplex chronicus (29.3%) and dermatoses due to venous stasis (19%) were most common among patients with noninfective dermatoses. The most commonly involved site was the shin, followed by the dorsum and sole of the foot.

CONCLUSIONS

The identification of high-risk patients is key in taking preventive measures to avoid complications.
The Effects of Hospital Delivery Volume and Travel Time on Perinatal Mortality and Delivery in Transit: Causal Inference with Triangulation
Authors: Asheim Andreas , Nilsen Sara Marie , Opdahl Signe , Risnes Kari , Balstad Magnussen Elisabeth , Carlsen Fredrik , Davies Neil Martin , Bjørngaard Johan Håkon
Published: January 2025

Background:

Hospital regionalization involves balancing hospital volume and travel time. We investigated how hospital volume and travel time affect perinatal mortality and the risk of delivery in transit using three different study designs.

Methods:

This nationwide cohort study used data from the Medical Birth Registry of Norway (1999-2016) and Statistics Norway. We compared estimates across three designs: (1) Observed confounder adjustment: Comparing women giving birth at hospitals of different sizes and travel times (1,066,332 births), (2) Sibling comparison: Comparing women who moved between hospital catchment areas between births (203,464 births), (3) Neighbor comparison: comparing women living in neighboring municipalities, but in different hospital catchment areas (460,776 births).

Results:

The study population included 5080 (0.48%) perinatal deaths and 7063 deliveries in transit (0.66%). For hospitals with 2000 compared with 500 births/year, observed confounder adjustment showed 1.81 times higher perinatal mortality (95% confidence interval [CI] 1.21-2.73). However, sibling and neighbor comparisons showed a factor 0.64 (95% CI 0.43-0.97) and 0.61% (95% CI 0.43-0.88) lower perinatal mortality, respectively. Increased travel time was strongly associated with higher perinatal mortality using observed confounder adjustment, but this was not supported by the other designs. Longer travel time was consistently linked to an increased risk of delivery in transit.

Conclusions:

Perinatal mortality was higher in high-volume hospitals when adjusting for observed confounders. However, triangulating inferences from the other designs suggested the opposite, estimating that observed confounder control was insufficient. This supports the idea that access to higher-volume hospitals could improve perinatal outcomes at the population level.
Interpretation of WFAS standard: general requirements for the risk control in the safe use of acupuncture
Authors: Luo Zhenshan , Wang Jingjing , Cui Shou , Liu Yaping , Ma Wenqian , Hu Jing , Chen Zhongjie , Wu Zhongchao
Published: January 2025

The international standard “General Requirements for the Risk Control in the Safe Use of Acupuncture” drafted by the Institute of Acupuncture and Moxibustion of the China Academy of Chinese Medical Sciences has been officially released by the World Federation of Acupuncture-Moxibustion Societies (WFAS). As the first general international standard in the field of acupuncture safety standards, in order to avoid the repetition of common problems, this standard specifies the basic requirements for the safe use of acupuncture, defines terms with common characteristics that are easily confused in the field of acupuncture safety, clarifies the scope and level of acupuncture risks, sorts out the sources of acupuncture risks, and formulates control processes and control measures for acupuncture risks, and lays the foundation for the establishment of subsequent related standards for specific needles. In order to help the developers of standards related to the safe use of acupuncture needles to better understand and apply this standard, this paper provides an in-depth interpretation of the development process and content of this standard. At the same time, it analyses the terminology definition process of this standard, the current research status of acupuncture risk and the sources of different types of acupuncture risk and corresponding control measures. This can provide a professional reference for the developers of subsequent related standards for specific needles and help promote the safe use of acupuncture techniques worldwide.
Status quo, problem and prospect for TCM international terminology standards
Authors: Song Meng , Fei Ni , Jiamei Li , Xinnuo Li , Keda Li
Published: January 2025

