bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling memory B cell responses in a lymphoid organ-chip to evaluate mRNA vaccine boosting
Authors: Jeger-Madiot Raphaël , Planas Delphine , Staropoli Isabelle , Debarnot Hippolyte , Kervevan Jérôme , Mary Héloïse , Collina Camilla , Fonseca Barbara F. , Robinot Rémy , Gellenoncourt Stacy , Schwartz Olivier , Ewart Lorna , Bscheider Michael , Gobaa Samy , Chakrabarti Lisa A.
Published: September 2024

Predicting the immunogenicity of candidate vaccines in humans remains a challenge. To address this issue, we developed a lymphoid organ-chip (LO chip) model based on a microfluidic chip seeded with human PBMC at high density within a 3D collagen matrix. Perfusion of the SARS-CoV-2 spike protein mimicked a vaccine boost by inducing a massive amplification of spike-specific memory B cells, plasmablast differentiation, and spike-specific antibody secretion. Features of lymphoid tissue, including the formation of activated CD4+ T cell/B cell clusters and the emigration of matured plasmablasts, were recapitulated in the LO chip. Importantly, myeloid cells were competent at capturing and expressing mRNA vectored by lipid nanoparticles, enabling the assessment of responses to mRNA vaccines. Comparison of on-chip responses to Wuhan monovalent and Wuhan/Omicron bivalent mRNA vaccine boosts showed equivalent induction of Omicron neutralizing antibodies, pointing at immune imprinting as reported in vivo. The LO chip thus represents a versatile platform suited to the preclinical evaluation of vaccine-boosting strategies.
Magnetotransport and angle-resolved photoemission spectroscopy of MnSb12Te19: a new member of MnSb

2
n

Te

3
n
+
1

family
Authors: Mudgal Mohit , Meena Priyanka , Tiwari Vishnu Kumar , Yenugonda Venkateswara , Malik Vivek Kumar , Buck Jens , Rossnagel Kai , Mahatha Sanjoy Kr , Nayak Jayita
Published: September 2024

The quest for intrinsically ferromagnetic topological materials is a focal point in the study of topological phases of matter, as intrinsic ferromagnetism plays a vital role in realizing exotic properties such as the anomalous Hall effect (AHE) in quasi-two-dimensional materials, and this stands out as one of the most pressing concerns within the field. Here, we investigate a novel higher order member of the MnSb

2
n

Te

3
n
+
1

family, MnSb12Te19, for the first time combining magnetotransport and angle-resolved photoemission spectroscopy (ARPES) measurements. Our magnetic susceptibility experiments identify ferromagnetic transitions at temperature Tc
= 18.7 K, consistent with our heat capacity measurements (T = 18.8 K). The AHE is observed for the field along the c-axis below Tc
. Our study of Shubinikov-de-Haas oscillations provides evidence for Dirac fermions with π Berry phase. Our comprehensive investigation reveals that MnSb12Te19 exhibits a FM ground state along with AHE, and hole-dominated transport properties consistent with ARPES measurements.
Influence of vacuum thermal annealing and air exposure on the performance of single-layer MoS2 devices
Authors: Bastante Pablo , Pucher Thomas , Castellanos-Gomez Andres
Published: September 2024

Two-dimensional semiconducting materials such as MoS2 have gained significant attention for potential applications in electronic components due to their reduced dimensionality and exceptional electrical and optoelectronic properties. However, when reporting the performance of such 2D-based devices, one needs to consider the effect of the environment in which the characterization is carried out. Air exposure has a non-negligible impact on the electronic performance and vacuum thermal annealing is an established method to decrease the effects of adsorbates. Nevertheless, when measurements are performed in ambient conditions these effects arise again. In this work, we study the changes in the electrical and optoelectronic properties of single-layer MoS2-based devices at air exposure after thermal annealing treatment. Measurements are carried out in an in-situ vacuum thermal annealing system, enabling the recording of electrical performance degradation over time. Moreover, this work shows how hexagonal boron nitride (hBN) capping improves device performance, both in vacuum and after venting, as well as stability, by decreasing the degradation speed by around six times. The results suggest that vacuum thermal annealing and hBN capping are methods to mitigate the effects of air environment on these devices.
Data-driven rapid 4D cone-beam CT reconstruction for new generation linacs
Authors: Gardner Mark , Dillon Owen , Byrne Hilary , Keall Paul , O’Brien Ricky
Published: September 2024

Objective. Newer generation linear accelerators (Linacs) allow 20 s cone-beam CT (CBCT) acquisition which reduces radiation therapy treatment time. However, the current clinical application of these rapid scans is only 3DCBCT. In this paper we propose a novel data-driven rapid 4DCBCT reconstruction method for new generation linacs. Approach. This method relies on estimating the magnitude of the diaphragm motion from an initial 3D reconstruction. This estimated motion is used to linearly approximate a deformation vector field (DVF) for each respiration phase. These DVFs are then used for motion compensated Feldkamp–Davis–Kress (MCFDK) reconstructions. This method, named MCFDK Data Driven (MCFDK-DD), was compared to a MCFDK reconstruction using a prior motion model (MCFDK-Prior), a 3D-FDK reconstruction, and a conventional acquisition (4 mins) conventional reconstruction 4DCBCT (4D-FDK). The data used in this paper were derived from 4DCT volumes from 12 patients from The Cancer Imaging Archives. Image quality was quantified using RMSE of line plots centred on the tumour, tissue interface width (TIW), the mean square error (MSE) and structural similarity index measurement (SSIM). Main Results. The tumour line plots in the Superior-Inferior direction showed reduced RMSE for the MCFDK-DD compared to the 3D-FDK method, indicating the MCFDK-DD method provided a more accurate tumour location. Similarly, the TIW values from the MCFDK-DD reconstructions (median 8.6 mm) were significantly reduced for the MCFDK-DD method compared to the 3D-FDK reconstructions (median 14.8 mm, (p < 0.001). The MCFDK-DD, MCFDK-Prior and 3D-FDK had median MSE values of

