bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementing Screening for Neonatal Delirium in the Neonatal Intensive Care Unit: A Quality Improvement Initiative
Authors: Karmarkar Meghana , Speziale Mark , Jenkins Willough , Heath Danielle , Kang Jane , Suvak Julia , Grimm Peggy , Moyer Laurel
Published: October 2024

Introduction:

Delirium is not commonly diagnosed in neonatal intensive care units and can adversely impact patient outcomes in the ICU setting. Recognition of delirium in the NICU is a necessary first step to address the potential impact on neonatal outcomes.

Methods:

We conducted a quality improvement initiative implementing screening for neonatal delirium. We aimed to increase screening in NICU patients from 0% to 85% by March 2022. Interdisciplinary meetings were held with key stakeholders to develop a clinical algorithm. We used standardized tools for delirium screening. Our process measures included weekly nursing compliance with Richmond Agitation Sedation Scale/Cornell Assessment of Pediatric Delirium/ scoring documentation (Fig. 1) and patients referred to psychiatry. Outcome measures included the percentage of patients screened for delirium before discharge. We conducted Plan-Do-Study Act cycles to optimize the screening process in the electronic medical record (EMR). This included creating an order set, documentation flowsheets, and prompts in the EMR for patients.

Results:

After initial implementation, we achieved an average weekly screening compliance of 76% (Fig. 1). Inclusion criteria expansion resulted in a downward compliance shift to 59%. Subsequently, the addition of the EMR checklist resulted in a center-line shift to a sustained average weekly screening compliance of 77%. An average of 82% of all eligible NICU patients received delirium screening before discharge (Fig. 2).

Conclusions:

Using quality improvement methodology, there was increased screening and recognition of delirium in our NICU. Future research efforts could focus on assessing preventive measures and the impact of neonatal delirium on patient outcomes.
Intelligent Verification Tool for Surgical Information of Ophthalmic Patients: A Study Based on Artificial Intelligence Technology
Authors: Lin Hui , Huang Xiaofang , Sheng Yaying , Tang Ning , Lian Hengli , Zhang Wenjie , Zhao Lvjun , Zhu Hanqing , Chang Pingjun , Guo Yingxuan
Published: October 2024

Objective:

With the development of day surgery, the characteristics of “short, frequent and fast” ophthalmic surgery are becoming more prominent. However, nurses are not efficient in verifying patients’ surgical information, and problems such as patient privacy leakage are becoming more prominent. To improve the situation, we developed a new augmented reality (AR)-based tool for visual recognition and artificial intelligent (AI) interpretation of the pattern and location of patient surgical skin markings for the verification of the correct surgical site and procedure. The tool can also display a variety of other verbally requested patient information. The purpose of this proposal is to evaluate its feasibility of use by surgical nurses in a real clinical setting.

Methods:

We developed a tool with image recognition technologies to interpretation patient surgical skin markings and match the information obtained with the patients surgical records, thus, verify the patient’s surgical information. Verification includes the proper surgical site and type of procedure to be performed. Nurses can interact with the device through its speech recognition capabilities and the device provides them with a variety of other requested patient information via a heads-up display. Three hundred patients in an outpatient ophthalmology clinic were divided into an AR intelligent verification experimental group and a manual verification control group. The accuracy of information verification, work time consumption, and economic cost data were compared between the 2 groups to evaluate the effectiveness of the AR Surgical Information Intelligent Verification Tool in clinical patient surgical information verification.

Results:

There was no statistically difference in the correct rates of patient surgical information review between the experimental group (95.33%) and the control group (98.67%) (χ2 = 2.934, P = 0.087). The median time for information verification was 10.00 (10.00, 11.00) seconds in the experimental group and 21.00 (20.00, 24.00) seconds in the control group, a statistically difference (Z = 0.000, P < 0.001). The experimental group saved 11 seconds per patient per review compared with the control group. Considering 10,531 surgeries in 2023, printing 1 page of surgical information per 9 patients and requiring 4 copies, 4680 pages of printing paper could be saved.

Conclusions:

The AR Surgical Information Intelligent Verification Tool has advantages in assisting medical staff in patient surgical information verification, improving nursing efficiency, preventing surgical mark errors or nonstandardization, protecting patient privacy, and saving costs. It has certain research and application value in the scenario of patient surgical information verification in ophthalmic day ward.
A Randomized Controlled Trial on Teaching the Safe Handling of Firearms Using a Simulation-Based Assessment
Authors: Hoyne Jake , Yee Jennifer , Lei Charles , Grossestreuer Anne V. , Li-Sauerwine Simiao , Burns William , Olson Nate , Pirotte Matthew , Dubosh Nicole , Ketterer Andrew R.
Published: October 2024

Introduction

Emergency providers risk encountering firearms in the emergency department, but a minority report familiarity with handling firearms. It may be unsafe if unfamiliar, untrained providers attempt to remove a firearm from the clinical care space. This study assessed the efficacy of an educational intervention training resident physicians in this task.

Methods

Five emergency medicine residency programs conducted a prospective, single-blinded randomized controlled trial assessing performance of safely removing a firearm from the clinical care space during a simulated patient encounter. The primary outcome was completion of critical actions previously assessed in a pilot study. Residents viewed a 5-minute educational video developed for this study detailing the principles of safely removing a firearm from the clinical care space. The training video was emailed to prospective participants in the intervention group ahead of the simulation session. Afterward, a debriefing session was held with all participants to review the safe handling of firearms.

