bluuebunny/crossref_metadata_2025 huggingface dataset:
Coherence of nonlinear Bloch dynamics of Bose–Einstein condensates in deep optical lattices
Authors: Zhang 张 Ai-Xia 爱霞 , Zhang 张 Wei 薇 , Wang 王 Jie 杰 , Hu 胡 Xiao-Wen 潇文 , Mi 米 Lai-Lai 来来 , Xue 薛 Ju-Kui 具奎
Published: January 2024

Atomic interaction leads to dephasing and damping of Bloch oscillations (BOs) in optical lattices, which limits observation and applications of BOs. How to obtain persistent BOs is particularly important. Here, the nonlinear Bloch dynamics of the Bose–Einstein condensate with two-body and three-body interactions in deep optical lattices is studied. The damping rate induced by interactions is obtained. The damping induced by two-body interaction plays a dominant role, while the damping induced by three-body interaction is weak. However, when the two-body and three-body interactions satisfy a threshold, long-lived coherent BOs are observed. Furthermore, the Bloch dynamics with periodical modulation of linear force is studied. The frequencies of linear force corresponding to resonance and pseudoresonance are obtained, and rich dynamical phenomena, i.e., stable and strong BOs, drifting and dispersion of wave packet, are predicted. The controllable Bloch dynamics is provided with the periodic modulation of the linear force.
High-speed readout system of X-ray CMOS image sensor for time domain astronomy
Authors: Ogino Naoki , Arimoto Makoto , Sawano Tatsuya , Yonetoku Daisuke , Shen Hsien-chieh , Sakamoto Takanori , Hiraga Junko S. , Yatsu Yoichi , Mihara Tatehiro
Published: January 2024

We developed an FPGA-based high-speed readout system for a complementary
metal-oxide-semiconductor (CMOS) image sensor to observe soft X-ray transients in future satellite
missions, such as HiZ-GUNDAM. Our previous research revealed that the CMOS image sensor
has low-energy X-ray detection capability (0.4–4 keV) and strong radiation tolerance, which
satisfies the requirements of the HiZ-GUNDAM mission. However, CMOS sensors typically
have small pixel sizes (e.g., ∼10 µm), resulting in large volumes of image data.
GSENSE400BSI has 2048×2048 pixels, producing 6 Mbyte per frame. These large volumes of
observed raw image data cannot be stored in a satellite bus system with a limited storage size.
Therefore, only X-ray photon events must be extracted from the raw image data. Furthermore, the
readout time of CMOS image sensors is approximately ten times faster than that of typical X-ray
CCDs, requiring faster event extraction on a timescale of ∼0.1 s. To address these issues,
we have developed an FPGA-based image signal processing system capable of high-speed X-ray event
extraction onboard without storing raw image data. The developed compact system enabled mounting
on a CubeSat mission, facilitating early in-orbit operation demonstration. Here, we present the
design and results of the performance evaluation tests of the proposed FPGA-based readout system.
Utilizing X-ray irradiation experiments, the results of the X-ray event extraction with the
onboard and offline processing methods were consistent, validating the functionality of the
proposed system.
Evaluation of the mean excitation energies of gaseous and liquid argon
Authors: Strait M.
Published: January 2024

Current and future experiments need to know the stopping
power of liquid argon. It is used directly in calibration, where
commonly the minimum-ionizing portion of muon tracks is used as a
standard candle. Similarly, muon range is used as a measure of muon
energy. More broadly, the stopping power figures into the simulation
of all charged particles, and so uncertainty propagates widely
throughout data analysis of all sorts. The main parameter that
controls stopping power is the mean excitation energy, or
I-value. Direct experimental information for argon's I-value come
primarily from measurements of gaseous argon, with a very limited
amount of information from solid argon, and none from liquid argon.
A powerful source of indirect information is also available from
oscillator strength distribution calculations. We perform a new
calculation and find that from oscillator strength information
alone, the I-value of gaseous argon is (187 ± 5) eV. In
combination with the direct measurements and other calculations, we
recommend (187 ± 4) eV for gaseous argon. For liquid argon, we
evaluate the difference in central value and uncertainty incurred by
the difference of phase and recommend (197 ± 7) eV. All
uncertainties are given to 68% C.L.
On sampling determinantal and Pfaffian point processes on a quantum computer
Authors: Bardenet Rémi , Fanuel Michaël , Feller Alexandre
Published: January 2024

DPPs were introduced by Macchi as a model in quantum optics the 1970s. Since then, they have been widely used as models and subsampling tools in statistics and computer science. Most applications require sampling from a DPP, and given their quantum origin, it is natural to wonder whether sampling a DPP on a quantum computer is easier than on a classical one. We focus here on DPPs over a finite state space, which are distributions over the subsets of

{
1
,
…
,
N
}

parametrized by an N × N Hermitian kernel matrix. Vanilla sampling consists in two steps, of respective costs

O

(

N
3

)

and

O

(
N

r
2

)

operations on a classical computer, where r is the rank of the kernel matrix. A large first part of the current paper consists in explaining why the state-of-the-art in quantum simulation of fermionic systems already yields quantum DPP sampling algorithms. We then modify existing quantum circuits, and discuss their insertion in a full DPP sampling pipeline that starts from practical kernel specifications. The bottom line is that, with P (classical) parallel processors, we can divide the preprocessing cost by P and build a quantum circuit with