1.08
×

10

−
6

m

m

−
1

,

1.11
×

10

−
6

m

m

−
1

and

1.17
×

10

−
6

m

m

−
1

respectively. The corresponding median SSIM values were 0.93, 0.92 and 0.92 respectively indicating the MCFDK-DD had good agreement with the conventional 4D-FDK reconstructions. Significance. These results demonstrate the feasibility of creating accurate data-driven 4DCBCT images for rapid scans on new generation linacs. These findings could lead to increased clinical usage of 4D information on newer generation linacs.
Deep learning–based statistical robustness evaluation of intensity-modulated proton therapy for head and neck cancer
Authors: Liang Danfu , Vazquez Ivan , Gronberg Mary P , Zhang Xiaodong , Zhu X Ronald , Frank Steven J , Court Laurence E , Martel Mary K , Yang Ming
Published: September 2024

Objective. Previous methods for robustness evaluation rely on dose calculation for a number of uncertainty scenarios, which either fails to provide statistical meaning when the number is too small (e.g., ∼8) or becomes unfeasible in daily clinical practice when the number is sufficiently large (e.g., >100). Our proposed deep learning (DL)-based method addressed this issue by avoiding the intermediate dose calculation step and instead directly predicting the percentile dose distribution from the nominal dose distribution using a DL model. In this study, we sought to validate this DL-based statistical robustness evaluation method for efficient and accurate robustness quantification in head and neck (H&N) intensity-modulated proton therapy with diverse beam configurations and multifield optimization. Approach. A dense, dilated 3D U-net was trained to predict the 5th and 95th percentile dose distributions of uncertainty scenarios using the nominal dose and planning CT images. The data set comprised proton therapy plans for 582 H&N cancer patients. Ground truth percentile values were estimated for each patient through 600 dose recalculations, representing randomly sampled uncertainty scenarios. The comprehensive comparisons of different models were conducted for H&N cancer patients, considering those with and without a beam mask and diverse beam configurations, including varying beam angles, couch angles, and beam numbers. The performance of our model trained based on a mixture of patients with H&N and prostate cancer was also assessed in contrast with models trained based on data specific for patients with cancer at either site. Results. The DL-based model’s predictions of percentile dose distributions exhibited excellent agreement with the ground truth dose distributions. The average gamma index with 2 mm/2%, consistently exceeded 97% for both 5th and 95th percentile dose volumes. Mean dose-volume histogram error analysis revealed that predictions from the combined training set yielded mean errors and standard deviations that were generally similar to those in the specific patient training data sets. Significance. Our proposed DL-based method for evaluation of the robustness of proton therapy plans provides precise, rapid predictions of percentile dose for a given confidence level regardless of the beam arrangement and cancer site. This versatility positions our model as a valuable tool for evaluating the robustness of proton therapy across various cancer sites.
Bipartite OTOC in open quantum systems: information scrambling and irreversibility
Authors: Bose Baibhab , Tiwari Devvrat , Banerjee Subhashish
Published: September 2024

The field of information scrambling has seen significant growth over the last decade, where the out-of-time-ordered correlator (OTOC) has emerged as a prominent tool to probe it. In this work, we use bipartite OTOC, a particular form of OTOC, to study information scrambling in the atom–field interaction models and the model of the Ising spin chain interacting with a tilted magnetic field. This is done considering the effects of open quantum systems. A relationship between information scrambling, using bipartite OTOC, and irreversibility, using entropy production, is probed under unitary dynamics. The equivalence of bipartite OTOC with operator entanglement is explicitly shown for the Ising model.
Fast and robust production of quantum superposition states by the fractional shortcut to adiabaticity
Authors: Li Guan-Qiang , Guo Hao , Zhang Yu-Qi , Yang Bo , Peng Ping
Published: September 2024

The fractional shortcut to adiabaticity (f-STA) for the production of quantum superposition states is proposed firstly via a three-level system with a Λ-type linkage pattern and a four-level system with a tripod structure. The fast and robust production of the coherent superposition states is studied by comparing the populations for the f-STA and the fractional stimulated Raman adiabatic passage (f-STIRAP). The states with equal proportions can be produced by fixing the controllable parameters of the driving pulses at the final moment of the whole process. The effects of the pulse intensity and the time delay of the pulses on the production process are discussed by monitoring the populations on all of the quantum states. In particular, the spontaneous emission arising from the intermediate state is investigated by the quantum master equation. The result reveals that the f-STA exhibits superior advantages over the f-STIRAP in producing the superposition states.
Study of singly anti-charmed pentaquark production in b-factory*
Authors: Hu 胡 Xiao-Hui 晓会 , Xing 邢 Ye 晔
Published: September 2024

