bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain-dependent transition of the relaxation dynamics in metallic glasses
Authors: Zhu Wenqing , Deng Yao , Liu Junjie , Yan Xin , Wei Xiaoding
Published: February 2024

Non-exponential relaxation is pervasive in glassy systems and intimately related to unique thermodynamic features, such as glass transition and aging; however, the underlying mechanisms remain unclear. The time scale of non-exponential relaxation goes beyond the time limit (nanosecond) of classic molecular dynamics simulation. Thus, the advanced time scaling atomistic approach is necessary to interpret the relaxation mechanisms at the experimental timescale. Here, we adopted autonomous basin climbing (ABC) to evaluate the long-time stress relaxation. At the same time, based on the energy minimization principle, we carried out simulations at continuum levels on the long-time stress relaxation kinetics of Cu–Zr metallic glass over timescales greater than 100 s. Combined with atomistic and continuum models, we demonstrate that a strain-dependent transition from compressed to stretched exponentials would happen, consistent with recent experimental observations on metallic glasses. Further examination of the spatial and temporal correlations of stress and plastic strain reveals two predominant driving forces: the thermal energy gradient governs in the compressed regime and leads to a release of the local internal stress; in the stretched regime, the strain energy gradient rules and causes long-range structural rearrangements. The discovery of the competition between two driving forces advances our understanding of the nature of aging dynamics in disordered solids.
Optimizing the traversal time for gantry trajectories for proton arc therapy treatment plans
Authors: Wase V , Marthin O , Fredriksson A , Finnson A
Published: February 2024

Background. Proton arc therapy (PAT) is an emerging radiation therapy technique where either the gantry or the patient continuously rotates during the irradiation treatment. One of the perceived advantages of PAT is the reduced treatment time, but it is still unclear exactly how long these treatment times will be, given that no machine capable of its delivery is available on the market at the time of writing. Objective. We introduce the algorithm arc trajectory optimization method (ATOM), which aims to determine an efficient velocity profile for the gantry for rapid delivery of a given proton arc treatment plan. This algorithm could be used to minimize the delivery time of a proton arc plan without changing the plan or updating the machine. Approach. ATOM computes the trajectory with the shortest delivery time while ensuring there is enough time to deliver all spots in each energy layer and switch energy between layers. The feasibility of the dynamic gantry movement was assured by enforcing maximum and minimum limits for velocity, acceleration, and jerk. This was achieved by discretizing the gantry velocity and combining the A* algorithm with the open-source motion generation library Ruckig. The algorithm was tested on a synthetic data set as well as a liver case, a prostate case and a head and neck case. Main results. Arc trajectories for plans with 360 energy layers were calculated in under a second using 256 discrete velocities. The delivery time of the liver case, the prostate case and the head and neck case were 284 s, 288 s and 309 s respectively, for 180 energy layers. Significance. ATOM is an open-source C++ library with a Python interface that rapidly generates velocity profiles, making it a highly efficient tool for determining proton arc delivery times, which could be integrated into the treatment planning process.
Coupling speckle noise suppression with image classification for deep-learning-aided ultrasound diagnosis
Authors: Wang Ruixin , Liu Xiaohui , Tan Guoping
Published: February 2024

Objective. During deep-learning-aided (DL-aided) ultrasound (US) diagnosis, US image classification is a foundational task. Due to the existence of serious speckle noise in US images, the performance of DL models may be degraded. Pre-denoising US images before their use in DL models is usually a logical choice. However, our investigation suggests that pre-speckle-denoising is not consistently advantageous. Furthermore, due to the decoupling of speckle denoising from the subsequent DL classification, investing intensive time in parameter tuning is inevitable to attain the optimal denoising parameters for various datasets and DL models. Pre-denoising will also add extra complexity to the classification task and make it no longer end-to-end. Approach. In this work, we propose a multi-scale high-frequency-based feature augmentation (MSHFFA) module that couples feature augmentation and speckle noise suppression with specific DL models, preserving an end-to-end fashion. In MSHFFA, the input US image is first decomposed to multi-scale low-frequency and high-frequency components (LFC and HFC) with discrete wavelet transform. Then, multi-scale augmentation maps are obtained by computing the correlation between LFC and HFC. Last, the original DL model features are augmented with multi-scale augmentation maps. Main results. On two public US datasets, all six renowned DL models exhibited enhanced F1-scores compared with their original versions (by 1.31%–8.17% on the POCUS dataset and 0.46%–3.89% on the BLU dataset) after using the MSHFFA module, with only approximately 1% increase in model parameter count. Significance. The proposed MSHFFA has broad applicability and commendable efficiency and thus can be used to enhance the performance of DL-aided US diagnosis. The codes are available at https://github.com/ResonWang/MSHFFA.
The biological effect of the physical energy of plasma
Authors: Li Y , Zhao F , Liu D , Nie L , Lu X
Published: February 2024