With the continuous development of standardization and internationalization of traditional Chinese medicine (TCM), the necessity and importance of TCM international standard composition is becoming more and more important. As the basis and premise of TCM internationalization, TCM international terminology standard is the key to bolster the international development of TCM and the dissemination of TCM culture. After thousands of years of development, traditional Chinese medicine has formed a unique set of terms with rich content, which need to be standardized to facilitate modern international use. The author introduced 4 TCM international standardization organizations and analized the necessity of composing international standards of TCM terminology. Then, the author found several problems in the field and put forward corresponding suggestions based on the collection and comparative study of the existing TCM international terminology standards. This paper was written to provide reference for TCM standardization learner, enthusiast and stakeholder by showcasing the current status and problems of TCM international terminology standards, spur the global spread of TCM and broaden the influence of Chinese culture.
Corticosteroids in severe alcohol-associated hepatitis? Not so fast: A systematic review of randomized controlled trials
Authors: Shi Michael A. , Pungwe Prisca , Comer Lauren LM. , Balakrishnan Maya , Lee Tzu-Hao , Cholankeril George , Patidar Kavish R. , Flores Avegail G. , Shah Vijay H. , Bataller Ramon , Asrani Sumeet K. , Arab Juan P. , Kanwal Fasiha , Hernaez Ruben
Published: January 2025

Background:

Severe alcohol-associated hepatitis (AH) is rising in incidence with a high mortality burden. While corticosteroids are recommended for eligible patients with severe AH, no guidance exists for the timing of steroid initiation, tapering regimens, and surveillance of adverse events.

Objective:

We aim to systematically review these variables and provide evidence-based recommendations for the inpatient and outpatient management of severe AH.

Design:

We performed a literature search from inception to 5/30/2024 to include clinical trials published in full form and assessed the quality of evidence using the Cochrane Risk of Bias tool. Data were collected on the timing of initiation, rate, and complications following steroid therapy, and taper regimens in the setting of severe AH.

Results:

Of 28 studies that fulfilled our inclusion criteria, median time from admission to steroid initiation was 6.5 days. The most common steroid dosing regimen was prednisolone 40 mg daily for 28 days. Twenty-five studies containing 3,196 subjects reported adverse events, with exactly 50% in the steroid arm and the other half in the comparison arm. Infections, gastrointestinal bleeds, and renal impairment were the most frequently reported adverse events. Most infections occurred within the first month of the study. A two-week steroid taper was the most frequently reported regimen.

Conclusion:

We recommend taking up to a week to systematically and thoroughly evaluate patients before initiating steroids, and vigilant monitoring in the first month of treatment. We also recommend the lowest possible steroid exposure with a two-week steroid taper and close outpatient follow-up.
Neurobehavioral Symptoms Partially Mediate the Effects of Depression and PTSD on Participation for Veterans With Mild Traumatic Brain Injury: A Cross-Sectional Study
Authors: Wyrwa Jordan M. , Brenner Lisa A. , Yan Xiang-Dong , Schneider Alexandra L. , Burke Lindsay , King Samuel E. , Forster Jeri E. , Kinney Adam R.
Published: January 2025

Objective:

To examine whether neurobehavioral symptoms mediate the relationship between comorbid mental health conditions (major depressive disorder [MDD] and/or posttraumatic stress disorder [PTSD]) and participation restriction among Veterans with mild traumatic brain injury (mTBI).

Setting:

Veterans Health Administration (VHA).

Participants:

National sample of Veterans with mTBI who received VHA outpatient care between 2012 and 2020.

Design:

Secondary data analysis of VHA clinical data. We specified a latent variable path model to estimate relationships between: (1) comorbid mental health conditions and 3 latent indicators of neurobehavioral symptoms (vestibular-sensory; mood-behavioral; cognitive); (2) latent indicators of neurobehavioral symptoms and 2 latent indicators of participation restriction (social and community participation; productivity); and (3) comorbid mental health conditions and participation restriction.

Main Measures:

International Classification of Diseases codes, Neurobehavioral Symptom Inventory, and Mayo-Portland Adaptability Inventory Participation Index to measure mental health conditions, neurobehavioral symptoms, and participation restrictions, respectively.

Results:

Indirect effect estimates indicated that comorbid MDD and/or PTSD was associated with greater social and community participation restrictions, as mediated by mood-behavioral (β = .22-.33; 99% CI 0.18-0.4; small to medium effect) and cognitive symptoms (β = .08-.13; 99% CI 0.05-0.18; small effect), and with greater productivity restrictions, as mediated by vestibular-sensory (β = .06-.11; 99% CI 0.04-0.15; small effect) and cognitive symptoms (β = .08-.13; 99% CI 0.05-0.18; small effect). Direct effect estimates indicated that comorbid MDD and/or PTSD was associated with greater challenges with both social and community participation (β = .19-.40; 99% CI 0.12-0.49; small to medium effect) and productivity (β = .08-.44; 99% CI −0.02 to 0.55; small to medium effect).