The b-factories, such as BelleII, BarBar, and LHCb, emphasize the increasing importance of exotic hadron research. In this paper, we discuss the possible production of singly anti-charmed pentaquark states

from B mesons in a b-factory under

(3) symmetry analysis. Discussions of both possibilities have been driven by the hypothesis that the pentaquark state considered in this work, known as the lowest lying state

, could be bound or unbound. We find the golden channels for the production of the pentaquark ground states, such as

. We further estimate the branching ratios for the production of the ground states

from B meson decays. Thus, multiple channels are available for experiments, which may remove certain obstacles to the discovery of new pentaquark states.
Comprehensive constraints on fermionic dark matter-quark tensor interactions in direct detection experiments*
Authors: Liang 梁 Jin-Han 锦汉 , Liao 廖 Yi 益 , Ma 马 Xiao-Dong 小东 , Wang 王 Hao-Lin 昊琳
Published: September 2024

Effective field theory (EFT) provides a model-independent framework for interpreting the results of dark matter (DM) direct detection experiments. In this study, we demonstrate that the two fermionic DM-quark tensor operators

and

can contribute to the DM electric and magnetic dipole moments via nonperturbative QCD effects, in addition to the well-studied contact DM-nucleon operators. We then investigate the constraints on these two operators by considering both the contact and dipole contributions using the XENON1T nuclear recoil and Migdal effect data. We also recast other existing bounds on the DM dipole operators, derived from electron and nuclear recoil measurements in various direct detection experiments, as constraints on the two tensor operators. For

, our results significantly extend the reach of constraints on the DM-quark tensor operators to masses as low as

, with the bound exceeding that obtained by the Migdal effect with only contact interactions by approximately an order of magnitude. In particular, for the operator

with DM mass

, the latest PandaX constraint on the DM electric dipole moment puts more stringent bounds than the previous direct detection limit. We also briefly discuss the constraints obtained from experiments other than direct detection.
Next-to-next-to-leading order QCD
EW corrections to Z-boson pair production at electron-positron colliders*
Authors: Li 黎 Zhe 哲 , Zhang 张 Ren-You 仁友 , Li 李 Shu-Xiang 书香 , Wang 王 Xiao-Feng 晓峰 , Li 李 Pan-Feng 攀峰 , Jiang 蒋 Yi 一 , Han 韩 Liang 良 , Wang 王 Qing-hai 清海
Published: September 2024

We present a comprehensive analytic calculation of the next-to-next-to-leading order

corrections to Z-boson pair production at electron-positron colliders. The two-loop master integrals essential to this calculation are evaluated using the differential equation method. In this paper, we detail the formulation and solution of the canonical differential equations for the two-loop three-point master integrals with two on-shell Z-boson external legs and a massive internal quark in the loops. These canonical master integrals are systematically expanded as a Taylor series in the dimensional regulator,

, up to the order of

, with coefficients expressed in terms of Goncharov polylogarithms up to weight four. Upon applying our analytic expressions of these master integrals to the phenomenological analysis of Z-pair production, we observe that the

corrections manifest at a level of approximately one percent when compared to the leading-order predictions, underscoring their significance for comparisons with future high-precision experimental data.
Conversion of a piston–cylinder dimensional dataset to the effective area of a mechanical pressure generator
Authors: Egan Patrick F , Stanfield Eric S , Stoup John R , Meyer Christopher W
Published: September 2024

Recent developments in diameter metrology at NIST have improved the dimensional characterization of piston–cylinder assemblies (PCAs) to unprecedented precision. For the newest generation of PCAs, the standard uncertainty in the measurement of the outer diameter is

12
 
nm

, while uncertainty in the measurement of the inner diameter is

14
 
nm

. With a high-accuracy dimensional dataset in hand, the task of determining the pressure generated by a specific PCA is reduced to converting the diameter (and straightness and roundness) to an effective area (and distortion coefficient). The details on how this was performed for the artifact PCA2062 are described. PCA2062 was dimensioned in 2017 and 2020; the area repeated within

0.2
×

10

−
6

⋅

A
0

. The calculation produced estimates of fall rate and rotation decay that agreed with experimental observations within 12 %. The fall rate is proportional to the square of the gap width; therefore, the agreement between calculation and measurement validates the dimensional estimate of the gap width within

(
36
±
42
)
 
nm

, where the

42
 
nm

standard uncertainty is governed by the present state of flow theory. The piston gage model is buttressed by three comparison tests against a laser barometer, which support a view that PCA2062 is linear and reproducible within

0.2
 
μ

Pa

 

Pa

−
1

. Finally, an estimate of uncertainty in the effective area of a dimensioned artifact is provided: as expected, the diameter measurement is the main culprit, but there are open questions regarding the flow model that preclude an accurate evaluation of the distortion coefficient. For the

530
 
kPa

operating range of PCA2062, distortion is not a significant problem, but the effect would be dominant in assemblies operating at

1
 
MPa

and above.
Neutron and gamma shielding capabilities of Li and Na borate glasses
Authors: Duru F. , Hughes D. , Christiansen M.M. , Caplice T. , Funk H. , Welch R.S. , Rusch M. , Simko S. , Keninger N.J. , Nimmagadda J.K. , Samant S.S. , Akgun U.
Published: September 2024