O

(
N
r
)

gates that sample a given DPP, with depth varying from

O

(
N
)

to

O
(
r
log
N
)

depending on qubit-communication constraints on the target machine. We also connect existing work on the simulation of superconductors to Pfaffian point processes (PfPP), which generalize DPPs and would be a natural addition to the machine learner’s toolbox. In particular, we describe ‘projective’ PfPPs, the cardinality of which has constant parity, almost surely. Finally, the circuits are empirically validated on a classical simulator and on 5-qubit IBM machines.
The effect of loss/gain and Hamiltonian perturbations of the Ablowitz—Ladik lattice on the recurrence of periodic anomalous waves
Authors: Coppini F , Santini P M
Published: January 2024

Using the finite gap method, in this paper we extend the recently developed perturbation theory for anomalous waves (AWs) of the periodic nonlinear Schrödinger (NLS) type equations to lattice equations, using as basic model the Ablowitz–Ladik (AL) lattices, integrable discretizations of the focusing and defocusing NLS equations. We study the effect of physically relevant perturbations of the AL equations, like linear loss, gain, and/or Hamiltonian corrections, on the AW recurrence, in the simplest case of one unstable mode. We show that these small perturbations induce O(1) effects on the periodic AW dynamics, generating three distinguished asymptotic patterns. Since dissipation and higher order Hamiltonian corrections can hardly be avoided in natural phenomena involving AWs, we expect that the asymptotic states described analytically in this paper will play a basic role in the theory of periodic AWs in natural phenomena described by discrete systems. The quantitative agreement between the analytic formulas of this paper and numerical experiments is excellent.
Homotopy truncations of homotopically stratified spaces
Authors: Chataur David , Saralegi-Aranguren Martintxo , Tanré Daniel
Published: January 2024

Intersection homology of Goresky and MacPherson can be defined from the Deligne sheaf, obtained from truncations of complexes of sheaves. As intersection homology is not the homology of a particular space, the search for a family of spaces whose homologies have properties analogous to intersection homology has developed. For some stratified spaces, M. Banagl has introduced such a family by using a topological truncation: the original link is replaced by a truncation of its homological Moore resolution.

In this work, we study the dual approach in the Eckmann-Hilton sense: we consider the stratified space obtained by replacing the original link by a Postnikov approximation. The main result is that our construction restores the space constructed by Gajer to establish an intersection Dold-Thom theorem. We are conducting this study within the general framework of Quinn’s homotopically stratified spaces.
Cinema, Displayed
Authors: Ponech Trevor
Published: January 2024

This essay details that which is arguably the essential nature of a ubiquitous kind of visual display prominently involved in a great many phenomena that people have in mind when they think and talk about the cinema. My argument begins with a summary and critique of an important precedent, Noël Carroll’s essentialist definition of the detached moving image display. The remainder of my discussion concentrates on the structure and dynamics of a particular sort of luminescent display. This display is essential to what I call the cinematic display. As I understand it, the cinematic display is neither the or a medium of cinema nor perforce a vehicle for artistic content. It is, rather, a luminescent display in service of someone’s presentational intentions. I conclude with thoughts about the ontological relation between cinematic displays and works, the latter tentatively defined as a display of expressive or artistic agency.
“I Want It to Look Natural”: Development and Validation of the FACE-Q Aesthetics Natural Module
Authors: Klassen Anne F , Cano Stefan , Mansouri Jasmine , Poulsen Lotte , Rae Charlene , Kaur Manraj , Dayan Steven , Tsangaris Elena , Armstrong Kathleen , Klok Jennifer , Santosa Katherine , Pusic Andrea
Published: January 2024

Background

The concept of “natural” after a facial aesthetic treatment represents an understudied area. We added scales to FACE-Q Aesthetics to provide a means to measure this concept from the patient's perspective.

Objectives

The objective of this study was to develop and validate the FACE-Q Aesthetic Natural module.

Methods

Concept elicitation interviews with people having minimally invasive treatments were conducted to explore the natural concept and develop scales. Patient and expert input refined scale content. An online sample (ie, Prolific) of people who had a facial aesthetic treatment was analyzed with Rasch measurement theory to examine psychometric properties. A test-retest reliability study was performed, and construct validity was examined.

Results

Interviews with 26 people were conducted. Three scales were developed and refined with input from 12 experts, 11 patients, and 184 online survey participants. Data from 1358 online participants provided evidence of scale reliability and validity. Reliability was high with person separation index, Cronbach alpha, and intraclass correlation coefficient values without extremes ≥0.82. Tests of construct validity confirmed that the scales functioned as hypothesized. Higher scores on the Expectations scale were associated with how important it was to have a natural look and movement after treatment. In addition, higher scores on the Natural Appearance and Natural Outcome scales correlated with better scores on other FACE-Q Aesthetics scales, and were associated with the face looking and feeling natural and with overall satisfaction with facial appearance.