Conclusion:

Neurobehavioral symptoms partially mediated the impact of MDD and/or PTSD on participation restrictions among Veterans with mTBI. These findings advance the understanding of explanatory mechanisms underlying participation challenges among Veterans with comorbid mTBI and mental health challenges, thereby informing the development of tailored intervention strategies.
Assessing Traumatic Brain Injury in Refugees: Feasibility, Usability, and Prevalence Insights From a US-Based Clinical Sample
Authors: Sherman Rosa Sofia , Nadal Rodrigo , Saadi Altaf
Published: January 2025

Objective:

This study assessed (1) the feasibility and usability of traumatic brain injury (TBI) assessment using the Ohio State University TBI Identification Method (OSU-TBI-ID) in a sample of English and Spanish-speaking refugees and asylum seekers (hereafter refugees), and (2) the prevalence and characteristics of TBI in this population.

Setting and Participants:

Refugees seeking care from Massachusetts General Hospital (MGH) Asylum Clinic, the MGH Chelsea HealthCare Center, and other asylum programs in the Greater Boston Area.

Design and Main Measures:

Bilingual clinical research coordinators screened 158 English and Spanish-speaking refugees using the OSU-TBI-ID. A “positive” screen for TBI was made if a participant reported loss of consciousness (LOC) or being dazed or confused following a head injury, with determinations of mild, moderate, and severe TBI based on established metrics of TBI severity using duration of LOC. We conducted descriptive statistics of the sample demographics and screening outcomes, including group comparisons between those with and without TBI and associated demographic characteristics.

Results:

The mean age was 36.8 years (SD: 9.1), with participants predominantly from Latin America and the Caribbean (51%), followed by Sub-Saharan Africa (35%). Less than half (43%) identified as men. The majority (59%) screened positive for having experienced at least 1 TBI in their lifetime. Among those with a TBI history, nearly three-quarters (73%) had a mild TBI, and about a third (38%) had sustained a moderate-to-severe TBI. A majority (56%) had more than 1 TBI and about 40% had sustained a childhood TBI. The most common mechanisms of injury were interpersonal assault (55%) and blunt trauma by an object (46%). There were no significant statistical differences in demographics and TBI characteristics.

Conclusion:

Our findings demonstrate the feasibility and usability of the OSU-TBI-ID in a sample of refugees. We call for greater and improved detection of TBI among refugees to ensure they receive the optimal care they need.
Removal of band keratopathy involving a LASIK flap with Amoils brush and ethylenediaminetetraacetic acid chelation
Authors: Khambati Alisha , Shean-Young Lee Patrick , Khambati Shabbir , McDermott Mark
Published: January 2025

Introduction:

To report a new method for ethylenediaminetetraacetic acid (EDTA) chelation with the use of an Amoils brush to debride calcium band keratopathy involving a laser-assisted in situ keratomileusis (LASIK) flap.

Patient and Clinical Findings:

A 77-year-old man with a history of bilateral LASIK presented with visually significant band keratopathy involving the flap.

Diagnosis, Intervention, and Outcomes:

We report the successful removal of the band keratopathy using EDTA chelation and debridement with an Amoils brush to prevent flap dislodgment. 1 month postoperatively, the patient experienced an improvement in corrected distance visual acuity with resolution of the band keratopathy.

Conclusions:

Debridement using an Amoils brush, in conjunction with EDTA chelation, is an effective and safe treatment for visually significant band keratopathy involving a LASIK flap.
Collaborative Core Curriculum Initiative
Authors: Palmer Brittany , Valido Laura , Tucker Ahquilah , Tanda Rika , Opperman Cathleen
Published: January 2025

Multiple intensive care units shared core knowledge, skills, and competencies but provided separate orientations leading to inconsistencies in practice, variations in onboarding, and poor use of resources. In this article, the methods of aligning the nursing professional development practitioner roles to the process of standardizing a core curriculum are described. This collaborative initiative sought to increase the knowledge and comfort of the new nurses while setting precedence for collaboration with educational endeavors between the units.
SMARCB1-deficient Sinonasal Carcinoma
Authors: Mittal Neha , Nagar Saurabh , Patil Asawari , Rane Swapnil Ulhas , Nisarga Palgun , Rabade Katha , Janu Amit , Nair Deepa , Thiagarajan Shiva , Laskar Sarbani Ghosh , Prabhash Kumar , Bal Munita
Published: January 2025