Glass is an increasingly popular candidate material for
radiation shielding in a variety of settings, including spacecraft
design and medical safety. This study investigates the gamma and
neutron shielding properties of various glass samples produced at
Coe College, including several sodium and lithium doped borate and
silicate glasses. The results are obtained through a series of test
beam trials at a nuclear reactor, which were further supported by
simulation in GATE, a Geant4-based tool. Evaluation tests included
simulation of photon energies from 0.01 MeV to 20 MeV and neutron
energies from 2 to 12 MeV. All candidate materials were poor
shields for gamma radiation, hovering around 10% prevention, the
glass samples with the highest packing fractions yielding the best
results. According to the mass attenuation coefficients (MAC), half
value layer (HVL), and tenth value layer (TVL) calculated in this
study, 0.6Na2O*SiO2 and 0.2Li2O*B2O3
provide the best shielding between 0.01–20 MeV of gamma radiation
among the glasses tested in this study. Neutron shielding tests were
more promising, with the borate glasses yielding the best
results. Among all glasses, 0.4Li2O*B2O3 provided the
best results blocking about 85% of the incident neutron radiation
and 0.6Na2O*SiO2 yielded the worst shielding, blocking
less than 20 % of the neutrons. Simulations show that the three
xLi2O*B2O3 glasses have the highest fast neutron
removal cross section (Σ
R
), indicating their higher level
of protection against fast neutrons, consistent with the test beam
results.
Financing diversified water strategies for megacities: the case of Mexico City and rainwater harvesting
Authors: Portal Carús Mariana , Paltán Homero
Published: September 2024

Megacities are increasingly confronted with water supply challenges, requiring innovative and diversified management strategies to ensure sustainability. This study examines Mexico City’s Cosecha de Lluvia program, a government initiative promoting residential rainwater harvesting (RWH). This case study offers valuable lessons for other megacities facing similar water security issues. The study particularly explores result-based financing (RBF) as a promising strategy to strengthen Mexico City’s RWH sector. Despite its potential, research on RBF for water supply diversification remains limited, especially from the perspective of practitioners. To address this gap, the study employs a systems thinking approach supported by qualitative methods, including a literature review and interviews. Thematic networks analysis revealed that RBF could enhance Cosecha de Lluvia by improving monitoring and results measurement, facilitating information exchange, and increasing transparency—key factors for successful water supply diversification. While these identified benefits do not address all of Cosecha de Lluvia’s challenges and RBF could have implementation challenges, there is a clear opportunity for this financial mechanism to enhance programs like the one studied and have a positive impact on several of its elements. As part of the RBF suitability assessment, three different funding sources were evaluated—public, private, and philanthropic—to determine their effectiveness in overcoming Cosecha de Lluvia’s challenges. The findings suggest that no single source of finance markedly influences the program’s effectiveness alone. Instead, a blended financing approach that integrates all three sources is recommended as a strategy to explore further for implementing RBF in water supply diversification efforts. Overall, the study highlights the necessity of diversifying water supply to build climate resilience in megacities. While programs like Cosecha de Lluvia are crucial, significant room for improvement exists. RBF offers a promising mechanism to enhance such initiatives, and its potential merits further exploration.
Agricultural tile drains increase the susceptibility of streams to longer and more intense streamflow droughts
Authors: Adelsperger Seth R , Ficklin Darren L , Robeson Scott M , Zimmer Margaret A , Hammond John C , Hall Damon M , Gannon J P
Published: September 2024

Streamflow droughts are receiving increased attention worldwide due to their impact on the environment and economy. One region of concern is the Midwestern United States, whose agricultural productivity depends on subsurface pipes known as tile drains to improve trafficability and soil conditions for crop growth. Tile drains accomplish this by rapidly transporting surplus soil moisture and shallow groundwater from fields, resulting in reduced watershed storage. However, no work has previously examined the connection between tile drainage and streamflow drought. Here, we pose the question: does the extent of watershed-level tile drainage lead to an increased susceptibly and magnitude of streamflow droughts? To answer this, we use daily streamflow data for 122 watersheds throughout the Midwestern United States to quantify streamflow drought duration, frequency, and intensity. Using spatial multiple regression models, we find that agricultural tile drainage generates statistically significant (p < 0.05) increases in streamflow drought duration and intensity while significantly reducing drought frequency. The magnitude of the effect of tile drainage on streamflow drought characteristics is similar to that of water table depth and precipitation seasonality, both of which are known to influence streamflow droughts. Furthermore, projected changes in regional precipitation characteristics will likely drive the installation of additional tile drainage. We find that for each 10% increase in tile-drained watershed area, streamflow drought duration and intensity increase by 0.03 d and 12%, respectively, while frequency decreases by 0.10 events/year. Such increases in tile drainage may lead to more severe streamflow droughts and have a detrimental effect on the socio-environmental usage of streams throughout the Midwest.
The future of Xenes beyond graphene: challenges and perspective
Authors: Grazianetti Carlo , Molle Alessandro , Martella Christian
Published: September 2024