Since the publication of the initial paper on atmospheric pressure plasma sterilization by Dr Laroussi in 1996, researchers have contributed to the field with an extensive number of papers on plasma medicine. However, these studies have primarily concentrated on the biological impacts of the chemical reactive components generated by plasma, specifically focusing on the effects of reactive oxygen and nitrogen species. Conversely, when plasma directly interacts with biological organisms, there are additional physical energies involved, such as electric fields, ultraviolet (UV)/vacuum ultraviolet (VUV) radiation, heat, etc., which may also play crucial roles in their interaction. This paper delves into this aspect by using the simplest bactericidal effect as a model for biological effects. Three dielectrics—Al2O3, quartz, and MgF2 glass—are employed to isolate the chemical active components, enabling the examination of the bactericidal effects of the electric field, UV, and VUV, respectively. The findings indicate that the plasma-induced electric field can induce irreversible electroporation, effectively eliminating bacteria at 27 kV cm−1. Notably, at a plasma-induced electric field of 40 kV cm−1, sterilization efficiency experiences a significant enhancement. The bactericidal effects of UV and VUV are closely linked to the choice of the plasma’s working gas. Specifically, when Ar is the working gas, the bactericidal effect of UV surpasses that of using only the plasma-induced electric field by two orders of magnitude, while using He results in only a one-order increase. Despite VUV radiation being considerably weaker than UV, its bactericidal effect remains substantial. In instances where He plasma is utilized, the addition of VUV doubles the bactericidal effect. In short, this paper pioneers the exploration of the biological effects of plasma’s physical energy, providing essential insights for the advancement of plasma medicine.
Drifts effect on the divertor W leakage mechanisms under different dissipative divertor conditions of EAST
Authors: Wang Hui , Xu Guoliang , Ding Rui , Si Hang , Jia Guozhang , Xie Hai , Hai Ran , Wang Zhibin , Zhu Dahuan , Yan Rong , Chen Junling
Published: February 2024

A new drift module has been developed in the DIVIMP code, enabling two-dimensional simulations of tungsten (W) transport in the edge plasma with full drifts included. By using the SOLPS-DIVIMP code package, the impact of drifts on W transport and screening has been investigated for various levels of dissipative divertor conditions and different divertor geometric configurations in EAST. Simulation results reveal that

E
⃗

×

B
⃗

drifts can enhance the W leakage by more than one order of magnitude. Under the favorable Bt
direction, W erosion mainly occurs on the outer divertor target, making the W leakage from the outer divertor region the dominator. A leakage path from the near-scrape-off layer (SOL) region is revealed by the modeling results. In the leakage path, both the ion temperature gradient force and the reversed poloidal

E
⃗

×

B
⃗

drift are pointing upstream. With the radial

E
⃗

×

B
⃗

drift pushing W ions from the well-screened far-SOL region to the near-SOL region, the leakage from the near-SOL region becomes significant. As the divertor condition varies from the low-recycling regime to the deep detachment regime, the decrease of the ion temperature gradient velocity and poloidal

E
⃗

×

B
⃗

drift velocity narrows the width of the near-SOL leakage tunnel and thus enhances W screening. While under the unfavorable Bt
, W erosion and leakage from the inner divertor target matters, the leakage mechanism especially the leakage path from the near-SOL region is similar as the favorable Bt
cases. Furthermore, the effect of different divertor geometries on the W screening has been investigated. The configuration with the outer strike point (OSP) on the horizontal divertor plate is proved to narrow the near-SOL leakage tunnel, and thus the unreversed poloidal

E
⃗

×

B
⃗

drift pointing to the divertor target dominates and helps to enhance the divertor W screening. For the same D
2 puffing rate, the W leakage ability of cases with the OSP on the horizontal target can be more than 10 times weaker than the cases with the OSP on the vertical target, especially when the divertor is detached.
Is deep learning a useful tool for the pure mathematician?
Authors: Williamson Geordie
Published: February 2024

A personal and informal account of what a pure mathematician might expect when using tools from deep learning in their research.
Project NextGen: Developing the Next Generation of COVID-19 Vaccines and Therapeutics to Respond to the Present and Prepare for the Future
Authors: Hofmeyer Kimberly A , Ventura Christy L , Armstrong Kimberly L , Houchens Christopher R , Patel Sandeep , Disbrow Gary L , Johnson Robert A ,   Project NextGen Line of Effort Leads, Bandremer Aaron C , Beigel John H , Belski Timothy T , Donis Ruben O , Jayashankar Lakshmi , Koup Richard A , Kovacs Gerald R , Link Malen A , Martins Karen A , Mason Robin M , Stronsky Sabrina M , Wolfe Daniel N
Published: February 2024