SMARCB1-deficient sinonasal carcinoma (SDSC) is a recently recognized rare malignancy. Despite growing awareness, SDSC remains susceptible to misdiagnosis owing to its rarity and overlapping features with diverse mimics. A retrospective review of the clinical and pathologic features of 32 SDSC including 4 SMARCB-1 deficient adenocarcinoma (SDAC) cases was performed. The patients were aged 19 to 76 years with a male predominance. Most tumors arose in the naso-ethmoid (75%), and advanced stage (93.6%), with frequent multi-sinus (90.5%) involvement. Histologically, tumors exhibited diverse morphologies, including basaloid (50%), rhabdoid (25%), and undifferentiated (12.5%) types. SDAC cases showed glandular differentiation with intraluminal and stromal mucin. Empty vacuoles (62.5%), pagetoid spread (31.3%), eosinophilic-granular bodies (18.8%), hyaline globules (15.2%), and florid glomeruloid neovascularization (15.6%) were additional findings. Yolk sac-like areas were encountered in 18.6%. Immunohistochemically, tumors were defined by a complete loss of SMARCB1 (100%); a variable reactivity for p40 (65.6%), synaptophysin (13.6%), glypican3 (6.1%), and CD34 (6.1%) was present. Notably, >90% of our patients had different initial diagnoses before referral. Lymph node metastasis, locoregional recurrence, and distant metastasis were seen in 23.3%, 24.1%, and 27.6% patients, respectively; 37.9% died of disease. In conclusion, SDSCs are rare and aggressive sinonasal malignancies that display a wide histologic spectrum including glandular differentiation. This study expands on the morphologic spectrum of SDSC by analyzing a large cohort of 32 cases, adding comprehensive clinical, histopathologic, and immunohistochemical data, and highlighting features to improve diagnostic accuracy. The emergence of targeted therapies, such as EZH2 inhibitors, further underscores the importance of accurate diagnosis.
Antiretroviral therapy in people with HIV and end-stage kidney disease
Authors: Spencer Matthew , Pieri Christopher , Hamzah Lisa , Popoola Joyce , Shah Sapna , Jones Rachael , Levy Jeremy , Murphy Maurice , Booth John , Post Frank A.
Published: January 2025

Objective:

To summarize antiretroviral therapy (ART) use in the setting of end-stage kidney disease (ESKD).

Design:

Cross-sectional analysis.

Methods:

Descriptive analysis of ART regimens and dose of nucleoside/nucleotide reverse-transcriptase inhibitors (NRTI) in people with HIV and ESKD (dialysis, kidney transplantation, or estimated glomerular filtration rate (eGFR) <15 mL/min/1.73m2) receiving HIV and renal care at five London centres. Exposures of interest were use of dual/unboosted ART regimens and higher than recommended doses of renally-cleared NRTI.

Results:

A total of 157 participants were included (median age 55 years, 66% male, 84% black ethnicity, median CD4 cell count 382 cells/mm3, 99% HIV RNA <200 copies/mL). Fifty-eight (37%) were on dual/unboosted ART regimens, mainly dolutegravir/lamivudine. Participants on dual/unboosted ART had similar rates of HIV suppression as those on triple-ART. Two participants currently virologically controlled on triple-ART had previously failed to suppress on dual/unboosted ART (dolutegravir/rilpivirine and dolutegravir/lamivudine [50 mg]). Lamivudine doses were higher than recommended in 75 (77%) and lower than recommended in 8 (8%) participants. Full dose lamivudine (300 mg daily) was used by 24 (32%) participants with eGFR <30 mL/min/1.73m2. None of those currently on reduced-dose lamivudine had required dose reductions for previous toxicity concerns.

Conclusions:

Dual/unboosted ART regimens such as dolutegravir/lamivudine provide robust viral efficacy in the setting of ESKD, and higher than recommended, including full-dose, lamivudine was well tolerated. The dolutegravir/lamivudine (300 mg) fixed-dose combination provides a single-tablet regimen for use across the eGFR spectrum, avoids under-exposure to lamivudine, and merits further evaluation in this population.
Assessing Readability of Patient Education Materials on Adult-Acquired Buried Penis
Authors: Thornton Sarah M. , Orgun Doruk , Bay Caroline C. , Seitz Allison J. , Poore Samuel O.
Published: January 2025

Introduction

Adult-acquired buried penis (AABP) is an increasingly prevalent condition characterized by the penis “buried” in prepubic/suprapubic tissue. AABP affects urinary and sexual function, hygiene, and psychosocial well-being. Because many affected individuals are unfamiliar with the condition or hesitant to seek medical help, accessible, high-quality patient education materials (PEMs) are necessary. The American Medical Association recommends that PEMs be written at or below a 6th-grade reading level. This study aimed to assess the readability of the most easily accessible AABP PEMs.