Results

Sixty-six of 170 prospective participants (38.8%) consented to participate. There were no significant differences in gender, clinical training level, environment of upbringing, confidence in handling firearms, firearm usage frequency, or prior firearm training. Twenty-nine participants handled the firearm during simulation. The intervention group performed significantly better than the control group, completing a median of 7 critical actions (interquartile range, 7–8) versus 6 critical actions (interquartile range, 5–7), P = 0.035. This effect held among participants who handle firearms outside of work and/or have prior firearms training.

Conclusions

This study demonstrates how a brief educational intervention was associated with improvement in participants' ability to safely remove a firearm from a simulated clinical care space. This approach can be integrated into existing curricula, and its success suggests broad applicability.
Aerobic Conditioning in Geriatric Rehabilitation
Authors: Moffat Marilyn , Park Ha Yeon
Published: October 2024

This article reviews the historical development of aerobic conditioning. The many physiological effects of aerobic conditioning are presented including the effects on cardiovascular, muscular, and neuromuscular health leading to increased physical endurance and increased lifespan. Aerobic exercise prescription follows the frequency, intensity, time, and type, as well as the volume and progression principles. Frequency recommendations are at least 3 d/wk and 3 to 5 d/wk appears to be conducive to meeting overall physical activity recommendations. Intensity determination is based on several methods that include heart rate methods, ratings of perceived exertion (Borg and OMNI), the talk test, and the counting talk test. Time recommendations include at least 150 to 300 minutes a week of moderate-intensity aerobic activity, 75 to 150 minutes a week of vigorous-intensity aerobic physical activity, or an equivalent combination of moderate- and vigorous-intensity aerobic activities. Type recommendations include any aerobic activities involving major muscle groups used in a continuous or intermittent manner. Volume recommendations include ≥500 to 1000 metabolic equivalent minutes per week and approximately 150 min/wk of moderate-intensity activity. Progression recommendations include the gradual advancing of the exercise duration, frequency, and intensity, making sure that the progressions allows for the best adherence to aerobic exercise on an ongoing basis. The benefits of aerobic exercise have been shown to be important for every aspect of living a healthy lifestyle across the age span, particularly for aging adults, adults with chronic conditions, and adults with disabilities.
Surgical Recovery Through the Lens of Patients with Colorectal Disease: A Qualitative Study in an Enhanced Recovery after Surgery Setting
Authors: Li Yaxin , Hajjar Rana , Gramlich Leah , Nelson Gregg , Ljungqvist Olle , Gillis Chelsia
Published: October 2024

BACKGROUND:

As perioperative care shifts to a more patient-centered model, understanding needs and experiences of patients is vital. Gaining such insight can enhance the alignment of care with patient priorities, encouraging adherence to recovery-oriented interventions. We aimed to explore patient-defined recovery and the elements that modify the recovery process for patients with colorectal disease under enhanced recovery after surgery (ERAS) care.

STUDY DESIGN:

A qualitative study was conducted at an ERAS-participating hospital in Alberta, Canada, between April 2018 and June 2019. A co-design focus group set the research direction, and semistructured interviews were conducted postoperatively in-hospital or within 3 months postdischarge. Diverse patient ages and colorectal conditions were targeted through purposive sampling. Interviews were transcribed verbatim and analyzed through manifest and latent content analysis.

RESULTS:

Twenty patients with mean age 62 (SD 13) years and 45% with cancer (17 interview, 2 focus group + interview, and 1 focus group only) were enrolled. Recovery was defined by patients as the return to normal routines and four themes were identified. First, phases of recovery: recovery was described as multidimensional phases distinctively as early, late or long-term, and the endpoint. Second, recovery facilitators: recovery was supported through positive mindsets, conscious recovery, and taking an active role. Third, recovery barriers: recovery was hindered by negative mindsets and treatment side effects. Finally, recovery catalysts: communication, autonomy, and expectations facilitated active or passive recovery.

CONCLUSIONS:

Our patient-oriented recovery model may contribute a new dimension to the ERAS framework by capturing patients’ recovery experiences. Further research is encouraged to explore its value in enhancing patient-centered care within ERAS.
Testing Neuroprotective Strategies in Prolonged Field Care Model of Traumatic Brain Injury and Hemorrhagic Shock
Authors: Bhatti Umar F , Dawood Zaiba Shafik , Shang Zhenhua , Jin Guang , Liggett Marjorie R , Chtraklin Kiril , Liu Baoling , Redondo Ramon-Lorenzo , Wang Bowen , Alam Hasan B
Published: October 2024

BACKGROUND:

Prolonged field care is a military adaptation of tactical combat casualty care providing extended prehospital management during delayed extrication. Effects of addition of valproic acid (VPA) to fresh–frozen plasma (FFP) in a prolonged field care model of hemorrhagic shock and traumatic brain injury are not known. We hypothesized that VPA is associated with decreased neurological impairment, and its protective changes are detected at the transcriptomic level.