Coronavirus disease 2019 (COVID-19) epidemiology and product landscapes have changed considerably since onset of the pandemic. Safe and effective vaccines and therapeutics are available, but the continual emergence of severe acute respiratory syndrome coronavirus 2 variants introduce limitations in our ability to prevent and treat disease. Project NextGen is a collaboration between the Biomedical Advanced Research and Development Authority, part of the Administration for Strategic Preparedness and Response, and the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, that is leveraging public–private partnerships to address gaps in the nation's COVID-19 vaccine and therapeutic capabilities. Targeted investments will advance promising next-generation candidates through the most difficult phases of clinical development to encourage further private sector interest for later stage development and commercial availability. New commercial vaccines and therapeutics that are more durable and effective across variants will improve our fight against COVID-19 and transform our response to future threats.
Evaluation of the effect of proximal massage and palm fisting in reducing the risk of peripheral venous catheter-related phlebitis: randomized control study
Authors: Tosun Betul , Güngör Serap , Ağkale Esengül , Andı Senem
Published: February 2024

Aims

Peripheral venous catheter (PVC) is a clinical procedure often performed by nurses in hospitals. Phlebitis can be prevented with more nursing care by applying PVC by trained nurses and using preventive methods. The aim of this study was to investigate the effect of proximal massage and palm fisting on the prevention of phlebitis in patients with a PVC.

Methods and results

This randomized controlled study was conducted with patients who were hospitalized in the orthopaedics and traumatology service of a state hospital and had PVC. While the study group (n = 36) received proximal massage and palm fisting on the side with a PVC, the control group (n = 36) received standard care for PVC. The data were collected by using the ‘Patient Demographics and Clinical Information Form’, ‘Peripheral Venous Catheter-Related Phlebitis Risk Scale’, and ‘Visual Infusion Phlebitis Assessment Scale’. There were no statistically significant differences between the groups regarding phlebitis development based on age, sex, chronic disease status, PVC insertion site, devices in the PVC, or fluids administered from the PVC. However, there was a significantly higher risk of PVC-induced phlebitis in patients who received proximal massage and palm fisting at 48 and 96 h, when the severity of phlebitis was evaluated on daily basis.

Conclusion

The study showed promising results, suggesting that proximal massage and palm fisting may be a simple and inexpensive technique to prevent the occurrence of phlebitis in PVC patients.

Registration

ClinicalTrials.gov: NCT05714137
Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp
Authors: Stuij Tamara M , Cleary Daniel F R , Rocha Rui J M , Polónia Ana R M , Silva Davide A M , Louvado Antonio , de Voogd Nicole J , Gomes Newton C M
Published: February 2024

Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
Development, characterization, and evaluation of a simple polymicrobial colony biofilm model for testing of antimicrobial wound dressings
Authors: Robertson Shaun N , Romero Manuel , Fenn Samuel , Kohler Riedi Petra L , Cámara Miguel
Published: February 2024

Chronic wound infections are generally of polymicrobial nature with aerobic and anaerobic bacteria, as well as fungi frequently observed in them. Wound treatment involves a series of steps, including debridement of the wound, flushing, and often the use of multiple wound dressings many of which are antimicrobial. Yet, many wound dressings are tested versus single species of planktonic microbes, which fails to mirror the real-life presence of biofilms.

Aims

Simple biofilm models are the first step to testing of any antimicrobial and wound dressing; therefore, the aim of this study was to develop and validate a simple polymicrobial colony biofilm wound model comprised of Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans on RPMI-1640 agar. The model was then used to evaluate the topical disinfectant chlorohexidine and four commercially available wound dressings using the polymicrobial model. The model used was as a starting point to mimic debridement in clinical care of wounds and the effectiveness of wound dressings evaluated afterwards.

Methods and Results

Planktonic assessment using AATCC100-2004 demonstrated that all antimicrobial wound dressings reduced the planktonic microbial burden below the limit of detection; however, when challenged with polymicrobial colony biofilms, silver wound dressings showed limited effectiveness (1–2 log CFU reductions). In contrast, a single iodine releasing wound dressing showed potent antibiofilm activity reducing all species CFUs below the limit of detection (>6–10 log) depending on the species. A disrupted biofilm model challenge was performed to represent the debridement of a wound and wound silver-based wound dressings were found to be marginally more effective than in whole colony biofilm challenges while the iodine containing wound dressing reduced microbial recovery below the limit of detection.

Conclusions

In this model, silver dressings were ineffective versus the whole colony biofilms but showed some recovery of activity versus the disrupted colony biofilm. The iodine wound dressing reduced the viability of all species below the level of detection. This suggests that mode of action of wound dressing should be considered for the type of biofilm challenge as should the clinical use, e.g. debridement.
One hundred optical emission lines of molecular hydrogen from a low-metallicity photodissociation region
Authors: Henney William J , Valerdi Mabel
Published: February 2024