Methods

After disabling user account information, the top 10 results for “buried penis treatment” from 3 search engines were collected. Academic journal articles, advertisements, and pediatric PEMs were excluded. Plain texts without graphics and extraneous information were copied to the Readability Test Tool (WebFX, Harrisburg, PA) to generate readability scores. Descriptive statistics were used to analyze the data.

Results

The top 10 results for each search engine, excluding duplicates, resulted in 12 unique articles. Of 5 readability tests used by the Readability Test Tool, the mean grade level necessary to comprehend resource content was 12.3, or about a 12th-grade level. The mean age estimated for understanding was 17.7, or an age range of 17–18 years old. Complex words comprised on average, 16.6% of a resource's material.

Conclusions

This study emphasizes the inadequate readability of current PEMs for AABP. The readability for most accessible materials exceeds the recommended reading level of at or below 6th grade. Providers should aim to publish easily comprehensible online PEMs to promote patient awareness and comprehension.
Protein profile of the Escherichia coli strain, BW25113, exposed to two novel iron-halide compounds: Fe(Hampy)2Cl4 and Fe(Hampy)2Br4
Authors: Abedin Nusrat , Wagner Sarah , Khalkar Yukta Sanjay , Johnson Zulekha , Egbowon Biola F. , Hargreaves Alan J. , Fitzpatrick Anthony J. , Miles Amanda K. , Dafhnis-Calas Felix
Published: January 2025

Graphical abstract

Characterizing the proteomic profile of the Escherichia coli strain, BW2513, exposed to two novel iron-halide complexes: iron tetrachloride and iron tetrabromide.
Biosynthetic plasticity enables CD8+ T cell functional resilience under nutrient stress
Authors: Scaglione Michael , Knight Montana , Trihemasava Krittin , Rome Kelly , Archambault Anne-Sophie , Oh Juhee , Tanaka Erin , Hall Elise , Van Le Tran Ngoc , Lines Caleb L. , Goldspiel Brian , Fazelinia Hossein , Queriault Clemence , Turner Lucien , Parnaik Tanay , Xu Jimmy , Spruce Lynn A. , Bartman Caroline , Mesaros Clementina , Klein Geltink Ramon I. , Conn Crystal S. , Bailis Will
Published: January 2025

Summary / Abstract

To maintain lineage-specific functions, cells must acquire and allocate nutrients across diverse cellular processes, even in metabolically-dysregulated environments. The mechanisms allowing CD8+ T cells to maintain immune function in perturbed environments are poorly understood. We find that CD8+ T cells adapt to nutrient stresses over time, reconfiguring gene-regulatory and metabolic networks to license functional recovery. Under acute stress, T cells reorient translational programming, limiting nutrient demand while prioritizing stress-sensitive metabolic and transcriptional responses. Within these responses, the transcription factors ATF4 and CEBPG jointly establish an adaptive metabolic program, promoting amino acid synthesis and uptake while maintaining mitochondrial anaplerosis. Despite diminished energetic capacity under environmental stress, this program prevents failure of central carbon metabolism, mitigating stress amplification and cellular dysfunction to potentiate anti-tumor immunity. Altogether, we demonstrate that biosynthetic plasticity via translational and metabolic reprioritization confers functional resilience to immune cells in unfavorable environments, offering novel strategies to enhance immunotherapies.
Acoustic pH sensor for dynamic ultrasound imaging of cellular acidification
Authors: Terwiel Dion , Park Byung Min , Heiles Baptiste , Waasdorp Rick , Muñoz-Ibarra Eleonora , Ara Tarannum , Gazzola Valeria , Maresca David
Published: January 2025