Conclusions

Many people seeking facial aesthetic treatments want to look natural after treatment. These new FACE-Q Aesthetics scales provide a means to measure the concept of natural from the patient's perspective.

Level of Evidence: 3
ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model
Authors: Lee Jin Seok , Karthikeyan Dhuvarakesh , Fini Misha , Vincent Benjamin G , Rubinsteyn Alex
Published: January 2024

The enzyme-linked immunosorbent spot (ELISpot) assay is a powerful in vitro immunoassay that enables cost-effective quantification of antigen-specific T-cell reactivity. It is used widely in the context of cancer and infectious diseases to validate the immunogenicity of predicted epitopes. While technological advances have kept pace with the demand for increased throughput, efforts to increase scale are bottlenecked by current assay design and deconvolution methods, which have remained largely unchanged. Current methods for designing pooled ELISpot experiments offer limited flexibility of assay parameters, lack support for high-throughput scenarios and do not consider peptide identity during pool assignment. We introduce the ACE Configurator for ELISpot (ACE) to address these gaps. ACE generates optimized peptide-pool assignments from highly customizable user inputs and handles the deconvolution of positive peptides using assay readouts. In this study, we present a novel sequence-aware pooling strategy, powered by a fine-tuned ESM-2 model that groups immunologically similar peptides, reducing the number of false positives and subsequent confirmatory assays compared to existing combinatorial approaches. To validate ACE’s performance on real-world datasets, we conducted a comprehensive benchmark study, contextualizing design choices with their impact on prediction quality. Our results demonstrate ACE’s capacity to further increase precision of identified immunogenic peptides, directly optimizing experimental efficiency. ACE is freely available as an executable with a graphical user interface and command-line interfaces at https://github.com/pirl-unc/ace.
Evolution in Islands: contrasting morph frequencies in damselfly populations of the Balearic Islands
Authors: Cordero-Rivera Adolfo , Rivas-Torres Anais , Sánchez-Guillén Rosa Ana
Published: January 2024

Colour polymorphism is an example of visible phenotypic variability that is often associated with ecological factors and may produce local adaptations. Small populations, particularly in islands, offer opportunities for evolutionary novelties, and are therefore of particular interest to the study of polymorphisms. Here we study the dynamics of female colour morphs in the damselfly Ischnura elegans in the Balearic Islands. We found that insular populations are small, show low density, low mating activity, and low androchrome frequency. Our surveys suggest that male harassment is a powerful force in the dynamics of this female-limited polymorphism, because high male densities result in lower presence of mature females around the water, where copulation takes place. Non-male-like (infuscans) females have higher mating frequency. Androchromes were rare (15%) in all populations, but the frequency of the two non-male like females (infuscans and aurantiaca) was reversed between islands, despite their geographical proximity. We found a possible novel morph, suggesting that insular conditions allow innovations. Fitness differences between the two non-male-like females of I. elegans are still understudied, because most previous research has concentrated on the maintenance of androchromes, and are therefore a priority for future research.
The biological basis for using optical signals to track evergreen needleleaf photosynthesis
Authors: Pierrat Zoe Amie , Magney Troy S , Cheng Rui , Maguire Andrew J , Wong Christopher Y S , Nehemy Magali F , Rao Mukund , Nelson Sara E , Williams Anneka F , Grosvenor Jeremy A Hoyne , Smith Kenneth R , Reblin Jaret S , Stutz Jochen , Richardson Andrew D , Logan Barry A , Bowling David R
Published: January 2024

Evergreen needleleaf forests (ENFs) play a sizable role in the global carbon cycle, but the biological and physical controls on ENF carbon cycle feedback loops are poorly understood and difficult to measure. To address this challenge, a growing appreciation for the stress physiology of photosynthesis has inspired emerging techniques designed to detect ENF photosynthetic activity with optical signals. This Overview summarizes how fundamental plant biological and biophysical processes control the fate of photons from leaf to globe, ultimately enabling remote estimates of ENF photosynthesis. We demonstrate this using data across four ENF sites spanning a broad range of environmental conditions and link leaf- and stand-scale observations of photosynthesis (i.e., needle biochemistry and flux towers) with tower- and satellite-based remote sensing. The multidisciplinary nature of this work can serve as a model for the coordination and integration of observations made at multiple scales.
Targeted Lung Health Check: breast related incidental findings—imaging appearances and lessons learned
Authors: Matthews Suzanne , Kyi Moe , Nasimudeen Abdul , Marusic Ante , Johns Christopher S , Page Jason
Published: January 2024

Objective

The introduction of Targeted Lung Health Checks (TLHC) to screen for lung cancer has highlighted that incidental findings are common and require management strategies. This study analyses retrospectively, incidentally detected breast lesions reported as part of the TLHC referred to the Breast Cancer clinicians.

Methods

All participants with incidental breast nodules referred to the Breast Cancer team in the first year of screening were reviewed.