After more than ten years since the silicene discovery, many Xenes, the class of elemental graphene-like lattices, have now enriched the two-dimensional periodic table of elements. Here, we provide a perspective on the future of the Xenes by briefly summarizing their properties and devices reported thus far. Two main challenges are expected to focus the scientists’ attention to bring the Xenes to the next level. To step over the current scenario the Xenes need standardization either in the growth or in the fabrication of devices, aiming at the wafer-scale and the reliability and stability, respectively. The benefits arising from these challenges will enable the concept of hybrid Xenes and hybrid Xenes-based devices, that is a combination of different Xenes with new properties and multifunctional Xenes-based devices, respectively, with potential unexpected fascinating properties to continue the journey.
Development of novel Gd-Fe/Ti composites with tunable thermal expansion property
Authors: Xia Feng , Yang Xigang , Yan Yiye , Liang Minxian , Guo Yongchun , Yang Siyu , Ma Zhijun , Wang Chan , Zhang Zhongwei , Zhou Qidi , Liu Jilin
Published: September 2024

Titanium alloys are considered one of the most promising materials. However, their poor thermal expansion property remains a major obstacle to their widespread application. In this study, we explored an innovative design strategy to tune the thermal expansion properties of titanium alloy. Specifically, we used rare earth iron intermetallic compounds (Gd-Fe IMCs) with low coefficient of thermal expansion (CTE) as expansion inhibitors to prepare composites with the required thermal expansion properties via in situ reaction. The morphology and size of Gd-Fe IMCs can be effectively controlled by electromagnetic and ultrasonic fields, resulting in a dense distribution of micro/nano-structured Gd-Fe IMCs and strong interfacial bonding of the composites. This alloy has an excellent CTE of 6.8 × 10−6/K and a high ultimate tensile strength of 921 MPa. The improvement in the physical properties (especially in thermal expansion properties) of titanium alloy can be attributed to the synergistic effect between Gd-Fe IMCs and Ti matrix. This design strategy can also be extended to other titanium alloys as a reference for designing low thermal expansion titanium alloys.
An integrated computer-aided diagnosis BCanD model for detection, segmentation and classification of breast cancer
Authors: Arfi Mehar , Yadav Subhash Chandra , Tripathi Suman Lata
Published: September 2024

A fully integrated Computer-Aided Diagnosis (CAD) system involves the integration of detection, segmentation, and classification, which makes it very useful for medical applications, particularly while dealing with the detection of breast mass and its classification into malignant and benign. The carried-out research work is intended to propose a Breast Cancer Detection (BCanD) model that is an integrated CAD system, where the system is capable enough for mass detection, its segmentation, and for the classification using mammograms. The proposed integrated system utilizes deep learning based YOLO model to detect the abnormality (mass) in the mammogram, where U-net is used for segmentation of the mass, as it has the capability to produce pixel level segmentation map, and at last stage that is the classification stage deep CNN is used for the classification. The proposed system is evaluated on open-source MIAS database. For the performance evaluation of the proposed BCanD, a three-fold cross-validation test was utilized. The mass detection accuracy of the BCanD is 98.99%, MCC is 97.96%, and F1-score is 98.87%. The model is evaluated with and without automated mass segmentation to study the impact of segmentation on the suggested CAD system. The best results was observed with the segmentation with the overall accuracy of 94.20%, F1-score (Dice) of 93.60%, MCC of 88.33%, and Jaccard of 88.08%. The proposed BCanD model surpasses the latest existing deep learning-based methodologies like fuzzy classifier, CNNI-BCC etc Hence, the proposed CAD system can be implemented and used by radiologists for all the stages from detection to diagnosis of breast mass.
Robust anomaly detection for particle physics using multi-background representation learning
Authors: Gandrakota Abhijith , Zhang Lily H , Puli Aahlad , Cranmer Kyle , Ngadiuba Jennifer , Ranganath Rajesh , Tran Nhan
Published: September 2024

Anomaly, or out-of-distribution, detection is a promising tool for aiding discoveries of new particles or processes in particle physics. In this work, we identify and address two overlooked opportunities to improve anomaly detection (AD) for high-energy physics. First, rather than train a generative model on the single most dominant background process, we build detection algorithms using representation learning from multiple background types, thus taking advantage of more information to improve estimation of what is relevant for detection. Second, we generalize decorrelation to the multi-background setting, thus directly enforcing a more complete definition of robustness for AD. We demonstrate the benefit of the proposed robust multi-background AD algorithms on a high-dimensional dataset of particle decays at the Large Hadron Collider.
Quality of life, pain and use of analgesic, anxiolytic and antidepressant medication, in people living in care homes
Authors: Collins Jemima T , Irvine Lisa , Logan Pip , Robinson Katie , Sims Erika , Gordon Adam L
Published: September 2024

Background

People living in care homes often have problems with pain, anxiety and depression. Whether being on analgesia, anxiolytics or antidepressants has any bearing on pain severity and quality of life (QoL) in this population, requires further investigation.

Objectives

(i) to examine the relationship between pain, anxiety and depression and medication use in care home residents and (ii) to compare those on medications to treat pain, anxiety and depression, and those who were not, and associations with pain severity and overall QoL.

Methods

This was a secondary analysis of a randomised controlled trial testing a falls prevention intervention in care homes. We recorded pain, anxiety and depression, QoL measurements and prescribed medication use.