Genetically encoded pH sensors based on fluorescent proteins enable dynamic optical imaging of cellular processes such as endocytosis and exocytosis. To date, light scattering in thick tissue as well as photobleaching of fluorescent proteins prevent deep cellular imaging over sustained periods of time. To visualize intracellular pH variations across opaque organs, we introduce a genetically encoded acoustic pH sensor dubbed ‘pHonon’. We modified the outer gas vesicle protein (GvpC) of echogenic protein nanostructures via histidine point mutations. At low pH, engineered gas vesicles exhibit an increased shell stiffness which switched their acoustic response from nonlinear to linear. By combining pHonons with nonlinear ultrasound imaging, we captured dynamic deep tissue images of lysosomal acidification by macrophages in murine liver. The combination of pHonon with nonlinear ultrasound creates the possibility for basic studies of endo- and exocytic activity in deep tissue of living opaque organisms.
Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq
Authors: Bristy Nishat Anjum , Schwartz Russell
Published: January 2025

Motivation

Reconstructing clonal lineage trees (“tumor phylogenetics”) has become a core tool of cancer genomics. Earlier approaches based on bulk DNA sequencing (DNA-seq) have largely given way to single-cell DNA-seq (scDNA-seq), which offers far greater resolution for clonal substructure. Available data has lagged behind computational theory, though. While single-cell RNA-seq (scRNA-seq) has become widely available, scDNA-seq is still sufficiently costly and technically challenging to preclude routine use on large cohorts. This forces difficult tradeoffs between the limited genome coverage of scRNA-seq, limited availability of scDNA-seq, and limited clonal resolution of bulk DNA-seq. These limitations are especially problematic for studying structural variations and focal copy number variations that are crucial to cancer progression but difficult to observe in RNA-seq.

Results

We develop a method, TUSV-int, combining advantages of these various genomic technologies by integrating bulk DNA-seq and scRNA-seq data into a single deconvolution and phylogenetic inference computation while allowing for single nucleotide variant (SNV), copy number alteration (CNA) and structural variant (SV) data. We accomplish this by using integer linear programming (ILP) to deconvolve heterogeneous variant types and resolve them into a clonal lineage tree. We demonstrate improved deconvolution performance over comparative methods lacking scRNA-seq data or using more limited variant types. We further demonstrate the power of the method to better resolve clonal structure and mutational histories through application to a previously published DNA-seq/scRNA-seq breast cancer data set.

Availability

The source code for TUSV-int is available athttps://github.com/CMUSchwartzLab/TUSV-INT.git
Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms
Authors: Johnson Nathan R. , Gonzalez-Toro Fabian , Bernal Gomez Barbara
Published: January 2025

Small RNAs (sRNAs) are important regulatory elements in eukaryotic organisms and comprise the functional elements of RNAi. Numerous classes of sRNAs have been annotated, however they vary greatly in their ease of annotation and compatibility with most annotators. Significant challenges exist for the annotation process, including variation in sRNA library quality, alignment depth, and poorly defined loci, collectively making this process difficult. Additionally, few annotators are fully agnostic to sRNA classes and may struggle identifying loci in less explored organisms (exceptional organisms, fungi). To address these problems, we present an integrated sRNA annotation suite, YASMA, which is specifically suited to finding reliable thresholds for locus annotation which balance sensitivity with specificity. By comparing YASMA with other annotators, we show that pipelines based on coverage-normalization methods have great advantages in balancing many metrics to produce a more reproducible annotation. We also demonstrate that YASMA produces more contiguous and representative loci, through the aggressive merging of similar adjacent expressed regions. Finally, we also show that the tool produces much more descriptive locus dimensions, a major advantage in species where sRNAs may be distinct or unique. Overall, we demonstrate substantial improvements in annotation accuracy, reproducibility, and description, particularly in non-model organisms and less-explored clades.
Resident Tissue Macrophages Govern Intraocular Pressure Homeostasis
Authors: Liu Katy C. , Grimsrud Aleksander O. , Suarez Maria Fernanda , Schuman Darren , De Ieso Michael L. , Kuhn Megan , Kelly Ruth A. , Mathew Rose , Kalnitsky Joan , Mack Matthias , Ginhoux Florent , Bupp-Chickering Violet , Balasubramanian Revathi , John Simon W. M. , Stamer W. Daniel , Saban Daniel R.
Published: January 2025