We report the detection of a rich spectrum of more than one hundred optical emission lines of vibrationally hot molecular hydrogen (H2) from the photodissociation region (PDR) around the mini-starburst cluster NGC 346 in the Small Magellanic Cloud. The lines are concentrated in the spectral range $6000 \, {{\mathring{\rm A}}}$ to $9300 \, {{\mathring{\rm A}}}$ and have observed brightnesses ranging from 0.01 per cent to 0.4 per cent times that of the H β λ4861 hydrogen recombination line. Analysis of the spatial distribution of the H2 lines shows that they originate from a range of depths in the PDR, intermediate between the shallow layers probed by fluorescent lines of neutral nitrogen and oxygen, and the more shielded layers probed by neutral carbon recombination lines. Comparison with other PDRs shows that the relative strength of the H2 lines with respect to the [$\mathrm{C\, \scriptstyle I}$] λ8727 line increases rapidly with decreasing metallicity, being at least 40 times larger in NGC 346 than in the prototypical PDR of the Orion Bar. The internal PDR dust extinction is also found to be anomalously low in NGC 346. A separate result is the discovery of a high-ionization bow shock around the O2 star Walborn 3.
The morphological mix of dwarf galaxies in the nearby Universe
Authors: Lazar I , Kaviraj S , Watkins A E , Martin G , Bichang’a B , Jackson R A
Published: February 2024

We use a complete, unbiased sample of 257 dwarf (10$^{8}\, {\rm M}_{\odot } \lt M_{\rm {\star }} \lt 10^{9.5}\, {\rm M}_{\odot }$) galaxies at z < 0.08, in the COSMOS field, to study the morphological mix of the dwarf population in low-density environments. Visual inspection of extremely deep optical images and their unsharp-masked counterparts reveals three principal dwarf morphological classes. 43 per cent and 45 per cent of dwarfs exhibit the traditional ‘early-type’ (elliptical/S0) and ‘late-type’ (spiral) morphologies, respectively. However, 10 per cent populate a ‘featureless’ class, that lacks both the central light concentration seen in early-types and any spiral structure – this class is missing in the massive-galaxy regime. 14 per cent, 27 per cent, and 19 per cent of early-type, late-type, and featureless dwarfs respectively show evidence for interactions, which drive around 20 per cent of the overall star formation activity in the dwarf population. Compared to their massive counterparts, dwarf early-types show a much lower incidence of interactions, are significantly less concentrated and share similar rest-frame colours as dwarf late-types. This suggests that the formation histories of dwarf and massive early-types are different, with dwarf early-types being shaped less by interactions and more by secular processes. The lack of large groups or clusters in COSMOS at z < 0.08, and the fact that our dwarf morphological classes show similar local density, suggests that featureless dwarfs in low-density environments are created via internal baryonic feedback, rather than by environmental processes. Finally, while interacting dwarfs can be identified using the asymmetry parameter, it is challenging to cleanly separate early and late-type dwarfs using traditional morphological parameters, such as ‘CAS’, M20, and the Gini coefficient (unlike in the massive-galaxy regime).
On the constraints on superconducting cosmic strings from 21-cm cosmology
Authors: Gessey-Jones T , Pochinda S , Bevins H T J , Fialkov A , Handley W J , de Lera Acedo E , Singh S , Barkana R
Published: February 2024

Constraints on the potential properties of superconducting cosmic strings provide an indirect probe of physics beyond the standard model at energies inaccessible to terrestrial particle colliders. In this study, we perform the first joint Bayesian analysis to extract constraints on superconducting cosmic strings from current 21-cm signal measurements while accounting rigorously for the uncertainties in foregrounds and high redshift astrophysics. We include the latest publicly available 21-cm power spectrum upper limits from HERA, 21-cm global signal data from SARAS 3, and the synergistic probe of the unresolved X-ray background in our final analysis. This paper thus constitutes the first attempt to use 21-cm power spectrum data to probe cosmic strings. In contrast to previous works, we find no strong constraints can be placed on superconducting cosmic strings from current 21-cm measurements. This is because of uncertainties in the X-ray emission efficiency of the first galaxies, with X-ray emissivities greater than 3 × 1040 erg s−1 M$_{\odot }^{-1}$ yr able to mask the presence of cosmic strings in the 21-cm signal. We conclude by discussing the prospects for future constraints from definitive 21-cm signal measurements and argue that the recently proposed soft photon heating should be cause for optimism due to its potential to break degeneracies that would have otherwise made the signatures of cosmic strings difficult to distinguish from those of astrophysical origin.
Lower Dorsal Putamen D2/3 Receptor Availability and Amphetamine-Induced Dopamine Release are Related to Poorer Cognitive Function in Recently Abstinent People Who Smoke and Healthy Controls
Authors: Cheung Frances , Calakos Katina C , Gueorguieva Ralitza , Hillmer Ansel T , Cosgrove Kelly P , Zakiniaeiz Yasmin
Published: February 2024

Introduction

In the dopamine system, the mesolimbic pathway, including the dorsal striatum, underlies the reinforcing properties of tobacco smoking, and the mesocortical pathway, including the dorsolateral prefrontal cortex (dlPFC), is critical for cognitive functioning. Dysregulated dopamine signaling has been linked to drug-seeking behaviors and cognitive deficits. The dorsal striatum and dlPFC are structurally and functionally connected and are key regions for cognitive functioning. We recently showed that people who smoke have lower dlPFC dopamine (D2/3R) receptor availability than people who do not, which is related to poorer cognitive function.