STUDY DESIGN:

Swine underwent traumatic brain injury and 40% blood volume hemorrhage. After 2 hours of shock, they were randomized to (1) normal saline (NS), (2) NS + 250 mL FFP (NS + FFP), or (3) NS + FFP + 150 mg/kg VPA (NS + FFP + VPA). At 72 hours, they were transfused packed RBCs before being euthanized. Intraoperative variables and neurological outcomes were compared. Brain lesion size was measured, and gene expression profiles were analyzed using RNA sequencing. Pathway and network analyses were performed on differentially expressed genes. Real-time polymerase chain reaction was performed to validate key genes.

RESULTS:

NS + FFP and NS + FFP + VPA required significantly less crystalloid resuscitation (974 mL: NS + FFP; 1,461 mL: NS + FFP + VPA vs 4,540 mL: NS, p < 0.001), had smaller brain lesion size (2,477 mm3: NS + FFP; 3,018.0 mm3: NS + FFP + VPA vs 4,517.0 mm3: NS, p < 0.01), and required less functional neurologic impairment compared with NS. Per pathway analysis of differentially expressed genes, VPA was associated with enrichment of numerous metabolic changes in injured brains, which were not observed with FFP. Network analysis showed enrichment of various gene networks. Mitochondrially encoded ATP synthase membrane subunit 8 gene was downregulated in VPA-treated animals.

CONCLUSIONS:

The addition of FFP to the resuscitation protocol resulted in a significant reduction in crystalloid requirements. Both the NS + FFP and NS + FFP + VPA groups showed improved neurological recovery compared with NS alone and had distinctive transcriptomic profiles in injured brains at 72 hours. The mitochondrially encoded ATP synthase membrane subunit 8 gene, involved in worsening ischemia following brain injury, was downregulated in VPA-treated animals.
Closed-loop fMRI at the mesoscopic scale of columns and layers: Can we do it and why would we want to?
Authors: Chaimow Denis , Lorenz Romy , Weiskopf Nikolaus
Published: October 2024

Technological advances in fMRI including ultra-high magnetic fields (≥ 7 T) and acquisition methods that increase spatial specificity have paved the way for studies of the human cortex at the scale of layers and columns. This mesoscopic scale promises an improved mechanistic understanding of human cortical function so far only accessible to invasive animal neurophysiology. In recent years, an increasing number of studies have applied such methods to better understand the cortical function in perception and cognition. This future perspective article asks whether closed-loop fMRI studies could equally benefit from these methods to achieve layer and columnar specificity. We outline potential applications and discuss the conceptual and concrete challenges, including data acquisition and volitional control of mesoscopic brain activity. We anticipate an important role of fMRI with mesoscopic resolution for closed-loop fMRI and neurofeedback, yielding new insights into brain function and potentially clinical applications.

This article is part of the theme issue ‘Neurofeedback: new territories and neurocognitive mechanisms of endogenous neuromodulation’.
On the origin of an insular hybrid butterfly lineage
Authors: Boman Jesper , Nolen Zachary J. , Backström Niclas
Published: October 2024

A new species can form through hybridization between species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process has been difficult to obtain. Recent access to whole-genome sequencing data have made it more feasible to detect hybrid lineages. Here we report the discovery of a European hybrid butterfly lineage, a finding that can be considered surprising given the intense and long-term study of European butterflies. The lineage we describe is mainly inhabiting an island in the Baltic Sea and was previously designated as a subspecies (horkei) of one of the parental species (Aricia artaxerxes). By analysing whole-genome resequencing data, we determine thathorkeioriginated by hybridization between the non-sister speciesA. artaxerxesandA. agestis. This hybridization event occurred approximately 54,000 years ago, predating the last glaciation of the current distribution range.Horkeimust therefore have persisted long enough to be able to colonize its current range, despite that this area lies between the current distributions of the parental species. The hybrid origin, the maintenance of genomic integrity across times of dramatic climate change and the expression of a combination of parental traits suggest thathorkeicould be in the process of hybrid speciation.
Cannabidiol (CBD) potentiates physiological and behavioral markers of hypothalamic-pituitary-adrenal (HPA) axis responsivity in female and male mice
Authors: Jenkins Bryan W. , Spina Hayley A. , Nicholson Kate , Newman Amy E. M. , Khokhar Jibran Y.
Published: October 2024

Rationale

Clinical literature indicates there may be a therapeutic use of cannabidiol (CBD) for stress-related disorders. Preclinical literature remains conflicted regarding the underlying neurobehavioral mechanisms, reporting mixed effects of CBD (increased, decreased, or no effect) on anxiety- and fear-related behaviors. Preclinical data demonstrated that CBD modulates hypothalamus-pituitary-adrenal (HPA) axis gene expression; it is unknown whether CBD changes HPA axis responsivity and how this relates to altered behavior.

Objectives

We aimed to evaluate whether acute or chronic CBD administration would alter physiological and behavioral measures of HPA axis responsivity in male or female mice.

Methods

C57BL/6 mice of both sexes were injected with vehicle or CBD (30 mg/kg, i.p.) daily for 26 days. Plasma corticosterone (CORT) levels were evaluated following dexamethasone suppression and adrenocorticotropin hormone stimulation tests after acute and chronic CBD exposure. After chronic CBD, mice were tested for anxiety-like behavior using an elevated plus maze (EPM) and associative fear learning and memory using a trace fear conditioning (FC) protocol.