Intraocular pressure is tightly regulated by the conventional outflow tissues, preventing ocular hypertension that leads to neurodegeneration of the optic nerve, or glaucoma. Although macrophages reside throughout the conventional outflow tract, their role in regulating intraocular pressure remains unknown. Using macrophage lineage tracing approaches, we uncovered a dual macrophage ontogeny with distinct spatial organizations across the mouse lifespan. Long-lived, resident tissue macrophages concentrated in the trabecular meshwork and Schlemm’s canal, whereas short-lived monocyte-derived macrophages, instead, were abundant around distal vessels. Specific depletion of resident tissue macrophages triggered elevated intraocular pressure and outflow resistance, linked to aberrant extracellular matrix turnover in the resistance-generating tissues of the trabecular meshwork. This dysregulated physiology and tissue remodeling were not observed when we depleted monocyte-derived macrophages. Results show ontogeny and tissue-specific macrophage function within the outflow tract, uncovering the integral homeostatic role of resident tissue macrophages in resistance-generating tissues whose dysfunction is responsible for glaucoma.
mzLearn, a data-driven LC/MS signal detection algorithm, enables pre-trained generative models for untargeted metabolomics
Authors: Pirhaji Leila , Eaton Jonah , Jeewajee Adarsh K. , Zhang Min , Morris Matthew , Karasarides Maria
Published: January 2025

Metabolite alterations are linked to diseases, yet large-scale untargeted metabolomics remains constrained by challenges in signal detection and integration of diverse datasets for developing pre-trained metabolic models. Here, we introduce mzLearn, a data-driven algorithm for untargeted metabolomic signal detection that requires no input parameters or metabolomics expertise. mzLearn outperforms existing methods in both signal quantity and quality, effectively correcting instrument drifts across large cohorts without experimental QC samples. mzLearn detected robust metabolite signals from 20,548 blood samples from diverse studies, enabling the development of first-in-class pre-trained generative models for untargeted metabolomics. Learned metabolite representations reflected demographic data and when fine-tuned on unseen renal cell carcinoma data, improved downstream clinical and survival tasks. Metabolite representation further facilitated joint and adversarial learning for prognostic and predictive patient stratification, outperforming clinical-grade risk criteria in survival prediction. mzLearn democratizes untargeted metabolomics data and paves the way for developing foundation models for untargeted metabolomics.
MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework
Authors: Ziemski Michal , Gehret Liz , Simard Anthony , Castro Dau Santiago , Risch Vinzent , Grabocka Doriela , Matzoros Christos , Wood Colin , Momo Cabrera Paula , Hernández-Velázquez Rodrigo , Herman Chloe , Evans Keegan , Robeson Michael S. , Bolyen Evan , Caporaso J. Gregory , Bokulich Nicholas A.
Published: January 2025

Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.
Contrasting genetic differentiation of urban and rural populations of two grassland lepidopterans across Europe
Authors: Kivelä Sami M. , Lee Kyung Min , Adamidis George C. , Bonelli Simona , Hendrickx Frederik , Huemer Peter , Kadlec Tomáš , Kankaanpää Tuomas , Minard Guillaume , Nielsen Matthew E. , Piano Elena , Tammaru Toomas , Zografou Konstantina , Merckx Thomas
Published: January 2025

Urbanisation is transforming environments globally. The altered abiotic conditions and biotic interactions in urban habitats inflict divergent selection pressures on urban versus rural populations. Genetic drift may simultaneously be significant in typically small urban populations. A key question in urban evolution is whether urban genotypes have a single or multiple origins, but such assessments remain rare, precluding generalizations. We expect similar patterns in species that share ecological traits, but such replicates are missing. To address whether urban and rural populations are genetically differentiated and what is the origin of urban genotypes, we conducted an extensive population genomic ddRADseq analysis of two non-model grassland lepidopterans,Coenonympha pamphilusandChiasmia clathrata, across Europe. Although the species share ecological traits, their genetic population structures were strikingly different:C. pamphilushad strong population differentiation, while this was almost absent inC. clathrata, which instead showed signs of recent strong population expansion. Although this signature of population expansion complicates inferences, it is nonetheless plausible that the urban populations of both species have multiple origins. This study highlights that urban evolution research needs to integrate phylogeography, because population history affects urban evolutionary dynamics.
A-TWAS: An aggregated transcriptome-wide association study model incorporating multiple Bayesian priors
Authors: Liang Yilan , Wang Han , Zhang Yan Dora
Published: January 2025