Aims and Methods

The goal of this study was to examine the same brain-behavior relationship in the dorsal striatum. Twenty-nine (18 males) recently abstinent people who smoke and 29 sex-matched healthy controls participated in 2 same-day [11C]-(+)-PHNO positron emission tomography scans before and after amphetamine administration to provoke dopamine release. D2/3R availability (binding potential; BPND) and amphetamine-induced dopamine release (%ΔBPND) were calculated. Cognition (verbal learning and memory) was assessed with the CogState computerized battery.

Results

There were no group differences in baseline BPND. People who smoke have a smaller magnitude %ΔBPND in dorsal putamen than healthy controls (p = .022). People who smoke perform worse on immediate (p = .035) and delayed (p = .011) recall than healthy controls. In all people, lower dorsal putamen BPND was associated with worse immediate (p = .006) and delayed recall (p = .049), and lower %ΔBPND was related to worse delayed recall (p = .022).

Conclusions

Lower dorsal putamen D2/3R availability and function are associated with disruptions in cognitive function that may underlie difficulty with resisting smoking.

Implications

This study directly relates dopamine imaging outcomes in the dorsal striatum to cognitive function in recently abstinent people who smoke cigarettes and healthy controls. The current work included a well-characterized subject sample in terms of demographics, smoking characteristics, and a validated neurocognitive test of verbal learning and memory. The findings of this study extend previous literature relating dopamine imaging outcomes to cognition in recently abstinent people who smoke and people who do not smoke, expanding our understanding of brain-behavior relationships.
Artificial intelligence compared with human-derived patient educational materials on cirrhosis
Authors: Pradhan Faruq , Fiedler Alexandra , Samson Kaeli , Olivera-Martinez Marco , Manatsathit Wuttiporn , Peeraphatdit Thoetchai
Published: February 2024

Background:

The study compared the readability, grade level, understandability, actionability, and accuracy of standard patient educational material against artificial intelligence chatbot-derived patient educational material regarding cirrhosis.

Methods:

An identical standardized phrase was used to generate patient educational materials on cirrhosis from 4 large language model-derived chatbots (ChatGPT, DocsGPT, Google Bard, and Bing Chat), and the outputs were compared against a pre-existing human-derived educational material (Epic). Objective scores for readability and grade level were determined using Flesch-Kincaid and Simple Measure of Gobbledygook scoring systems. 14 patients/caregivers and 8 transplant hepatologists were blinded and independently scored the materials on understandability and actionability and indicated whether they believed the material was human or artificial intelligence-generated. Understandability and actionability were determined using the Patient Education Materials Assessment Tool for Printable Materials. Transplant hepatologists also provided medical accuracy scores.

Results:

Most educational materials scored similarly in readability and grade level but were above the desired sixth-grade reading level. All educational materials were deemed understandable by both groups, while only the human-derived educational material (Epic) was considered actionable by both groups. No significant difference in perceived actionability or understandability among the educational materials was identified. Both groups poorly identified which materials were human-derived versus artificial intelligence-derived.

Conclusions:

Chatbot-derived patient educational materials have comparable readability, grade level, understandability, and accuracy to human-derived materials. Readability, grade level, and actionability may be appropriate targets for improvement across educational materials on cirrhosis. Chatbot-derived patient educational materials show promise, and further studies should assess their usefulness in clinical practice.
Sintilimab plus bevacizumab combined with radiotherapy as first-line treatment for hepatocellular carcinoma with portal vein tumor thrombus: A multicenter, single-arm, phase 2 study
Authors: Zhu Meiyan , Liu Zelong , Chen Shuling , Luo Zhenhua , Tu Jianfei , Qiao Liangliang , Wu Jian , Fan Wenzhe , Peng Zhenwei
Published: February 2024

Background and Aims:

Systemic treatments are listed as first-line therapies for HCC with portal vein tumor thrombus (PVTT), resulting in modest efficacy. We aimed to evaluate the efficacy and safety of sintilimab plus bevacizumab combined with radiotherapy in HCC with PVTT and to identify prognostic biomarkers.

Approach and Results:

This open-label, multicenter, single-arm, phase 2 clinical trial was conducted at 3 tertiary hospitals in China. A total of 46 patients with HCC with PVTT were enrolled. All the patients received the first cycle of i.v. sintilimab (200 mg, day 1) plus bevacizumab (15 mg/kg, day 1) within 3 days after enrollment. Radiotherapy (30–50 Gy/10 fractions) was administered after 2 cycles of Sin-Bev. Sin-Bev was disrupted during radiotherapy and resumed 2 weeks after radiotherapy and continued every 3 weeks thereafter until disease progression, unacceptable toxicity, or withdrawal of consent. The primary end point was objective response rate. Patients obtained an objective response rate of 58.7% and a disease control rate of 100%. After a median follow-up time of 26.0 months (95% CI: 24.0–26.0), the median OS was 24.0 months (95% CI: 19.0 to not applicable) and the median progression-free survival was 13.8 months (95% CI: 12.0–21.0), respectively. No unexpected adverse events or treatment-related deaths occurred. Mutations of PCTMD1 were predictive of shorter OS and progression-free survival.

