bluuebunny/crossref_metadata_2025 huggingface dataset:
ALLIN: A tool for annotation of a protein alignment combined with structural visualization
Authors: Picollo Alessandra , Pusch Michael
Published: December 2024

The physiological, functional, and structural properties of proteins and their pathogenic variants can be summarized using many tools. The information relating to a single protein is often spread among different sources requiring different programs for access. It is not always easy to select, simultaneously visualize, and compare specific properties of different proteins. On the other hand, comparing members of the same protein family could suggest conserved properties or highlight significant differences. We have thus developed a web interface, ALLIN (Annotation of sequence aLignment and structuraL proteIn visualizatioN) for the simultaneous visualization of multi-sequence protein alignments, including comments and annotations, and the related three-dimensional structures. This interface permits the inclusion of comments and coloring of residues in the alignment section, according to a user-defined color code, allowing a quick overview of specific properties. The interface does not require training or coding expertise, and the result is a unique “memo” web page that combines data from different sources, with the flexibility to highlight only the information of interest. The output provides an overview of the state of art of a protein family that is easily shared among researchers and new data can be conveniently added as it emerges. We believe the ALLIN tool can be useful for all scientists working on the structure–function analysis of proteins, in particular on those involved in human genetic diseases.
Magnetic flux transitions in two-band single-junction superconductors with time-reversal symmetry breaking
Authors: Wang 王 Guo 果 , Han 韩 Tian-Yi 天意 , Huang 黄 Hai 海
Published: December 2024

Based on Ginzburg–Landau theory, we investigate the electromagnetic properties of two-band superconductors with broken time-reversal symmetry. We propose an apparatus of a superconducting ring integrated with a microbridge structure to probe the peculiar topological excitations in the chiral system. The phase difference of two order parameters in the superconductor satisfies the double sine-Gordon equation, and a linear relationship between the phase difference at the two ends of the junction and the total magnetic flux in the ring can be obtained. Then with the Josephson current–phase relation, we establish the dependence of the circulating current and magnetic flux on the applied external magnetic field. Our results show that this single-junction system will exhibit the irreversible behaviors and two different types of fractional flux transitions can clearly manifest the time-reversal symmetry breaking in two-component superconductors.
Possible coexistence of superconductivity and topological electronic states in 1T-RhSeTe
Authors: Zhang 张 Tengdong 腾东 , Fan 樊 Rui 睿 , Gao 高 Yan 炎 , Wu 吴 Yanling 艳玲 , Xu 徐 Xiaodan 晓丹 , Yao 姚 Dao-Xin 道新 , Li 李 Jun 军
Published: December 2024

Transition metal dichalcogenides (TMDs), exhibit a range of crystal structures and topological quantum states. The 1T phase, in particular, shows promise for superconductivity driven by electron–phonon coupling (EPC), strain, pressure, and chemical doping. In this theoretical investigation, we explore 1T-RhSeTe as a novel type of TMD superconductor with topological electronic states. The optimal doping structure and atomic arrangement of 1T-RhSeTe are constructed. Phonon spectrum calculations validate the integrity of the constructed doping structure. The analysis of the electron–phonon coupling using the electron–phonon Wannier (EPW) method has confirmed the existence of a robust electron–phonon interaction in 1T-RhSeTe, resulting in total EPC constant λ = 2.02, the logarithmic average frequency ω
log = 3.15 meV and T
c = 4.61 K, consistent with experimental measurements and indicative of its classification as a BCS superconductor. The band structure analysis revealed the presence of Dirac-like band crossing points. The topological non-trivial electronic structures of the 1T-RhSeTe are confirmed via the evolution of Wannier charge centers (WCCs) and time-reversal symmetry-protected topological surface states (TSSs). These distinctive properties underscore 1T-RhSeTe as a possible candidate for a topological superconductor, warranting further investigation into its potential implications and applications.
An adjustment-free laser resonator based on micron-scale corner cube array
Authors: Chang 常 Pengyuan 鹏媛 , Huang 黄 Xinrong 欣荣 , Fu 傅 Caolei 曹雷 , Liu 刘 Aiping 爱萍 , Pan 潘 Duo 多 , Wang 王 Zhiyang 志洋 , Chen 陈 Jingbiao 景标
Published: December 2024