Results

In 1589 participants, the mean age was 84.7 years (±9.3 SD), 32.2% were male and 67.3% had a diagnosis of dementia. 54.3% and 53.2% of participants had some level of pain and anxiety or depression respectively, regardless of prescribed medication use. There was a direct association between pain severity and being on any analgesia, opioid analgesia, and antidepressants, but no associations between pain severity and use of paracetamol and anxiolytics. QoL was best for residents with no pain and not on any analgesia, anxiolytics or antidepressants and worst for those with moderate-extreme pain and taking at least two of these classes of medications.

Conclusion

Many care home residents live with pain, anxiety and depression. Addressing residents’ pain may also increase their quality of life, but using medication alone to reach this goal may be inadequate.
Bin2cell reconstructs cells from high resolution Visium HD data
Authors: Polański Krzysztof , Bartolomé-Casado Raquel , Sarropoulos Ioannis , Xu Chuan , England Nick , Jahnsen Frode L , Teichmann Sarah A , Yayon Nadav
Published: September 2024

Visium HD by 10X Genomics is the first commercially available platform capable of capturing full scale transcriptomic data paired with a reference morphology image from archived FFPE blocks at sub-cellular resolution. However, aggregation of capture regions to single cells poses challenges. Bin2cell reconstructs cells from the highest resolution data (2 μm bins) by leveraging morphology image segmentation and gene expression information. It is compatible with established Python single cell and spatial transcriptomics software, and operates efficiently in a matter of minutes without requiring a GPU. We demonstrate improvements in downstream analysis when using the reconstructed cells over default 8 μm bins on mouse brain and human colorectal cancer data.

Availability and implementation

Bin2cell is available at https://github.com/Teichlab/bin2cell, along with documentation and usage examples, and can be installed from pip. Probe design functionality is available at https://github.com/Teichlab/gene2probe.
Effect of radiotherapy on long-term quality of life in recurrence-free rectal cancer survivors (LaTE study): nationwide inverse probability of treatment-weighted registry-based cohort study and survey
Authors: Malik Yasir G , Benth Jūratė Šaltytė , Hamre Hanne M , Færden Arne E , Schultz Johannes K
Published: September 2024

Background

Radiotherapy reduces local recurrence in locally advanced rectal cancer, but may cause harm in patients who do not experience recurrence. The aim was to investigate the impact of radiotherapy on long-term quality of life after curative treatment for rectal cancer, i.e. in patients without a recurrence during the follow-up.

Methods

All patients operated on for rectal cancer in Norway under 75 years of age between 30 September 2007 and 1 October 2020 were identified using the Cancer Registry of Norway. Exclusion criteria were distant metastasis, recurrence and dementia. The primary outcome measure was the Gastrointestinal Quality of Life Index. Secondary outcome measures included the 36-item Short Form Survey. Inverse probability weights based on a multiple logistic regression model were used to balance prechosen covariates between the radiotherapy and no radiotherapy groups when assessing differences in outcomes.

Results

Of 5014 invited patients, 2142 (43%) eligible patients answered the questionnaires. Of these 762 (36%) were treated with neoadjuvant radiotherapy plus surgery and 1380 (64%) with surgery alone. The mean follow-up time was 6.4 and 7.4 years respectively. After propensity score matching, the Gastrointestinal Quality of Life Index differed significantly between irradiated and non-irradiated patients ((mean(s.d.), mean score 103.8(19.4) versus 110.8(19.6) respectively, mean difference: −6.96 (95% c.i. −8.72 to −5.19); P < 0.001). Among patients without a stoma the mean difference was −8.1 points, whereas it was −5.7 for patients with a stoma. The radiotherapy group also scored significantly lower in 7 of 8 36-item Short Form Survey domains compared with the surgery alone group.

Conclusion

Long-term quality of life was significantly lower in patients without a recurrence during the follow-up who received radiotherapy compared with patients who did not. These findings warrant a critical re-evaluation of the use of radiotherapy both in traditional neoadjuvant treatment and in modern organ-preserving treatment regimens.
Arctic cooperation with Russia: at what price?
Authors: Paukkunen Samu , Black James
Published: September 2024

After February 2022, it seemed that a breakdown of political, economic and scientific cooperation in the Arctic would be one of the many examples of collateral damage from Russia's war of aggression in Ukraine. Two years on from the invasion, however, the Arctic 7 (the United States, Canada and the Nordic countries) have renewed their engagement with Russia on polar issues. The Arctic Council has emerged as the exceptional case of a regional body in which Russia and NATO nations continue to collaborate, albeit at a more limited level through the working groups. This article examines the dilemmas facing the Arctic 7 as they seek to balance a values-based policy and strong stance against Russia in solidarity with Ukraine, with a desire to ensure the continuing survival of the Arctic Council and its primacy in regional governance. We argue that Russia has sought to weaponize the Council—withholding vital climate data and threatening to bring China further into regional politics—as part of a wider strategy of coercive diplomacy and hybrid threats in the Arctic. The Arctic 7 should recognize that they ultimately stand to lose more from giving into Russian tactics than from freezing Moscow out of the Arctic Council while the war in Ukraine continues.
Adaptive modeling and analysis of distributed photovoltaic absorptive capacity based on improved simulated annealing algorithm
Authors: Rong Shimin , Wang Cong , Dong Yawei , Shi Biwei , Ma Huiqing
Published: September 2024