Motivation

Transcriptome-wide association study (TWAS) is a significant methodology utilized for identifying associations between genes and diseases by integrating transcriptome and genome-wide association studies (GWAS) data. The approach has been successful in pinpointing risk genes for various diseases, including Alzheimer’s disease, schizophrenia, and different types of cancers. TWAS typically involves two key steps: imputation and association analysis. In the imputation step, the original PrediXcan employs the elastic-net model, while subsequent research endeavors have delved into more intricate models such as FUSION and TIGAR. Despite these advancements, the existing individual methods may not capture the intricate genotype-expression relationships in a comprehensive way. Given the complexity of genetic contributions of genotypes to gene expression, sophisticated modeling techniques are imperative. In response to this, we have introduced Aggregated-TWAS (A-TWAS), a comprehensive tool that amalgamates multiple imputation models to accommodate diverse genetic architectures. A-TWAS utilizes several continuous shrinkage priors, including Laplace, Horseshoe, and Horseshoe+, to ensure precise imputation results while incorporating the benefits of Bayesian variable selection methods. In the association phase of TWAS, we employ the aggregated Cauchy association test (ACAT) to obtain an omnibusp-value.

Result

We demonstrate the effectiveness of A-TWAS through comprehensive simulations and real data analyses. Simulation studies highlight that A-TWAS produces substantial improvements in predictiveR2and statistical power, while maintaining the type error I at a low level. Furthermore, TWASs are conducted on schizophrenia and obsessive-compulsive symptoms datasets. In comparison to standard methods, the Bayesian imputation model demonstrates superior accuracy, and A-TWAS, by integrating multiple Bayesian priors, identifies a notably greater number of disease-relevant genes.

Availability and Implementation

The source code of A-TWAS is available athttps://github.com/Yilan-Liang/A-TWAS.
Ultraviolet-Complete Local Field Theory of Persistent Symmetry Breaking in
2+1
Dimensions
Authors: Hawashin Bilal , Rong Junchen , Scherer Michael M.
Published: January 2025

Spontaneous symmetry breaking can persist at all temperatures in certain biconical O(N)×Z2 vector models when the underlying field theories are ultraviolet complete. So far, the existence of such theories has been established in fractional dimensions for local but nonunitary models or in 2+1 dimensions but for nonlocal models. Here, we study local models at zero and finite temperature directly in 2+1 dimensions employing functional methods. At zero temperature, we establish that our approach describes the quantum critical behavior with good accuracy for all N≥2. We then exhibit the mechanism of discrete symmetry breaking from O(N)×Z2→O(N) for increasing temperature near the biconical critical point when N is finite but large. We calculate the corresponding finite-temperature phase diagram and further show that the Hohenberg-Mermin-Wagner theorem is fully respected within this approach, i.e., symmetry breaking only occurs in the Z2 sector. Finally, we determine the critical N above which this phenomenon can be observed to be Nc≈15.

Published by the American Physical Society
2025
Motivation, demographics, and engagement during COVID-19 in an astrobiology massive open online course
Authors: Grayson Skylar , Simon Molly N. , Buxner Sanlyn , Wenger Matthew , Impey Chris
Published: January 2025

Massive open online courses (MOOCs) experienced a resurgence in popularity due to the COVID-19 pandemic. In this work, we studied participants in an astrobiology MOOC offered on Coursera since April 2019. Using a modified version of the Science Motivation Questionnaire II, we examined the primary motivational factors of the participants, how those factors related to demographics and course performance, and how participants in our MOOC compared to those in a general astronomy MOOC as well as traditional undergraduate students. Participants in the astrobiology MOOC were more highly motivated when compared to the general astronomy MOOC across all five motivational factors we surveyed: intrinsic, career, grade, self-determination, and self-efficacy. Compared to the undergraduate population, astrobiology MOOC participants reported higher motivations in all the factors except for career and grade. We found that demographics had some impact on these results, with older participants reporting lower career and grade motivations and female participants having generally higher motivations compared to males. Despite this, male participants and those older than 40 were more likely to complete the course. As the astrobiology MOOC was initially offered prior to the COVID-19 pandemic, we also looked at the impact the pandemic had on these results. The demographics of participants changed significantly, with the percentage of participants under the age of 30 and the percentage of those identifying as full-time students doubling compared to prepandemic. The motivations of participants also changed, with participants showing more career and grade motivation since the pandemic. Interestingly, the increase in younger and more full-time student participants has continued even with the return of in-person learning. This suggests that the pandemic introduced MOOCs to a new population of learners who have continued to utilize them in the years since.

Published by the American Physical Society
2025