The topic of improving the mechanical stability of external cavity diode lasers (ECDLs) has recently attracted widespread attention and interest. The use of corner-cube-array (CCA)-based resonators provides a potential solution for this purpose, although continuous oscillation at super large incident angle remains challenging. In this work, we employ the CCA resonator to generate continuous oscillation within ±20° angular misalignment of cavity mirror in experiment. On the basis of retroreflection theory, the retroreflectivity of a CCA is analyzed by using optical simulation software. Notably, the experiment verifies the advantage of using a CCA over a plane mirror in laser resonator, thereby providing a promising approach for ECDLs. The threshold characteristic curves measured at different incident angles in the experiment verify that the CCA possesses an obvious anti-angle misalignment performance. This research introduces an alternative solution of using CCA resonator instead of parallel plane cavity, thereby realizing an adjustment-free ECDL with enhanced mechanical stability.
Experimental investigation of the mechanical properties of Al6061-TiB2-fly ash reinforced monolithic and hybrid composites
Authors: Nithesh K , B M Karthik , Sharma Sathyashankara , Anne Gajanan , Hegde Ananda
Published: December 2024

This study investigates the mechanical properties of Al6061-TiB2-fly ash reinforced monolithic and hybrid composites, fabricated using the stir casting technique. The experiment involved the preparation of both monolithic composites by varying TiB2 (3–6 wt%) and hybrid composites by varying TiB2 (1–3 wt%) and fly ash (3–5 wt%) within the Al6061 matrix. Preheated reinforcement particles were introduced to the matrix alloy under controlled stirring conditions to ensure proper dispersion. Mechanical testing was conducted on the fabricated composites to evaluate their hardness and tensile strength. The results indicate that the hybrid composites exhibit superior mechanical properties compared to the base Al6061 alloy and the monolithic composites. The hardness of the hybrid composites A1T3F (Al6061 + 1%TiB2 + 3% fly ash) and A3T5F (Al6061 + 3%TiB2 + 5% fly ash) were significantly improved, reaching 134 HV and 146 HV, respectively, compared to 74 HV for the base alloy. The tensile strength of the hybrid composites also exceeded that of the monolithic composites, demonstrating the synergistic reinforcement effect of TiB2 and fly ash. However, attempts to incorporate higher levels of reinforcement (TiB2 5% and fly ash 7%) were unsuccessful due to agglomeration issues. The results indicate that the hybrid composites provide a cost-effective solution with enhanced mechanical properties, making them a more economical and efficient alternative to monolithic composites reinforced solely with TiB2.
New players, same problems: Michael Lee-Chin v Dominican Republic, and the rising tide of inconsistency in South–South ISDS
Authors: Haynes Jason
Published: December 2024

This article provides a critical analysis of the Michael Lee-Chin v Dominican Republic arbitral award, highlighting its problematic reasoning and inconsistencies. Despite being a rare South–South investment dispute, the case demonstrates many of the same shortcomings criticized in North–South arbitrations. The tribunal’s expansive interpretation of investor protections, particularly regarding fair and equitable treatment and the umbrella clause, raises concerns about potential overreach. Most troublingly, the tribunal’s restrictive approach to the national security exception imposes a high threshold that may undermine states’ ability to respond to genuine environmental and public health crises. The award stands in stark contrast to the more balanced approach adopted in the recent Seda v Colombia case. By exposing these issues, the article argues that the problems plaguing investment arbitration are not merely a product of North–South power dynamics, but are deeply entrenched in how investment treaties are interpreted and applied. It calls for a fundamental reassessment of investment treaty interpretation that gives due weight to state regulatory space and public interest concerns, regardless of the geographical context of the dispute.
STNGS: a deep scaffold learning-driven generation and screening framework for discovering potential novel psychoactive substances
Authors: Liu Dongping , Liu Dinghao , Sheng Kewei , Cheng Zhenyong , Liu Zixuan , Qiao Yanling , Cai Shangxuan , Li Yulong , Wang Jubo , Chen Hongyang , Hu Chi , Xu Peng , Di Bin , Liao Jun
Published: December 2024

The supervision of novel psychoactive substances (NPSs) is a global problem, and the regulation of NPSs was heavily relied on identifying structural matches in established NPSs databases. However, violators could circumvent legal oversight by altering the side chain structure of recognized NPSs and the existing methods cannot overcome the inaccuracy and lag of supervision. In this study, we propose a scaffold and transformer-based NPS generation and Screening (STNGS) framework to systematically identify and evaluate potential NPSs. A scaffold-based generative model and a rank function with four parts are contained by our framework. Our generative model shows excellent performance in the design and optimization of general molecules and NPS-like molecules by chemical space analysis and property distribution analysis. The rank function includes synthetic accessibility score and frequency score, as well as confidence score and affinity score evaluated by a neural network, which enables the precise positioning of potential NPSs. Applied STNGS framework with molecular docking and a G protein-coupled receptor (GPCR) activation-based sensor (GRAB), we successfully identify three novel synthetic cannabinoids with activity. STNGS constrains the chemical space to generate NPS-like molecules database with diversity and novelty, which assists in the ex-ante regulation of NPSs.
Histologic and Endoscopic Findings Are Highly Correlated in a Prospective Cohort of Patients With Inflammatory Bowel Diseases
Authors: Di Vincenzo Federica , Quintero Maria A , Serigado Joao M , Koru-Sengul Tulay , Killian Rose Marie , Poveda Julio , England Jonathan , Damas Oriana , Kerman David , Deshpande Amar , Abreu Maria T
Published: December 2024