Results

Compared to vehicle, CBD induced a state of HPA axis hyperactivation, an effect which was significant in males; it also normalized anxiety-like behavior in female mice classified as having HPA axis hypofunction and primed all female mice for enhanced conditioned responding. Significant sex differences were also detected: females had greater plasma CORT levels and HPA axis responsivity than males, exhibited less EPM anxiety-like behavior, and were more responsive during FC.

Conclusions

CBD potentiated physiological and behavioral markers of HPA axis function and normalized anxiety-like behavior in a sex-specific manner. This observation has implications for cannabinoid-based drug development targeting individuals with stress-related disorders involving HPA axis hypofunction pathology.
Evaluation of post-acute COVID-19 health outcomes (ECHOES) in England: The development of national surveillance system for long- term health outcomes following COVID-19
Authors: Allen Hester , Hassell Katie , Rawlinson Christopher , Pullen Owen , Campbell Colin , Jödicke Annika M. , Català Martí , Uribe Albert Prats , Dabrera Gavin , Prieto-Alhambra Daniel , Campos-Matos Ines
Published: October 2024

Introduction

Electronic health records can be used to understand the diverse presentation of post-acute and long-term health outcomes following COVID-19 infection. In England, the UK Health Security Agency in collaboration with the University of Oxford have created the ECHOES dataset to monitor how an initial SARS-CoV-2 infection episode is associated with changes in the risk of health outcomes that are recorded in routinely collected health data.

Methods

The ECHOES dataset is as a national level dataset combining national level surveillance, administrative, and healthcare data. Entity resolution and data linkages methods are used to create a cohort of individuals who have tested positive and negative for SARS-CoV-2 in England throughout the COVID-19 pandemic, alongside information on a range of health outcomes including diagnosed clinical conditions and mortality, and risk factor information.

Results

The dataset contains comprehensive COVID-19 testing data and demographic, socio economic and health related information for 44 million individuals, who tested for SARS-CoV-2 between March 2020 and April 2022, representing 15,720,286 individuals who tested positive and 42,351,016 individuals who tested negative.

Discussion

With the application of epidemiological and statistical methods, this dataset allows a range of clinical outcomes to be investigated, including pre-specified health conditions and mortality. Furthermore, understanding of potential determinants of health outcomes can be gained, including pre-existing health conditions, acute disease characteristics, SARS-CoV-2 vaccination status and genomic variant.
Incident COVID-19 infections before Omicron in the U.S
Authors: Lobay Rachel , Srivastava Ajitesh , Tibshirani Ryan J. , McDonald Daniel J.
Published: October 2024

The timing and magnitude of COVID-19 infections are of interest to the public and to public health, but these are challenging to ascertain due to the volume of undetected asymptomatic cases and reporting delays. Accurate estimates of COVID-19 infections based on finalized data can improve understanding of the pandemic and provide more meaningful quantification of disease patterns and burden. Therefore, we retrospectively estimate daily incident infections for each U.S. state prior to Omicron. To this end, reported COVID-19 cases are deconvolved to their date of infection onset using delay distributions estimated from the CDC line list. Then, a novel serology-driven model is used to scale these deconvolved cases to account for the unreported infections. The resulting infections incorporate variant-specific incubation periods, reinfections, and waning antigenic immunity. They clearly demonstrate that the reported cases fail to reflect the full extent of disease burden in all states. Most notably, infections were severely underreported during the Delta wave, with an estimated reporting rate as low as 6.3% in New Jersey, 7.3% in Maryland, and 8.4% in Nevada. Moreover, in 44 states, fewer than 1/3 of infections appear as cases reports. Therefore, while reported cases offer a convenient proxy of disease burden, they fail to capture the full extent of infections, and can severely underestimate the true disease burden. This retrospective analysis also estimates other important quantities for every state, including variant-specific deconvolved cases, time-varying case ascertainment ratios, and infection-hospitalization ratios.
Functional and pangenomic exploration of Roc two-component regulatory systems identifies novel players acrossPseudomonasspecies
Authors: Simon Victor , Trouillon Julian , Attrée Ina , Elsen Sylvie
Published: October 2024

The opportunistic pathogenPseudomonas aeruginosacounts on a large collection of two-component regulatory systems (TCSs) to sense and adapt to changing environments. Among them, the Roc (Regulationofcup) system is a one-of-a-kind network of branched TCSs, composed of two histidine kinases (HKs) (RocS1 and RocS2) interacting with three response regulators (RRs) (RocA1, RocR and RocA2), which regulate virulence, antibiotic resistance and biofilm formation. Based on extensive work on the Roc system, previous data suggested the existence of other key regulators yet to be discovered. In this work, we identified PA4080, renamed RocA3, as a fourth RR that is activated by RocS1 and RocS2 and that positively controls the expression of thecupBoperon. Comparative genomic analysis of the locus identified a gene -rocR3- adjacent torocA3in a subpopulation of strains which encodes a protein with structural and functional similarity to the c-di-GMP phosphodiesterase RocR. Furthermore, we identified a fourth branch of the Roc system consisting of the PA2583 HK, renamed RocS4, and of the Hpt protein HptA. Using a bacterial two-hybrid system, we showed that RocS4 interacts with HptA, which in turn interacts with RocA1, RocA2 and RocR3. Finally, we mapped the pangenomic RRs repertoire establishing a comprehensive view of the plasticity of such regulators among clades of the species. Overall, our work provides a comprehensive inter-species definition of the Roc system, nearly doubling the number of proteins known to be involved in this interconnected network of TCSs controlling pathogenicity inPseudomonasspecies.