In order to improve the adaptive modeling and operational stability of distributed photovoltaic absorption capacity, a distributed photovoltaic absorption capacity adaptive modeling method based on improved simulated annealing algorithm is proposed. This method constructs a level source network load storage model for distributed photovoltaic consumption and establishes a control parameter analysis model through consumption scheduling and active/reactive power coordination control methods to analyze the dynamic limit load characteristics of the distribution network. Using an improved simulated annealing algorithm to analyze the constraint characteristics of distributed photovoltaic consumption patterns, in order to achieve adaptive modeling of the absorption capacity of distributed photovoltaic systems based on actual needs and grid transmission limitations. The test results show that this method has good dynamic ultimate bearing capacity and optimization performance, achieving the optimal economic and safety solution for distributed photovoltaic absorption.
Tangle Free Permutations and the Putman–Wieland Property of Random Covers
Authors: Klukowski Adam , Marković Vladimir
Published: September 2024

Let $\Sigma ^{p}_{g}$ denote a surface of genus $g$ and with $p$ punctures. Our main result is that the fraction of degree $n$ covers of $\Sigma ^{p}_{g}$ that have the Putman–Wieland property tends to $1$ as $n\to \infty $. In addition, we show that the monodromy of a random cover of $\Sigma ^{p}_{g}$ is asymptotically almost surely tangle free.
Sampling poorly studied lineages improves resolution in mitogenome-based phylogenies of leafhoppers (Hemiptera: Cicadellidae)
Authors: Liang Zonglei , Zhang Junru , Dietrich Christopher H , Du Yimin , Dai Wu
Published: September 2024

Cicadellidae (leafhoppers) may be the most diverse and abundant insect herbivores in terrestrial ecosystems worldwide, with more than 23,000 described species in 20 extant subfamilies. Although prior studies have supported the monophyly of most recognized subfamilies, relationships among these groups remain inconsistently resolved and previous molecular phylogenies have failed to support the monophyly of a few subfamilies. To help address this deficiency, we combined 24 new complete mitogenomes representing 6 previously unsequenced subfamilies and 13 tribes with previously available data to create a dataset of 79 cicadellid taxa representing 16 subfamilies for phylogenetic analysis. The new analyses confirm that leafhopper mitochondrial genomes are highly conservative in overall structure, with only a few rare rearrangements of tRNAs. All phylogenetic analyses consistently supported the monophyly of previously recognized cicadellid tribes for which more than 1 representative was included and all of the included subfamilies were also consistently recovered as monophyletic with the exception of Aphrodinae and Eurymelinae. Bayesian inference and Maximum Likelihood analyses with site-homogeneous models are only slightly affected by nucleotide compositional heterogeneity and yield more stable phylogenetic relationships of family-group taxa than analyses with a heterogeneous-site mixture model using PhyloBayes. Molecular divergence time estimates indicate that the main lineages of Cicadellidae, most corresponding to recognized subfamilies, diverged during the Cretaceous period (93–121 Mya).
The lonely algorithm problem: the relationship between algorithmic personalization and social connectedness on TikTok
Authors: Taylor Samuel Hardman , Chen Y Anthony
Published: September 2024

Many major social media companies have claimed that their social feed algorithms were designed to promote relational well-being and enhance social connection. This project tested part of these claims by investigating if algorithmic personalization predicted social connectedness on TikTok, where connecting with identity-relevant media content is prioritized over interpersonal interaction. Drawing from the algorithm responsiveness process, we identified perceived algorithm responsiveness (PAR) and perceived algorithm insensitivity (PAI) as perceptual mechanisms of how algorithmic personalization relates to social connectedness. In two preregistered studies, an online survey and a 2-week daily diary survey, results suggested that the TikTok For You algorithm curating frequent and positively valenced identity-relevant content was associated with higher PAR and less PAI. In turn, higher levels of PAR predicted more social connectedness, but PAI did not. These findings highlight the sociotechnical dynamics of algorithms, suggesting human–algorithm interaction predicted social connectedness not only an algorithm’s code.
Civil Society’s Endgame
Authors: Sutherland Kirsty
Published: September 2024

This article seeks to examine the contributions of civil society to modern peoples’ tribunals, the extent to which adherence to ‘legal’ processes serves the victims of serious human rights violations, and how these efforts have interacted with ‘formal’ legal spaces. While recognizing that every situation responds to and raises distinct and complex issues and needs, a look at the history, contexts, and development of civil society-led accountability efforts illuminates their contributions to stemming the impunity gulf of today’s ‘formal’ accountability architecture. The article specifically examines the Uyghur Tribunal and the Democratic People’s Republic of Korea Inquiries as examples of recent civil society-led tribunals, considering the modalities and contexts of their establishment, the evidential contributions of civil society, the legal attitudes assumed by the tribunals, and — to the extent possible — their impact on ‘formal’ accountability spaces. In so doing, it aims to highlight identifiable features of these recent ‘informal’ tribunals to encourage a discussion of the opportunities and challenges that might be encountered in future civil society-led accountability efforts. Notwithstanding the structured gaze of legal categorizations and its modulation of victims’ voices and witnesses’ experiences, this article suggests that close adherence to formal legal standards and procedures may serve to optimize the opportunity to secure, test, and enhance the evidential value of the material arduously collected by civil society, and thus best serve the interests of victims and survivors of violations of international law.
Comparative dissection of transcriptional landscapes of human iPSC-NK differentiation and NK cell development
Authors: Zhang Li , Weiskittel Taylor M , Zhu Yuqing , Xue Dixuan , Zhang Hailing , Shen Yuxuan , Yu Hua , Li Jingyu , Hou Linxiao , Guo Hongshan , Dai Zhijun , Li Hu , Zhang Jin
Published: September 2024