Background and Aims

The advantages of endoscopic vs histologic assessments of inflammation in inflammatory bowel disease remain unclear. We compared endoscopic and histologic inflammation in a prospective cohort. Furthermore, in patients with discordant findings, we compared the ability of endoscopy vs histology to predict disease course.

Methods

Ulcerative colitis (UC) or Crohn’s disease (CD) patients underwent routine colonoscopies with intestinal biopsies, which included ratings of inflammation severity. Tetrachoric correlation analysis between the endoscopic and histologic inflammation ratings was performed. In postsurgical CD patients, major adverse outcomes (MAOs) were recorded.

Results

The analysis included 749 patients (60.2% CD patients), with 2807 biopsied segments. We found high concordance between endoscopist and pathologist inflammation ratings (0.84, 95% confidence interval, 0.81-0.87, p < 0.0001). Only 12.5% of biopsied segments exhibited microscopic inflammation without endoscopic inflammation. Neo-terminal ileum (neo-TI) biopsies exhibited the highest discordance; UC colonic biopsies had the highest concordance. Postsurgical CD patients who completed the 48-month follow-up (n = 138) were included in the survival analysis. The probability of MAO-free survival was significantly higher in patients with a Rutgeerts score of i0 at baseline than in those with higher scores. Microscopic inflammation in the neo-TI did not predict a higher risk of MAOs (p = 1.00).

Conclusions

In a real-world setting, endoscopic inflammation predicted histologic inflammation with high accuracy. In patients with a Rutgeerts score of i0, microscopic inflammation in neo-TI biopsies did not predict more aggressive disease behavior over the next 4 years. These results have implications for the design of clinical trials, suggesting the use of endoscopic healing as an endpoint.
Potential of Bacillus thuringiensis isolates to manage Gonipterus platensis (Coleoptera: Curculionidae) larvae populations
Authors: Jordan Carolina , de Carvalho Vanessa Rafaela , Horta André Ballerini , Lemos Manoel Victor Franco , Barbosa Rodrigues Jardel Diego , Passos José Raimundo de Souza , Domingues Maurício Magalhães , Zanuncio José Cola , Wilcken Carlos Frederico
Published: December 2024

The growing expansion of eucalyptus plantations in Brazil and the impact of exotic pests, such as Gonipterus platensis, demand effective, and sustainable biological control strategies. The aim of this study was to assess the pathogenicity of 10 Bacillus thuringiensis (Bt) isolates to neonate Gonipterus platensis larvae, commonly known as the eucalyptus weevil (Coleoptera: Curculionidae) with the specific focus of evaluating their potential to manage this pest while preserving its egg parasitoid, Anaphes nitens. To achieve this, the genomic DNA of the 10 Bt isolates was extracted using the thermal lysis method for molecular characterization of their Cry and Vip proteins. Neonate G. platensis larvae were subjected to bioassays with each isolate, at a concentration of 1 × 109 spores/ml, was applied on 10 larvae per replication (3 replications). The concentration and lethal time to kill 50% of the larvae were determined for the most effective isolates. The Bt isolates 107 and 178 isolates even at concentrations 10× lower than those recommended for commercial Bacillus thuringiensis var. tenebrionis (Btt) formulations against Coleoptera pests, achieved 100% mortality of G. platensis larvae. These isolates, with coleopteran-specific genes, caused high mortality of neonate Gonipterus platensis larvae. This indicates their potential for the biological control of this pest and maybe of other Coleoptera pests. Their use poses minimal risk to non-target organisms such as the egg parasitoid A. nitens and indicates a promising avenue for integrated pest management strategies with effective pest control while preserving the ecological balance.
Vein watershed analysis locational method versus computed tomography-guided percutaneous localization for detecting non-palpable peripheral pulmonary nodules: a real-world study of non-inferiority
Authors: Huang Chen , Chen Zi-Hao , Peng Li-Shan , Zhang Jia-Tao , Lin Jun-Tao , Zhang Sheng , Yang Jie , Jiang Ben-Yuan , Yang Xue-Ning , Zhong Wen-Zhao , Nie Qiang
Published: December 2024