GRAPHICAL ABSTRACT

ABBREVIATED SUMMARY

Roc system account for a particularly interconnected yet incomplete network of two-component regulatory system involved in the virulence ofPseudomonas aeruginosa. Our work identified the missing RocA3 regulator and propose new players of the system delineating their conservation between the clade of the species.
miR-210 locus deletion disrupts cellular homeostasis; an integrated genetic study
Authors: Preda Mihai Bogdan , Rusu-Nastase Evelyn Gabriela , Neculachi Carmen Alexandra , Zhong Xiaoling , Voellenkle Christine , Mazure Nathalie M. , Balacescu Ovidiu , Ivan Cristina , Zheng Xiao-Wei , Gherghiceanu Mihaela , Lebrigand Kevin , Simionescu Maya , Martelli Fabio , Mari Bernard , Catrina Sergiu-Bogdan , Burlacu Alexandrina , Ivan Mircea
Published: October 2024

MiR-210 is widely recognized as the quintessential hypoxia-responsive miRNA and thought to fine-tune various facets of cellular homeostasis. We hereby present an integrative appraisal of phenotypic and molecular repercussions of disrupting the corresponding locus in human and mouse cells using multiple genetic strategies. Briefly, MIR210 deletion led to decreased cellular fitness and suboptimal responses to several stress types. Transcriptomic comparisons using different profiling platforms, performed independently by members of this collaboration, revealed consistent deregulation of neighboring genes, in locus-disrupted cells. Interestingly, the anticipated enrichment in miR-210 targets failed to materialize in unbiased analyses. Our results point to the biological significance of unrecognized regulatory elements that overlap miRNA genes and should serve as note of caution for studies based for genetic disruption of such loci.
Detection and electron microscopic study of thick cross-striated linear fibrils in mammalian cell nuclei
Authors: Mosevitsky Mark I.
Published: October 2024

Using an electron microscope, cross-striated fibrils with an axial repeat of about 65 nm were detected in the cell nuclei of rat and calf tissues. The nuclei were purified and processed using a “complete medium” (CM) simulating the composition of salts of the intranuclear medium. These fibrils are not the filaments of the nuclear matrix described in the literature. In particular, they are thicker and not branched. The axial repeat in these fibrils is similar to that in extracellular collagen fibrils. Therefore, in this work, the main efforts were aimed at demonstrating the nuclear origin of the observed fibrils. Their presence in the material of nuclei destroyed by ultrasound, their contact with isolated nucleoli and their presence in residual nuclei are shown on samples prepared for electron microscopy in the form of “whole mounts”. The sites of attachment of chromatin and of nuclear matrix network to thick cross-striated fibrils were detected. As axial components of condensed chromosomes, thick cross-striated fibrils are preserved during mitosis. Probably, their contacts with chromatin and with elements of nuclear matrix network are also preserved providing reproduction of the internal structure of the nuclei in daughter cells. It is logical to assume that the cross-striated fibrils perform important functions attributed to the nuclear matrix.

Highlights

Thick cross-striated fibrils with an axial repeat of about 65 nm are present in mammalian cell nuclei.

Areas of dense contact between thick cross-striated fibrils and chromatin are observed.

Nucleoli are attached to thick cross-striated fibrils.

Nuclear matrix network is tightly adherent to thick cross-striated fibrils.

Thick cross-striated fibrils can be retained in mitosis as axial elements of chromosomes.
Greater recalled pain and movement-evoked pain are associated with longer 400-meter walk and repeat stair climb time: the Study of Muscle, Mobility and Aging
Authors: Mau Theresa , Barnes Haley N. , Simon Corey B. , Hetherington-Rauth Megan , Bauer Scott R. , Strotmeyer Elsa S. , Lane Nancy E. , Rowbotham Michael C. , Weaver Ashley A. , Blackwell Terri L. , Cai Yurun , Glynn Nancy W. , Goodpaster Bret H. , Cummings Steven R. , Newman Anne B. , Cawthon Peggy M. , Kritchevsky Stephen B.
Published: October 2024

Background

Musculoskeletal pain frequently accompanies the development of mobility disability and falls in old age. To better understand this, we aimed to quantify the impact of different pain measures—recalled pain and movement-evoked pain—on 400-meter walk and stair climb time in older adults participating in the Study of Muscle, Mobility and Aging (SOMMA).

Methods

In SOMMA (N=879, age=76.3 ± 5.0 years, 59% women, 84% Non-Hispanic White), participants completed usual pace 400m walk (avg=6.6 ± 1.2 min.) and repeat stair climb tests (avg=26.6 ± 7.2 sec.). Assessments of recalled pain included the Brief Pain Inventory short form (BPI-sf), total lower body pain (lower back, hips, knees, feet/ankles), stiffness (hip or knee), and Neuropathy Total Symptom Score (NTSS-6). Movement-evoked pain was assessed separately before and after the 400m walk and repeat stair climb tasks. Multivariable linear regression modeled the associations of pain with time to complete the tasks, reported as β[95%CI] expressed per SD increment of pain measure or β[95%CI] per pain categories, adjusted for age, sex, race, ethnicity, body mass index, prescription medications, and depressive symptoms.