Conclusions:

Sintilimab plus bevacizumab combined with radiotherapy provides favorable treatment response and survival outcomes along with an acceptable safety profile in the first-line setting for patients with HCC with PVTT (ClinicalTrials.gov Identifier: NCT05010434).
Effects of High-Intensity Resistance Versus Aerobic Training in PCOS Women at Risk for Psychological Trauma
Authors: Riaz Huma , Maqsood Mobeena , Afridi Ayesha , Ehsan Sarah , Jan Sadiq
Published: February 2024

Background:

Polycystic ovarian syndrome (PCOS) is a prevalent and complex endocrine disorder that affects women of reproductive age. Its physical manifestations as the change in body image, fertility challenges, menstrual irregularities, and associated chronic health conditions increase their vulnerability to psychological trauma. Negative effects on psychological health significantly impact their quality of life.

Objectives:

The current study aimed to compare the effects of high-intensity resistance versus aerobic training on psychological health and quality of life in women with PCOS.

Study Design:

This was a single-blinded, randomized controlled trial.

Methods:

A randomized controlled trial was conducted from November 22 to April 23 at Riphah Rehabilitation Center, Islamabad, Pakistan. The female university students (n = 60), with an age range of 18 to 30 years, who were not part of any planned physical activity program, were not taking any medication, and were willing to participate in the exercise trial, were recruited. They were randomly allocated into 2 groups: high-intensity resistance (HIRG) and high-intensity aerobic (HIAG) groups. Both groups underwent exercise interventions for a duration of 12 weeks. Clinical and psychological health and quality of life were assessed using validated measures, including the polycystic ovary syndrome questionnaire (PCOS-Q) and the 36-item Short Form Survey (SF-36). Assessments were conducted at baseline, 6th, and 12th weeks. Data analysis was done using SPSS-21.

Results:

The mean age of women in the HIRG (n = 30) versus the HIAG (n = 30) was 22.40 ± 2.4 years versus 20.63 ± 2.1 years. Between-group analysis revealed no significant difference (P > .05) between the groups in terms of postintervention total scores of the PCOS-Q and SF-36 quality of life. However, within-group analysis has shown statistically significant improvement (P < .01) in both outcome measures.

Conclusion:

It is concluded that both high-intensity modes of exercise, resistance, and aerobic training were found to be equally effective interventions for improving psychological health and quality of life in women with PCOS. Individualizing exercise programs to meet individual needs and preferences may aid in maximizing the psychological benefits of each exercise modality. Further investigation into the underlying processes and long-term impact of these therapies in this vulnerable population is required.
Mixing studies for lupus anticoagulant: does it matter how we mix?
Authors: Radišić Biljak Vanja , Tomas Matea , Lapić Ivana
Published: February 2024

Although clear and detailed recommendation regarding the lupus anticoagulant mixing test exist, various sources of NPP are used. We decided to inspect the possible differences in mixing studies depending on the mixing media. Four types of mixing media were prepared for 45 random remnant plasma samples: standard human plasma, control plasma N, previously analyzed patient with normal coagulation values, and home-made normal pool plasma (NPP). Samples were analyzed by using Siemens Dade Actin FSL Activated PTT Reagent on BCS XP analyzer. The median aPTT values of mixing studies with commercial lyophilized NPP, with commercial IQC, as well as with a patient did not differ (26.6, 26.3, and 26.8 s, respectively). Median value of a mixing study with home-made NPP was significantly higher from the rest of the group (27.9 s) (P < 0.05). According to the obtained results, we decided to employ the commercial lyophilized NPP for future lupus anticoagulant mixing studies.
Comparison of Surgical Outcomes of Transoral Versus Open Thyroidectomy for Graves Disease
Authors: Wang Suo-Hsien , Chao Wu-Po , Lo Ta-You , Ng Soh-Ching , Chen Yu-Hsien
Published: February 2024

Introduction:

The transoral endoscopic thyroidectomy vestibular approach (TOETVA) is a safe alternative to thyroidectomy for thyroid goiter and provides the benefit of being scarless. However, the data on the use of TOETVA in patients with Graves disease are limited. This retrospective study compared the outcomes of Graves disease patients who underwent TOETVA versus those who underwent open thyroidectomy (OT).

Materials and Methods:

Patients with Graves disease who received TOETVA or OT for bilateral total thyroidectomy between September 2017 and October 2022 were included. Patient demographics and surgical outcomes, including operation time, blood loss, length of stay, and complications, were compared.

Results:

There were 15 patients in each group. The mean age in the TOETVA group was 35.80±8.13 years, which was significantly younger than that in the OT group, which was 51.53±14.22 years. Females predominated in both groups. The other demographic characteristics were similar in both groups. The operation time and intraoperative blood loss were also comparable. The postoperative stay and complications, including hypoparathyroidism, recurrent laryngeal nerve injury, surgical site infection, postoperative hemorrhage, and recurrence of hyperthyroidism, were not different between the 2 groups. There were 11 patients in the TOETVA group and 10 in the OT group who had thyroglobulin levels <0.1 ng/dL, indicating the completeness of total thyroidectomy in the 2 groups. There was no conversion of TOETVA to an open procedure.