Clinical and preclinical research has demonstrated that iPSC-derived NK (iNK) cells have a high therapeutic potential, yet poor understanding of the detailed process of their differentiation in vitro and their counterpart cell development in vivo has hindered therapeutic iNK cell production and engineering. Here we dissect the crucial differentiation of both fetal liver NK cells and iNK cells to enable the rational design of advanced iNK production protocols. We use a comparative analysis of single-cell RNA-seq (scRNA-seq) to pinpoint key factors lacking in the induced setting which we hypothesized would hinder iNK differentiation and/ or functionality. By analyzing key transcription factor regulatory networks, we discovered the importance of TBX21, EOMES, and STAT5A in the differentiation timeline. This analysis provides a blueprint for further engineering new iPSC lines to obtain iNK cells with enhanced functions. We validated this approach by creating a new line of STAT5A-iPSCs which can be differentiated to STAT5A-expressing macrophages with both NK cell and macrophage features such as perforin production, phagocytosis, and anti-tumor functions.
The structural properties of nearby dwarf galaxies in low-density environments – size, surface brightness, and colour gradients
Authors: Lazar I , Kaviraj S , Watkins A E , Martin G , Bichang’a B , Jackson R A
Published: September 2024

We use a complete sample of 211 nearby ($z< 0.08$), dwarf (10$^{8}$ M$_{\odot }$ < $M_{\rm {\star }}$ < 10$^{9.5}$ M$_{\odot }$) galaxies in low-density environments, to study their structural properties: effective radii ($R_{\rm e }$), effective surface brightnesses ($\langle \mu \rangle _{\rm e}$), and colour gradients. We explore these properties as a function of stellar mass and the three principal dwarf morphological types identified in a companion paper – early-type galaxies (ETGs), late-type galaxies (LTGs), and featureless systems. The median $R_{\rm e }$ of LTGs and featureless galaxies are factors of $\sim$2 and $\sim$1.2 larger than the ETGs. While the median $\langle \mu \rangle _{\rm e}$ of the ETGs and LTGs is similar, the featureless class is $\sim$1 mag arcsec$^{-2}$ fainter. Although they have similar median $R_{\rm e }$, the featureless and ETG classes differ significantly in their median $\langle \mu \rangle _{\rm e}$, suggesting that their evolution is different and that the featureless galaxies are not a subset of the ETGs. While massive ETGs typically exhibit negative or flat colour gradients, dwarf ETGs generally show positive colour gradients (bluer centres). The growth of ETGs therefore changes from being ‘outside-in’ to ‘inside-out’ as we move from the dwarf to the massive regime. The colour gradients of dwarf and massive LTGs are, however, similar. Around 46 per cent of dwarf ETGs show prominent, visually identifiable blue cores which extend out to $\sim$1.5$R_{\rm e}$. Finally, compared to their non-interacting counterparts, interacting dwarfs are larger, bluer at all radii and exhibit similar median $\langle \mu \rangle _{\rm e}$, indicating that interactions typically enhance star formation across the entire galaxy.
Most Pleiotropic Effects of Gene Knockouts Are Evolutionarily Transient in Yeasts
Authors: Liu Li , Liu Yao , Min Lulu , Zhou Zhenzhen , He Xingxing , Xie YunHan , Cao Waifang , Deng Shuyun , Lin Xiaoju , He Xionglei , Chen Xiaoshu
Published: September 2024

Pleiotropy, the phenomenon in which a single gene influences multiple traits, is a fundamental concept in genetics. However, the evolutionary mechanisms underlying pleiotropy require further investigation. In this study, we conducted parallel gene knockouts targeting 100 transcription factors in 2 strains of Saccharomyces cerevisiae. We systematically examined and quantified the pleiotropic effects of these knockouts on gene expression levels for each transcription factor. Our results showed that the knockout of a single gene generally affected the expression levels of multiple genes in both strains, indicating various degrees of pleiotropic effects. Strikingly, the pleiotropic effects of the knockouts change rapidly between strains in different genetic backgrounds, and ∼85% of them were nonconserved. Further analysis revealed that the conserved effects tended to be functionally associated with the deleted transcription factors, while the nonconserved effects appeared to be more ad hoc responses. In addition, we measured 184 yeast cell morphological traits in these knockouts and found consistent patterns. In order to investigate the evolutionary processes underlying pleiotropy, we examined the pleiotropic effects of standing genetic variations in a population consisting of ∼1,000 hybrid progenies of the 2 strains. We observed that newly evolved expression quantitative trait loci impacted the expression of a greater number of genes than did old expression quantitative trait loci, suggesting that natural selection is gradually eliminating maladaptive or slightly deleterious pleiotropic responses. Overall, our results show that, although being prevalent for new mutations, the majority of pleiotropic effects observed are evolutionarily transient, which explains how evolution proceeds despite complicated pleiotropic effects.