Results

Greater degree of any pain measure was associated with longer physical performance time, though intercorrelations between recalled pain measures varied (r=0.13-0.57,p<0.05 for all). For each SD increment in lower body pain, participants had longer walk time (by 10.5 sec [6.1, 14.8]) and stair climb (by 0.6 sec [0.1, 1.1]). Compared to participants with no change in pain upon movement, walk time was longer in those with more pain upon movement (19.5 sec [10.3, 28.7]) (p<0.001) but not those with less pain upon movement; stair climb showed similar patterns.

Conclusions

Recalled and movement-evoked pain measures were weakly correlated with one another but similarly associated with time to complete 400m walk and stair climb tests. Different pain assessments capture different functional domains of pain but have similar associations with physical performance in these older adults.
Distinct patterns of bioscience doctoral publication disparities by gender and race/ethnicity
Authors: Leap Katie , Payne Gregory S. , Sinsheimer Janet S. , Azurdia Diana E.
Published: October 2024

The ability to address the lack of diversity in the Science, Technology, Engineering and Math workforce depends on inclusive and equitable training of doctoral students to succeed in the profession. An important metric used to assess equitable training in bioscience doctoral programs is the number of publications that result from a student’s research. The purpose of this study was to investigate whether there are demographic differences in publication rates among all students in a cohort of bioscience Ph.D. programs at the University of California Los Angeles who graduated between 2011 and 2019. Using institutional data and publication database queries, we determined the number of doctoral publications parsed by authorship position, and the timing of the first publication for each student. The resulting dataset was then analyzed for the relationships between publication categories and student gender, race/ethnicity, and citizenship status. We find that female students published significantly fewer total and co-author papers compared to male students, but had the same number of first-author publications. In contrast, students from underrepresented racial/ethnic groups had fewer first-author papers compared to students from well-represented groups, but similar numbers of total and co-author publications. Publication of the first doctoral paper occurred later for female versus male, and underrepresented versus well-represented students. These results provide evidence for distinct patterns of doctoral publication disparities by gender and race/ethnicity, offering insights into a key metric of bioscience student success and informing potential strategies to achieve equitable outcomes in bioscience doctoral education.
Prevalence of subpatentPlasmodium falciparuminfections in regions with varying transmission intensities and implications for malaria elimination in Mainland Tanzania
Authors: Seth Misago D. , Popkin-Hall Zachary R. , Madebe Rashid A. , Budodo Rule , Bakari Catherine , Lyimo Beatus M. , Giesbrecht David , Moshi Ramadhani , Mbwambo Ruth B. , Francis Filbert , Pereus Dativa , Mbata Doris , Challe Daniel P. , Mandai Salehe S. , Chacha Gervas A. , Kisambale Angelina J. , Mbwambo Daniel , Aaron Sijenunu , Lusasi Abdallah , Lazaro Samwel , Mandara Celine I. , Bailey Jeffrey A. , Juliano Jonathan J. , Gutman Julie R. , Ishengoma Deus S.
Published: October 2024

Background

SubpatentPlasmodium falciparuminfections, defined as infections with parasitaemia density below the detection limit of routine malaria diagnostic tests, contribute to infectious reservoirs, sustain transmission, and cause the failure of elimination strategies in target areas. This study assessed the prevalence of and factors associated with subpatentP. falciparuminfections in 14 regions of Mainland Tanzania with varying endemicity.

Methods

The study used samples randomly selected from RDT-negative dried blood spots (DBS) (n = 2,685/10,121) collected in 2021 at 100 health facilities across 10 regions of Mainland Tanzania, and four communities in four additional regions. The regions were selected from four transmission strata; high (five regions), moderate (three), low (three), and very low (three regions). DNA was extracted by Tween-Chelex method, and thePf18SrRNA gene was amplified by quantitative polymerase chain reaction (qPCR). Logistic regression analysis was used to assess the associations between age groups, sex, fever status, and transmission strata with of subpatent infections status, while linear regression analysis was used to assess the association between these factors and subpatent parasite density.

Results

Of the selected samples, 525/2,685 (19.6%) were positive by qPCR forP. falciparum, and the positivity rates varied across different regions (range: 4.8 to 39.6%). Under-fives (aOR: 1.4, 95% CI 1.04-1.88; p<0.05) from health facilities had higher odds of subpatent infections compared to other groups, while those from community surveys (aOR: 0.33, 95% CI 0.15-0.72; p = 0.005) had lower odds. Participants from very low transmission stratum had significantly lower odds of subpatent infection compared to those from high transmission straum (aOR=0.53, 95% CI=0.37-0.78; p < 0.01). The log-transformed median parasite density (interquartile range) was 6.9 (5.8 - 8.5) parasites/µL, with significantly higher parasitaemia in the low transmission stratum compared to very low (11.4 vs 7.0 parasites/µL, p<0.001).