Results

Fifty-two participants (48 female; 92.3%) were referred to the Breast Multidisciplinary Team Meeting for assessment of 43 breast nodules, 8 breast asymmetry/dense breasts, and 2 likely breast related metastatic disease. One participant declined breast team referral. For the 42 breast nodules investigated, the final diagnoses were 5 breast carcinomas, 10 normal breast tissue, and 27 benign nodules. One male patient was diagnosed with breast carcinoma. The 29 breast nodules classified as smooth and well defined were all benign. No malignancy was demonstrated in the group with asymmetric or dense breast tissue. Metastatic breast carcinoma was confirmed in two participants. Twenty-six out of thirty-seven (54%) females had prior breast screening mammograms precluding further investigation.

Conclusion

Incidental breast nodules are common on THLC scans. Smooth, sharply defined breast nodules are likely to be benign but low-dose CT is poor at accurately assessing breast nodules. Agreed breast referral pathways prior to starting the Lung Cancer Screening programme are recommended. Access to screening mammograms can reduce referrals to the Breast clinic.

Advances in knowledge

Lessons learned from TLHC pilot studies can be useful to sites commencing national TLHC programme.
Foreign Policy as the Continuation of Domestic Politics by Other Means: Pathways and Patterns of Populist Politicization
Authors: Cadier David
Published: January 2024

This article argues that populism in power translates into a greater tendency to politicize foreign policy, in the sense of defining and articulating foreign policy preferences in opposition to political predecessors, using foreign policy as an instrument and ground to battle political opponents, and over-prioritizing domestic incentives and considerations over external ones. Paradoxically, compared to other classical determinants of foreign policy, how populism relates to domestic political competition has received scant attention. Yet, populist actors’ strategies in dealing with political opposition are at the same time distinctive and consequential. This article advances a typological theoretical framework shedding light on the pathways, patterns, and implications of populist politicization, which it illustrates empirically with reference to the case of Poland.
Dietary Patterns and Risk of Inflammatory Bowel Disease: A Systematic Review of Observational Studies
Authors: Khademi Zainab , Pourreza Sanaz , Amjadifar Anis , Torkizadeh Mohammadsadegh , Amirkhizi Farshad
Published: January 2024

Background

The incidence of inflammatory bowel disease (IBD) is increasing worldwide. Dietary patterns may be associated with odds of this disease. Although previous reviews have attempted to summarize the evidence in this field, the growing body of investigations prompted us to conduct an updated comprehensive systematic review.

Methods

We used the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines to evaluate the association between dietary patterns before disease onset and the risk of IBD. PubMed, SCOPUS, and Web of Science were searched using structured keywords up to November 20, 2023.

Results

Twenty-four publications (13 case-control, 1 nested case-control, and 10 cohort studies) were included in this review. The sample size of these studies ranged from 181 to 482 887 subjects. The findings were inconsistent across the included studies, showing inverse, direct, or no association between different dietary patterns and the risk of IBD.

Conclusions

This review provides comprehensive data on the link between dietary patterns prior to IBD diagnosis and risk of this condition. The explicit finding of present review is the extent gap in our knowledge in this field. Therefore, large-scale, high-quality studies are warranted to improve our understanding of the relationship between dietary patterns and IBD risk.
Regulation of innate immune and inflammatory responses by supersulfides
Authors: Tsutsuki Hiroyasu , Zhang Tianli , Akaike Takaaki , Sawa Tomohiro
Published: January 2024

Innate immunity plays an important role in host defense against microbial infections. It also participates in activation of acquired immunity through cytokine production and antigen presentation. Pattern recognition receptors such as Toll-like receptors and nucleotide oligomerization domain-like receptors sense invading pathogens and associated tissue injury, after which inflammatory mediators such as pro-inflammatory cytokines and nitric oxide are induced. Supersulfides are molecular species possessing catenated sulfur atoms such as persulfide and polysulfide moieties. They have recently been recognized as important regulators in cellular redox homeostasis by acting as potent antioxidants and nucleophiles. In addition, recent studies suggested that supersulfides are critically involved in the regulation of innate immune and inflammatory responses. In this review, we summarize current knowledge of the chemistry and biology of supersulfides, with particular attention to their roles in regulation of innate immune, and inflammatory responses. Studies with animal models of infection and inflammation demonstrated the potent anti-inflammatory functions of supersulfides such as blocking pro-inflammatory signaling cascades, reducing oxidative stresses, and inhibiting replication of microbial pathogens including severe acute respiratory syndrome coronavirus 2. Precise understanding of how supersulfides regulate innate immune responses is the necessary requirement for developing supersulfide-based diagnostic as well as therapeutic strategies against inflammatory disorders.
Pathomolecular epidemiology, antimicrobial resistance, and virulence genes of Streptococcus dysgalactiae subsp. equisimilis isolates from slaughtered pigs in India
Authors: Patel Sagar M , Sahoo Monalisa , Thakor Jigarji Chaturji , Murali Dinesh , Kumar Pradeep , Singh Rajendra , Singh Karam Pal , Saikumar G , Jana Chandrakanta , Patel Shailesh Kumar , Mote Akash B , Karthikeyan Ravichandran , Vandre Rajesh Kumar , Biswal Jitendra Kumar , Sahoo Nihar Ranjan
Published: January 2024

Aims

We aimed to investigate the prevalence, pathology, and characterization of Streptococcus dysgalactiae subsp. equisimilis (SDSE) in slaughtered pigs of India.