Conclusions:

For carefully selected Graves patients, TOETVA offers a safe, scarless, and feasible alternative to conventional open thyroidectomy.
Effect of Intraperitoneal Instillation of Dexmedetomidine With Local Anesthetics in Laparoscopic Cholecystectomy: A Systematic Review and Meta-analysis of Randomized Trials
Authors: Sun Chenxu , He Zhengguang , Feng Biao , Huang Yaping , Liu Dawei , Sun Zhihua
Published: February 2024

Objective:

Dexmedetomidine (DEX) can strengthen the analgesic effects of local anesthetics (LAs) when used as an adjuvant through intrathecal, perineural, and intraperitoneal routes. Many studies have used intraperitoneal instillation of DEX with LAs in laparoscopic cholecystectomy (LC) to relieve postoperative pain. We performed a systematic review and meta-analysis to synthesize evidence of the efficacy and safety of intraperitoneal instillation of DEX as an adjuvant of LAs in patients undergoing LC.

Methods:

A comprehensive literature search of the MEDLINE, PubMed, EMBASE, and Cochrane Library databases was performed to identify randomized controlled trials in which patients received intraperitoneal instillation of DEX combined with LAs during LC. A meta-analysis and sensitivity analysis of the results were conducted. We also performed a subgroup analysis to investigate the source of heterogeneity. The Egger test was used to check for publication bias.

Results:

Eleven randomized controlled trials involving 890 patients were analyzed. We found that the addition of DEX to LAs significantly decreased pain scores at six postoperative time points (0.5, 1, 2, 4, 12, and 24 h) and significantly prolonged the time to the first analgesic request by patients. In addition, 24-hour postoperative analgesic consumption was decreased in the experimental group, and no significant difference in the incidence of nausea and vomiting was observed.

Conclusion:

Our findings indicate that intraperitoneal instillation of DEX with LAs can reduce postoperative pain and prolong the time to first request analgesia after LC.
Outcomes of Endoscopic Sleeve Gastroplasty Following Laparoscopic Adjustable Gastric Band: A Propensity Score–matched Analysis
Authors: Maselli Daniel B. , Wooley Chase , Lee Daniel , Waseem Areebah , Donnangelo Lauren L. , Secic Michelle , Coan Brian , McGowan Christopher E.
Published: February 2024

Background:

The performance of endoscopic sleeve gastroplasty (ESG) in patients with prior laparoscopic adjustable gastric band (LAGB) has not been characterized.

Materials and Methods:

This is a retrospective propensity score–matched study of ESG after LAGB at 2 centers with expertise in bariatric endoscopy. The primary outcome was total weight loss (TWL) at 12 months. Secondary outcomes included TWL at 3 and 6 months, 12-month excess weight loss (EWL), procedural characteristics, predictors of TWL, and serious adverse events.

Results:

Twenty-six adults (88.5% female, age 50.8 y, BMI 36.5 kg/m2) with prior LAGB (median duration 8 y) underwent ESG at a median of 3 years after LAGB removal. A 2:1 age-matched, sex-matched, and BMI-matched comparator group was created, comprising ESG patients from the same organization and time frame but without prior LAGB. TWL for the LAGB-to-ESG cohort versus the ESG-only cohort was 10.1±5.5% versus 13.0±4.4% at 3 months (P=0.0256), 12.4±7.2% versus 16.0±5.4% at 6 months (P=0.0375), and 12.7±8.2% versus 18.4±6.5% at 12 months (P=0.0149). At 12 months, the LAGB-to-ESG cohort had an EWL of 52.5±50.0%, and 75% achieved TWL ≥10%. There was no association between TWL at 3, 6, or 12 months and the following traits: age or BMI at the time of ESG, patient sex, and time from LAGB removal to ESG. No serious adverse events occurred in either cohort.

Conclusion:

ESG after LAGB facilitates safe and clinically meaningful weight loss but is attenuated compared to primary ESG.
Erysipelothrix amsterdamensis sp. nov., associated with mortalities among endangered seabirds
Authors: Zhong Jiadong , Medvecky Matej , Tornos Jérémy , Clessin Augustin , Le Net Rozenn , Gantelet Hubert , Gamble Amandine , Forde Taya L. , Boulinier Thierry
Published: February 2024