Conclusion

Even in very low transmission settings, the prevalence of subpatent infections was 13%, and in low transmission settings it was even higher at 29.4%, suggesting a substantial reservoir which is likely to be missed by routine malaria case management strategies. Thus, control and elimination programmes may benefit from adoption of more sensitive detection methods to ensure that a higher proportion of subpatent infections are detected.
Statistical Relationship Between Wastewater Data and Case Notifications for COVID-19 Surveillance in the United States, 2020-2023: A Bayesian Hierarchical Model
Authors: Haraguchi Masahiko , Klaassen Fayette , Cohen Ted , Salomon Joshua A. , Menzies Nicolas A.
Published: October 2024

During the COVID-19 pandemic a number of jurisdictions in the United States began to regularly report levels of SARS-CoV-2 in wastewater for use as a proxy for SARS-CoV-2 incidence. Despite the promise of this approach for improving situational awareness, the degree to which viral levels in wastewater track with other outcome data has varied, and better evidence is needed to understand the situations in which wastewater surveillance tracks closely with traditional surveillance data. In this study, we quantified the relationship between wastewater data and traditional case-based surveillance data for multiple jurisdictions. To do so, we collated data on wastewater SARS-CoV-2 RNA levels and COVID-19 case reports from July 2020 to March 2023, and employed Bayesian hierarchical regression modeling to estimate the statistical relationship between wastewater data and reported cases, allowing for variation in this relationship across counties. We compared different model structural approaches and assessed how the strength of the estimated relationships varied between settings and over time. These analyses revealed a strong positive relationship between wastewater data and COVID-19 cases for the majority of locations, with a median correlation coefficient between observed and predicted cases of 0.904 (interquartile range 0.823 – 0.943). Across locations, the COVID-19 case rate associated with a given level of wastewater SARS-CoV-2 RNA concentration declined over the study period. Counties with higher population size and of higher levels of urbanicity had stronger concordance between wastewater data and COVID-19 cases. Ideally, use of wastewater data for decision-making should be based on an understanding of their local historical performance.
Replication-dependent histone (Repli-Histo) labeling dissects the physical properties of euchromatin/heterochromatin in living human cells
Authors: Minami Katsuhiko , Ide Satoru , Nakazato Kako , Kaizu Kazunari , Higashi Koichi , Tamura Sachiko , Toyoda Atsushi , Takahashi Koichi , Kurokawa Ken , Maeshima Kazuhiro
Published: October 2024

A string of nucleosomes, where genomic DNA is wrapped around histones, is organized in the cell as chromatin. Chromatin in the cell varies greatly, from euchromatin to heterochromatin, in its genome functions. It is important to understand how heterochromatin is physically different from euchromatin. However, their specific labeling methods in living cells are limited. To address this, we have developed replication-dependent histone labeling (Repli-Histo labeling) to label nucleosomes in euchromatin and heterochromatin based on DNA replication timing. We investigated local nucleosome motion in the four chromatin classes from euchromatin to heterochromatin of living human and mouse cells. We found that more euchromatic regions (earlier replicated regions) show greater nucleosome motion. Notably, the motion profile in each chromatin class persists throughout interphase. Genome chromatin is essentially replicated from regions with greater nucleosome motions, even though the replication timing program is perturbed. Our findings, combined with computational modeling, suggest that earlier replicated regions have more accessibility and local chromatin motion can be a major determinant of genome-wide replication timing.
Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos
Authors: Jiang Yi , Wang Haoyu , Boergens Kevin , Rzepka Norman , Wang Fangfang , Hua Yunfeng
Published: October 2024

Recent technical advances in volume electron microscopy (vEM) and artificial intelligence-assisted image processing have facilitated high throughput quantifications of cellular structures, such as mitochondria that are ubiquitous and morphologically diversified. A still often overlooked computational challenge is to assign cell identity to numerous mitochondrial instances, for which both mitochondrial and cell membrane contouring used to be required. Here, we present a vEM reconstruction procedure (called mito-SegEM) that utilizes virtual path-based annotation to assign automatically segmented mitochondrial instances at the cellular scale, therefore bypassing the requirement of membrane contouring. The embedded toolset in webKnossos (an open-source online annotation platform) is optimized for fast annotation, visualization, and proofreading of cellular organelle networks. We demonstrate broad applications of mito-SegEM on volumetric datasets from various tissues, including the brain, intestine, and testis, to achieve an accurate and efficient reconstruction of mitochondria in a use-dependent fashion.
Cooperative motility emerges in crowds of T cells but not neutrophils
Authors: Wortel Inge MN , Postat Jérémy , Mihaylova Mihaela , Merino Mauricio , Bhagrath Aanya , Harris Maryl , Wouters Lin , Wiebke Lucas , Parisi Daniel R , Mandl Judith N , Textor Johannes
Published: October 2024

T cells are among the most motile immune cells in the body, and their migration into and within tissues is key to their function. Remarkably, T cells can maintain their motility even in highly crowded environments like the densely packed T cell areas of lymphoid organs, but how they do so remains incompletely understood. Here, we use microfluidic devices andin silicomodels to study T cells from a crowd dynamics perspective, focusing on a hallmark scenario that has proven instrumental in characterizing other crowded systems such as pedestrians and ants: single-lane traffic. Unexpectedly, T cells in narrow, straight microchannels synchronize their speeds and form stable, motile trains. We show that this behavior can be explained by a preference of T cells to maintain contact with each other after collisions, and an ability of faster T cells to “push” slower ones. We demonstrate that this behavior does not extend to all immune cells; neutrophils in the same settings slow down with increasing cell density. Cooperative motion may benefit T cell motility in difficult and crowded tissue environments, ultimately preventing jams that impair motion in other crowded systems.
Muon spin force
Authors: Ema Yohei , Gao Ting , Pospelov Maxim
Published: October 2024