Methods and results

We collected 1254 morbid tissues (lungs—627 and spleen—627) and 627 heart-blood from 627 slaughtered pigs. The bacterial isolation, antibiogram, virulence gene profiling, and mouse pathogenicity testing were performed for the detection and characterization of SDSE. A total of 177 isolates (heart-blood—160 and tissues—17) were recovered from 627 slaughtered pigs with higher isolation rate in heart-blood (25.51%). The prevalence of SDSE was 11% in morbid tissues by polymerase chain reaction. Majority of isolates showed higher detection of streptolysin O, followed by streptokinase and extracellular phospholipase A virulence genes with higher degree of resistance to azithromycin, clindamycin, erythromycin, and penicillin antibiotics. Mouse pathogenicity testing confirmed virulence based on histopathological lesions and re-isolation of SDSE.

Conclusions

Our findings highlight the high prevalence of SDSE in slaughtered pigs. The presence of virulence genes and mouse pathogenicity testing confirm their pathogenic potential.
Effects of bacterial direct-fed microbial mixtures offered to beef cattle consuming finishing diets on intake, nutrient digestibility, feeding behavior, and ruminal kinetics/fermentation profile
Authors: Silva Kaliu G Scaranto , Sarturi Jhones O , Johnson Bradley J , Woerner Dale R , Lopez Alejandra M , Rodrigues Barbara M , Nardi Kaue T , Rush Camron J
Published: January 2024

Effects of bacterial direct-fed microbial (DFM) mixtures on intake, nutrient digestibility, feeding behavior, ruminal fermentation profile, and ruminal degradation kinetics of beef steers were evaluated. Crossbred Angus ruminally cannulated steers (n = 6; body weight [BW] = 520 ± 30 kg) were used in a duplicated 3 × 3 Latin square design and offered a steam-flaked corn-based finisher diet to ad libitum intake for 3, 28-d periods. Treatments were 1) Control (no DFM, lactose carrier only); 2) Treat-A (Lactobacillus animalis, Propionibacterium freudenreichii, Bacillus subtilis, and Bacillus licheniformis), at 1:1:1:3 ratio, respectively; totaling 6 × 109 CFU (50 mg)/animal-daily minimum; and 3) Treat-B, the same DFM combination, but doses at 1:1:3:1 ratio. Bacterial counts were ~30% greater than the minimum expected. Data were analyzed using the GLIMMIX procedure of SAS with the model including the fixed effect of treatment and the random effects of square, period, and animal (square). For repeated measure variables, the fixed effects of treatment, time, and their interaction, and the random effects of square, period, animal (square), and animal (treatment) were used. Preplanned contrasts comparing Control × Treat-A or Treat-B were performed. Intake and major feeding behavior variables were not affected (P ≥ 0.17) by treatments. Steers offered Treat-A had an increased (P = 0.04) ADF digestibility compared with Control. Steers offered Treat-A experienced daily 300 min less (P = 0.04) time under ruminal pH 5.6, a greater (P = 0.04) ruminal pH average and NH3–N concentration (P = 0.05) and tended (P = 0.06) to have a lower ruminal temperature compared to Control. Ruminal VFA was not affected (P ≥ 0.38) by treatments. Steers offered Treat-A increased (P = 0.02) and tended (P = 0.08) to increase the ruminal effective degradable NDF and ADF fractions of the diet-substrate, respectively. When the forage-substrate (low quality) was incubated, steers offered Treat-A tended (P = 0.09) to increase the effective degradable hemicellulose fraction compared to Control. In this experiment, the bacterial combinations did not affect intake and feeding behavior, while the combination with a greater proportion of B. licheniformis (Treat-A) elicited an improved core-fiber digestibility and a healthier ruminal pH pattern, in which the ruminal environment showed to be more prone to induce the effective degradability of fiber fractions, while also releasing more NH3–N.
Social Distancing or Socially Dividing? A Greater Proportion of Vulnerable Patients Admitted to a Metropolitan Burn Center During the COVID-19 Pandemic
Authors: Choe Deborah , Won Paul , Stanton Eloise , Abu-Ghazaleh Joshua , Collier Zachary , Panhassi Daniel , Yenikomshian Haig A , Gillenwater Justin
Published: January 2024

Due to stay-at-home mandates and social distancing, we hypothesized the coronavirus disease 2019 global pandemic altered the epidemiology of burn injuries that presented to a single-institution, metropolitan burn center. A retrospective review of adult and pediatric patients admitted to the center during a 3-year period: 3/20/19-3/19/20 (pre-pandemic year), 3/20/20-3/19/21 (pandemic year 1), and 3/20/21-3/19/22 (pandemic year 2). Variables included patient demographics, burn injury, and hospitalization characteristics. A greater proportion of males compared to females were admitted during the pre-pandemic year with a significant increase in this difference during pandemic year 1 (P < .05). There was a significant increase in the proportion of undomiciled patients admitted between the pre-pandemic year and pandemic year 2 (P < .01). There were significant increases in the proportion of admitted patients who were uninsured, had a history of mental illness and/or substance abuse between pandemic years 1 and 2 (P < .001, P < .05, P < .01) and between the pre-pandemic year and pandemic year 2 (P < .001, P < .01, P < .001). There were significant differences in deepest burn depth and burn etiology between individual years. The proportion of patients with burns treated purely non-operatively significantly increased during pandemic year 1 (P < .05). Greater changes in the demographics of patients with burns admitted after the onset of the pandemic were reported compared to the characteristics and management of their burn injuries. Overall, this study demonstrated that a greater proportion of vulnerable patients were admitted during the pandemic, providing a better understanding of existing health disparities and the differential impact of the pandemic on lower socioeconomic populations.
Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera
Authors: Blackmon Heath , Jonika Michelle M , Alfieri James M , Fardoun Leen , Demuth Jeffery P
Published: January 2024

Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (Ne) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant mutations by genetic drift is greater. Thus, it is possible that ecological and phenotypic transitions that modulate Ne facilitate the fixation of chromosome changes, increasing the rate of karyotype evolution. We synthesize all available chromosome number data in Coleoptera and estimate the impact of traits expected to change Ne on the rate of karyotype evolution in the family Carabidae and 12 disparate clades from across Coleoptera. Our analysis indicates that in Carabidae, wingless clades have faster rates of chromosome number increase. Additionally, our analysis indicates clades exhibiting multiple traits expected to reduce Ne, including strict inbreeding, oligophagy, winglessness, and island endemism, have high rates of karyotype evolution. Our results suggest that chromosome number changes are likely fixed by genetic drift despite an initial fitness cost and that chromosomal speciation models may be important to consider in clades with very small Ne.
Decreased percentages of plasmacytoid dendritic cells predict survival in critically ill patients
Authors: Steinacher Eva , Lenz Max , Krychtiuk Konstantin A , Hengstenberg Christian , Huber Kurt , Wojta Johann , Heinz Gottfried , Niessner Alexander , Speidl Walter S , Koller Lorenz
Published: January 2024

Critically ill patients admitted to intensive care units (ICUs) experience a broad variety of life-threatening conditions. Irrespective of the initial cause of hospitalization, many experience systemic immune dysregulation. Dendritic cells (DCs) are the most potent antigen-presenting cells and play a pivotal role in regulating the immune response by linking the innate to the adaptive immune system. The aim of this study was to analyze whether DCs or their respective subsets are associated with 30-d mortality in an unselected patient cohort admitted to a medical ICU with a cardiovascular focus. A total of 231 patients were included in this single-center prospective observational study. Blood was drawn at admission and after 72 h. Subsequently, flow cytometry was utilized for the analysis of DCs and their respective subsets. In the total cohort, low percentages of DCs were significantly associated with sepsis, respiratory failure, and septic shock. In particular, a significantly lower percentage of circulating plasmacytoid DCs (pDCs) was found to be a strong and independent predictor of 30-d mortality after adjustment for demographic and clinical variables with an hazard ratio of 4.2 (95% confidence interval: 1.3–13.3, P = 0.015). Additionally, low percentages of pDCs were correlated with additional markers of inflammation and organ dysfunction. In conclusion, we observed low percentages of DCs in patients admitted to an ICU experiencing sepsis, respiratory failure, and cardiogenic shock, suggesting their depletion as a contributing mechanism for the development of immune paralysis. In our cohort, pDCs were identified as the most robust subset to predict 30-d mortality.
Colorectal cancer screening test exposure patterns in US adults 45 to 49 years of age, 2019-2021
Authors: Star Jessica , Siegel Rebecca L , Minihan Adair K , Smith Robert A , Jemal Ahmedin , Bandi Priti
Published: January 2024

Several organizations now recommend that individuals at average risk for colorectal cancer (CRC) begin screening at 45 rather than 50 years of age. We present contemporary estimates of CRC screening in newly eligible adults aged 45 to 49 years between 2019 and 2021. Nationally representative prevalence estimates and population number screened were estimated based on the National Health Interview Survey. A logistic regression model assessed CRC screening prevalence differences by survey year and sociodemographic characteristics. In 2021, 19.7%—that is, fewer than 4 million of the eligible 19 million adults aged 45 to 49 years—were up-to-date on CRC screening. Screening was lowest in those who were uninsured (7.6%), had less than a high school diploma (15.4%), and Asian (13.1%). Additionally, fecal occult blood test and/or fecal immunochemical testing was underused, with only 2.4% (<460 000 people) reporting being up-to-date with screening using this modality in 2021. CRC screening in eligible young adults remains low. Concerted efforts to improve screening are warranted, particularly in underserved populations.
Policy evaluation for temporal and/or spatial dependent experiments
Authors: Luo Shikai , Yang Ying , Shi Chengchun , Yao Fang , Ye Jieping , Zhu Hongtu
Published: January 2024

The aim of this article is to establish a causal link between the policies implemented by technology companies and the outcomes they yield within intricate temporal and/or spatial dependent experiments. We propose a novel temporal/spatio-temporal Varying Coefficient Decision Process model, capable of effectively capturing the evolving treatment effects in situations characterized by temporal and/or spatial dependence. Our methodology encompasses the decomposition of the average treatment effect into the direct effect (DE) and the indirect effect (IE). We subsequently devise comprehensive procedures for estimating and making inferences about both DE and IE. Additionally, we provide a rigorous analysis of the statistical properties of these procedures, such as asymptotic power. To substantiate the effectiveness of our approach, we carry out extensive simulations and real data analyses.
Sigmoid colon pseudotumor of actinomycosis: a rare case
Authors: Lesmana Andy , Wirdhani Vika , Perangin Angin Lenti B R , Muzakky Muhamad I , Hayon Stefi G V , Sholihah Mentari M , Hanif Muhammad I
Published: January 2024