Infectious diseases threaten endangered species, particularly in small isolated populations. Seabird populations on the remote Amsterdam Island in the Indian Ocean have been in decline for the past three decades, with avian cholera caused by Pasteurella multocida proposed as the primary driver. However, Erysipelothrix species have also been sporadically detected from albatrosses on Amsterdam Island and may be contributing to some of the observed mortality. In this study, we genomically characterized 16 Erysipelothrix species isolates obtained from three Indian yellow-nosed albatross (Thalassarche carteri) chick carcasses in 2019. Histological analyses suggest that they died of bacterial septicaemia. Two isolates were sequenced using both Illumina short-read and MinION long-read approaches, which – following hybrid assembly – resulted in closed circular genomes. Mapping of Illumina reads from the remaining isolates to one of these new reference genomes revealed that all 16 isolates were closely related, with a maximum of 13 nucleotide differences distinguishing any pair of isolates. The nucleotide diversity of isolates obtained from the same or different carcasses was similar, suggesting all three chicks were likely infected from a common source. These genomes were compared with a global collection of genomes from Erysipelothrix rhusiopathiae and other species from the same genus. The isolates from albatrosses were phylogenetically distinct, sharing a most recent common ancestor with E. rhusiopathiae. Based on phylogenomic analysis and standard thresholds for average nucleotide identity and digital DNA–DNA hybridization, these isolates represent a novel Erysipelothrix species, for which we propose the name Erysipelothrix amsterdamensis sp. nov. The type strain is A18Y020dT (=CIP 112216T=DSM 115297T). The implications of this bacterium for albatross conservation will require further study.
Developing machine-learning-based amyloid predictors with Cross-Beta DB
Authors: Gonay Valentin , Dunne Michael P. , Caceres-Delpiano Javier , Kajava Andrey V.
Published: February 2024

Due to shifts in environmental conditions, mutations, or interactions with other biomolecules, some proteins that would normally be soluble can undergo aggregation, resulting in the formation of clumps of amyloid fibrils. Understanding of this phenomenon is of paramount importance due not only to its association with various diseases (including Alzheimer’s disease), but also due to increasingly abundant evidence for its functional roles. Numerous studies have demonstrated that the propensity to form amyloids is coded by the amino acid sequence and this finding has paved the way for the development of several computational predictors of amyloidogenicity. The ultimate objective of computational methods is to accurately predict the formation of disease-related and functionally relevant amyloids that occurin vivo. These amyloid fibrils are known to form very specific “cross-β” structures of protein regions longer than about 15 residues. Remarkably, despite the significance of the naturally occurring amyloids, there has been a lack of datasets specifically dedicated to them. Hence, we built Cross-Beta DB, a database composed of cross-β amyloids formed in natural conditions. This database is expected to be indispensable for benchmarking amyloid predictors. We used the Cross-Beta DB to train and benchmark several such algorithms, using machine learning. The best-performing of these, the random-forest-based Cross-Beta RF Predictor, demonstrated superior performance over the other existing methods, fostering high expectations for an improved prediction of naturally occurring amyloids.
Metal ion activation and DNA recognition by theDeinococcus radioduransmanganese sensor DR2539
Authors: Mota Cristiano , Webster Myles , Saidi Melissa , Kapp Ulrike , Zubieta Chloe , Giachin Gabriele , Manso José Antonio , de Sanctis Daniele
Published: February 2024

The accumulation of manganese ions is crucial for scavenging reactive oxygen species (ROS) and protecting the proteome ofDeinococcus radiodurans(Dr). However, metal homeostasis still needs to be tightly regulated to avoid toxicity. DR2539, a dimeric transcription regulator, plays a key role inDrmanganese homeostasis. Despite comprising three well-conserved domains: a DNA binding domain, a dimerization domain, and an ancillary domain, both the metal ion activation mechanism and the DNA recognition mechanism remain elusive. In this study, we present biophysical analyses and the structure of the dimerization and DNA binding domains of DR2539 in its holo form and in complex with the 21 bp pseudo-palindromic repeat of thedr1709promotor region. These findings shed light into the activation and recognition mechanisms. The dimer presents eight manganese binding sites that induce structural conformations essential for DNA binding. The analysis of the protein-DNA interfaces elucidates the significance of Tyr59 and helix H3 sequence in the interaction with the DNA. Finally, the structure in solution as determined by small angle X-ray scattering experiments and supported by AlphaFold modelling provides a model illustrating the conformational changes induced upon metal binding.
Deciphering Peptide-Protein Interactions via Composition-Based Prediction: A Case Study with Survivin/BIRC5
Authors: Anindya Atsarina Larasati , Olsson Torbjörn Nur , Jensen Maja , Garcia-Bonete Maria-Jose , Wheatley Sally P. , Bokarewa Maria I. , Mezzasalma Stefano A. , Katona Gergely
Published: February 2024

In the realm of atomic physics and chemistry, composition emerges as the most powerful means of describing matter. Mendeleev’s periodic table and chemical formulas, while not entirely free from ambiguities, provide robust approximations for comprehending the properties of atoms, chemicals, and their collective behaviours, which stem from the dynamic interplay of their constituents.

Our study illustrates that protein-protein interactions follow a similar paradigm, wherein the composition of peptides plays a pivotal role in predicting their interactions with the protein survivin, using an elegantly simple model. An analysis of these predictions within the context of the human proteome not only illuminates the known cellular locations of survivin and its interaction partners, but also introduces novel insights into biological functionality. It becomes evident that an electrostatic- and primary structure-based descriptions fall short in predictive power, leading us to speculate that protein interactions are orchestrated by the collective dynamics of functional groups.