Current discrepancy between the measurement and the prediction of the muon anomalous magnetic moment can be resolved in the presence of a long-range force created by ordinary atoms acting on the muon spin via axial-vector and/or pseudoscalar coupling, and requiring a tiny O(10−13  eV) spin energy splitting between muon state polarized in the vertical direction. We suggest that an extension of the muon spin resonance (μSR) experiments can provide a definitive test of this class of models. We also derive indirect constraints on the strength of the muon spin force by considering the muon-loop-induced interactions between nuclear spin and external directions. The limits on the muon spin force extracted from the comparison of Hg199/Hg201 and Xe129/Xe131 spin precession are strong for the pseudoscalar coupling but are significantly relaxed for the axial-vector one. These limits suffer from significant model uncertainties, poorly known proton/neutron spin content of these nuclei, and therefore do not exclude the possibility of a muon spin force relevant for the muon g−2.

Published by the American Physical Society
2024
Generating variable length full events from partons
Authors: Quétant Guillaume , Raine John Andrew , Leigh Matthew , Sengupta Debajyoti , Golling Tobias
Published: October 2024

This paper presents a novel approach for directly generating full events at detector-level from parton-level information, leveraging cutting-edge machine learning techniques. To address the challenge of multiplicity variations between parton and reconstructed object spaces, we employ transformers, score-based models and normalizing flows. Our method tackles the inherent complexities of the stochastic transition between these two spaces and achieves remarkably accurate results. The combination of innovative techniques and the achieved accuracy demonstrates the potential of our approach in advancing the field and opens avenues for further exploration. This research contributes to the ongoing efforts in high-energy physics and generative modeling, providing a promising direction for enhanced precision in fast detector simulation.

Published by the American Physical Society
2024
Scalable Architecture for Trapped-Ion Quantum Computing Using rf Traps and Dynamic Optical Potentials
Authors: Schwerdt David , Peleg Lee , Shapira Yotam , Priel Nadav , Florshaim Yanay , Gross Avram , Zalic Ayelet , Afek Gadi , Akerman Nitzan , Stern Ady , Kish Amit Ben , Ozeri Roee
Published: October 2024

Qubits based on ions trapped in linear radio-frequency traps form a successful platform for quantum computing, due to their high fidelity of operations, all-to-all connectivity, and degree of local control. In principle, there is no fundamental limit to the number of ion-based qubits that can be confined in a single 1D register. However, in practice, there are two main issues associated with long trapped-ion crystals, that stem from the “softening” of their modes of motion, upon scaling up: high heating rates of the ions’ motion and a dense motional spectrum; both impede the performance of high-fidelity qubit operations. Here, we propose a holistic, scalable architecture for quantum computing with large ion crystals that overcomes these issues. Our method relies on dynamically operated optical potentials that instantaneously segment the ion crystal into cells of a manageable size. We show that these cells behave as nearly independent quantum registers, allowing for parallel entangling gates on all cells. The ability to reconfigure the optical potentials guarantees connectivity across the full ion crystal and also enables efficient midcircuit measurements. We study the implementation of large-scale parallel multiqubit entangling gates that operate simultaneously on all cells and present a protocol to compensate for crosstalk errors, enabling full-scale usage of an extensively large register. We illustrate that this architecture is advantageous both for fault-tolerant digital quantum computation and for analog quantum simulations.

Published by the American Physical Society
2024
Development of crystal optics for X-ray multi-projection imaging for synchrotron and XFEL sources
Authors: Bellucci Valerio , Birnsteinova Sarlota , Sato Tokushi , Letrun Romain , Koliyadu Jayanath C. P. , Kim Chan , Giovanetti Gabriele , Deiter Carsten , Samoylova Liubov , Petrov Ilia , Lopez Morillo Luis , Graceffa Rita , Adriano Luigi , Huelsen Helge , Kollmann Heiko , Tran Calliste Thu Nhi , Korytar Dusan , Zaprazny Zdenko , Mazzolari Andrea , Romagnoni Marco , Asimakopoulou Eleni Myrto , Yao Zisheng , Zhang Yuhe , Ulicny Jozef , Meents Alke , Chapman Henry N. , Bean Richard , Mancuso Adrian , Villanueva-Perez Pablo , Vagovic Patrik
Published: October 2024

X-ray multi-projection imaging (XMPI) is an emerging experimental technique for the acquisition of rotation-free, time-resolved, volumetric information on stochastic processes. The technique is developed for high-brilliance light-source facilities, aiming to address known limitations of state-of-the-art imaging methods in the acquisition of 4D sample information, linked to their need for sample rotation. XMPI relies on a beam-splitting scheme, that illuminates a sample from multiple, angularly spaced viewpoints, and employs fast, indirect, X-ray imaging detectors for the collection of the data. This approach enables studies of previously inaccessible phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. In this work, we discuss in detail the beam-splitting scheme of XMPI. More specifically, we explore the relevant properties of X-ray splitter optics for their use in XMPI schemes, both at synchrotron insertion devices and XFEL facilities. Furthermore, we describe two distinct XMPI schemes, designed to faciliate large samples and complex sample environments. Finally, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL. This detailed overview aims to state the challenges and the potential of XMPI and act as a stepping stone for future development of the technique.