Actinomycosis is a chronic suppurative infection caused by gram-positive bacteria, Actinomyces, which commonly colonize the oral cavity, urogenital tract and gastrointestinal tract. It causes opportunistic infection where the mucosal barrier is compromised and is often misdiagnosed as malignancy. We report a case of a 58-year-old female with severe abdominal pain and a palpable tender mass in the left lower quadrant. Computed tomography scan with contrast showed thickening of the transverse, descending to sigmoid colon wall and intense contrast enhancement resembling colitis with mesenteritis. At laparotomy, we found an adherent mass involving sigmoid colon with adjacent small bowel and peritoneum. We decided to perform adhesiolysis and Hartmann procedure. The culture result was negative, whereas the biopsy of sigmoid colon revealed characteristic sulfur granules of actinomycosis colony. Intravenous antibiotic combination of ceftazidime and metronidazole was administered for 14 days followed by complete resolution of symptoms. Histopathological and bacteriological examinations are keys to diagnose actinomycosis. Patients require long-term antibiotic therapy, but surgery is often required because preoperative diagnosis is difficult.

Main novel aspects?
Conjugate Multimode Heat Transfer Analysis of Cryogenic EXLO Manipulation
Authors: Beggs Kyle W , Kassab Alain J , Colletta Michael , Yu Yue , Kourkoutis Lena F , Darwish Ahmed A , Giannuzzi Lucille A
Published: January 2024

In this study, a conjugate radiation/conduction multimode heat transfer analysis of cryogenic focused ion beam (FIB) milling steps necessary for producing ex situ lift out specimens under cryogenic conditions (cryo-EXLO) is performed. Using finite volume for transient heat conduction and enclosure theory for radiation heat transfer, the analysis shows that as long as the specimen is attached or touching the FIB side wall trenches, the specimen will remain vitreous indefinitely, while actively cooled at liquid nitrogen (LN2) temperatures. To simulate the time needed to perform a transfer step to move the bulk sample containing the FIB-thinned specimen from the cryo-FIB to the cryo-EXLO cryostat, the LN2 temperature active cooling is turned off after steady-state conditions are reached and the specimen is monitored over time until the critical devitrification temperature is reached. Under these conditions, the sample will remain vitreous for >3 min, which is more than enough time needed to perform the cryo-transfer step from the FIB to the cryostat, which takes only ∼10 s. Cryo-transmission electron microscopy images of a manipulated cryo-EXLO yeast specimen prepared with cryo-FIB corroborates the heat transfer analysis.
Revisiting the membership, multiplicity, and age of the Beta Pictoris Moving Group in the Gaia era
Authors: Lee Rena A , Gaidos Eric , van Saders Jennifer , Feiden Gregory A , Gagné Jonathan
Published: January 2024

Determining the precise ages of young (tens to a few hundred Myr) kinematic (‘moving’) groups is important for placing star, protoplanetary disc, and planet observations on an evolutionary timeline. The nearby ∼25 Myr-old β Pictoris Moving Group (BPMG) is an important benchmark for studying stars and planetary systems at the end of the primordial disc phase. Gaia DR3 astrometry and photometry, combined with ground-based observations and more sophisticated stellar models, permit a systematic re-evaluation of BPMG membership and age. We combined Gaia astrometry with previously published radial velocities to evaluate moving group membership in a Bayesian framework. To minimize the effect of unresolved stellar multiplicity on age estimates, we identified and excluded multistar systems using Gaia astrometry, ground-based adaptive optics imaging, and multi-epoch radial velocities, as well as literature identifications. We estimated age using isochrone and lithium-depletion-boundary fitting with models that account for the effect of magnetic activity and spots on young, rapidly rotating stars. We find that age estimates are highly model-dependent; Dartmouth magnetic models with ages of 23 ± 8 and 33$^{+9}_{-11}$ Myr provide best fits to the lithium depletion boundary and Gaia MG versus BP–RP colour–magnitude diagram, respectively, whereas a Dartmouth standard model with an age of 11$^{+4}_{-3}$ Myr provides a best fit to the 2-Micron All-Sky Survey-Gaia$M_{K_S}$ versus BP–RP colour–magnitude diagram.
Assessment of the three-test genetic toxicology battery for groundwater metabolites
Authors: Fowler Paul , Bearzatto Alessandra , Beevers Carol , Booth Ewan D , Donner E Maria , Gan Lin , Hartmann Kerstin , Meurer Krista , Schutte Maaike E , Settivari Raja S
Published: January 2024

The two-test in vitro battery for genotoxicity testing (Ames and micronucleus) has in the majority of cases replaced the three-test battery (as two-test plus mammalian cell gene mutation assay) for the routine testing of chemicals, pharmaceuticals, cosmetics, and agrochemical metabolites originating from food and feed as well as from water treatment. The guidance for testing agrochemical groundwater metabolites, however, still relies on the three-test battery. Data collated in this study from 18 plant protection and related materials highlights the disparity between the often negative Ames and in vitro chromosome aberration data and frequently positive in vitro mammalian cell gene mutation assays. Sixteen of the 18 collated materials with complete datasets were Ames negative, and overall had negative outcomes in in vitro chromosome damage tests (weight of evidence from multiple tests). Mammalian cell gene mutation assays (HPRT and/or mouse lymphoma assay (MLA)) were positive in at least one test for every material with this data. Where both MLA and HPRT tests were performed on the same material, the HPRT seemed to give fewer positive responses. In vivo follow-up tests included combinations of comet assays, unscheduled DNA synthesis, and transgenic rodent gene mutation assays, all gave negative outcomes. The inclusion of mammalian cell gene mutation assays in a three-test battery for groundwater metabolites is therefore not justified and leads to unnecessary in vivo follow-up testing.
Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome
Authors: Li Shijun , Liu Bing , Tan Min , Juillard Franceline , Szymula Agnieszka , Álvarez Ángel L , Van Sciver Nicholas , George Athira , Ramachandran Akshaya , Raina Komal , Tumuluri Vinayak Sadasivam , Costa Catarina N , Simas J Pedro , Kaye Kenneth M
Published: January 2024

To establish lifelong, latent infection, herpesviruses circularize their linear, double-stranded, DNA genomes through an unknown mechanism. Kaposi's sarcoma (KS) herpesvirus (KSHV), a gamma herpesvirus, is tightly linked with KS, primary effusion lymphoma, and multicentric Castleman's disease. KSHV persists in latently infected cells as a multi-copy, extrachromosomal episome. Here, we show the KSHV genome rapidly circularizes following infection, and viral protein expression is unnecessary for this process. The DNA damage response (DDR) kinases, ATM and DNA-PKcs, each exert roles, and absence of both severely compromises circularization and latency. These deficiencies were rescued by expression of ATM and DNA-PKcs, but not catalytically inactive mutants. In contrast, γH2AX did not function in KSHV circularization. The linear viral genomic ends resemble a DNA double strand break, and non-homologous DNA end joining (NHEJ) and homologous recombination (HR) reporters indicate both NHEJ and HR contribute to KSHV circularization. Last, we show, similar to KSHV, ATM and DNA-PKcs have roles in circularization of the alpha herpesvirus, herpes simplex virus-1 (HSV-1), while γH2AX does not. Therefore, the DDR mediates KSHV and HSV-1 circularization. This strategy may serve as a general herpesvirus mechanism to initiate latency, and its disruption may provide new opportunities for prevention of herpesvirus disease.
Intein-based thermoregulated meganucleases for containment of genetic material
Authors: Foo Gary W , Leichthammer Christopher D , Saita Ibrahim M , Lukas Nicholas D , Batko Izabela Z , Heinrichs David E , Edgell David R
Published: January 2024

Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18°C and not at higher temperatures. We constructed an orthogonal set of temperature-sensitive meganucleases (TSMs) by inserting the yeast VMA1 L212P temperature-sensitive intein into the coding regions of LAGLIDADG homing endonucleases. We showed that the TSMs eliminated plasmids carrying the cognate TSM target site from laboratory strains of Escherichia coli at the permissive 18°C but not at higher restrictive temperatures. Plasmid elimination is dependent on both TSM endonuclease activity and intein splicing. TSMs eliminated plasmids from E. coli Nissle 1917 after passage through the mouse gut when fecal resuspensions were incubated at 18°C but not at 37°C. Collectively, our data demonstrates the potential of thermoregulated meganucleases as a means of restricting engineered plasmids and probiotics to the mammalian gut.
CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions
Authors: Schubach Max , Maass Thorben , Nazaretyan Lusiné , Röner Sebastian , Kircher Martin
Published: January 2024

Machine Learning-based scoring and classification of genetic variants aids the assessment of clinical findings and is employed to prioritize variants in diverse genetic studies and analyses. Combined Annotation-Dependent Depletion (CADD) is one of the first methods for the genome-wide prioritization of variants across different molecular functions and has been continuously developed and improved since its original publication. Here, we present our most recent release, CADD v1.7. We explored and integrated new annotation features, among them state-of-the-art protein language model scores (Meta ESM-1v), regulatory variant effect predictions (from sequence-based convolutional neural networks) and sequence conservation scores (Zoonomia). We evaluated the new version on data sets derived from ClinVar, ExAC/gnomAD and 1000 Genomes variants. For coding effects, we tested CADD on 31 Deep Mutational Scanning (DMS) data sets from ProteinGym and, for regulatory effect prediction, we used saturation mutagenesis reporter assay data of promoter and enhancer sequences. The inclusion of new features further improved the overall performance of CADD. As with previous releases, all data sets, genome-wide CADD v1.7 scores, scripts for on-site scoring and an easy-to-use webserver are readily provided via https://cadd.bihealth.org/ or https://cadd.gs.washington.edu/ to the community.