OBJECTIVES

In recent years, with the advancement of sublobar resection, a safe, painless method for locating peripheral pulmonary nodules was needed. Previously, an alternative method of arterial watershed localization was introduced to remedy the shortcomings of preoperative computed tomography (CT)-guided localization or other methods for locating pulmonary nodules, but its technical limitations were discovered during clinical applications. Therefore, we developed a technique to localize non-subpleural nodules using basin analysis of the target vein and validated its feasibility and safety.

METHODS

We performed a retrospective analysis of surgical cases of pulmonary nodules smaller than 2 cm in our centre. The vein watershed locational method (V-WALM) was compared with CT-guided percutaneous puncture localization wedge dissection in terms of success rate, the mean duration of the operation, mean volume of intraoperative bleeding and median postoperative stay, mean postoperative drainage and mean drainage tube indwelling time.

RESULTS

V-WALM and CT-guided localization were used for localized resection of pulmonary nodules in 50 patients. The localization success rates were 94.0% for V-WALM and 90.0% for CT-guided localization, respectively, with no statistical difference noted. In addition, no statistical difference in patient population distribution between the 2 groups was noted. The operating time was 95.5 ± 26.4 min for V-WALM and 94.3 ± 37.5 min for CT-guided localization, with no statistical difference. Neither were there statistical differences in intraoperative bleeding, postoperative drainage and drainage tube indwelling time. The lymph node sampling rate of V-WALM was 48.0%, which was much higher than the 24% noted in the CT-guided localization group.

CONCLUSIONS

The results of this study demonstrate that V-WALM is a safe and feasible intraoperative localization method for peripheral lung nodules. It provides a high-precision, fast and minimally invasive approach to intraoperative localization.
Environmental sustainability—an essential component of rational use of medicines
Authors: Giunchi Valentina , Fusaroli Michele , Linder Elkanah , Villén Johanna , Raschi Emanuel , Lunghi Carlotta , Wettermark Björn , Poluzzi Elisabetta , Nekoro Marmar
Published: December 2024

Human-use medicines are introduced into surface water throughout their entire life cycle, from manufacturing and consumption to improper disposal, resulting in negative effects on aquatic flora and fauna. Sustainability approaches have addressed this issue, proposing frameworks like the One Health approach. A revised definition of the rational use of medicines has also been proposed, taking into account their environmental sustainability. Building on this updated definition, this paper presents a decision-making flowchart to integrate the assessment of the impact of human medicines on surface water, outlining existing actions and proposing new ones. These actions are categorized into those with primary clinical benefits and those focused solely on environmental concerns. They include both upstream and downstream measures, such as implementing regulations similar to those in the EU and the USA, educating future healthcare practitioners, promoting green pharmacy innovations, and establishing proper disposal practices.
Effect of feeding high oleic soybean oil to finishing pigs on growth performance, carcass characteristics, and meat quality
Authors: Atoo Ashir F , Levesque Crystal L , Thaler Robert , Underwood Keith , Beyer Erin , Perez-Palencia Jorge Y
Published: December 2024

This study aimed to evaluate the effects of dietary fat source and feeding duration on growth performance, carcass characteristics, and meat quality of finishing pigs. A total of 450, 21-wk-old finishing pigs with an average body weight of 113.7 ± 8 kg were housed in 90 pens assigned to one of five dietary treatments in a 2 × 2 + 1 factorial design. Dietary treatments consisted of two fat sources (CWG: 4% inclusion of choice white grease and HOSO: 4% inclusion of high oleic soybean oil) each provided 2 or 4 wk before marketing. The “+1” diet was corn-based without fat inclusion (CON). Observations included growth performance, carcass characteristics, fatty acid (FA) profile, and sensory evaluation. Data was analyzed using PROC MIXED in SAS considering dietary treatment as a main effect, feeding duration, and their interactions. Preplanned contrasts were used to compare dietary treatments with the control. From day 14 to 28 and the overall experimental period (day 0–28), pigs fed fat-supplemented diets had a greater (P < 0.05) average daily gain and gain-to-feed ratio than CON-fed pigs. There was no significant difference (P > 0.05) in growth performance when comparing fat sources or feeding periods. Pigs supplemented with either CWG or HOSO showed a tendency to have a greater (P < 0.10) belly weight and belly yield, and a lesser (P < 0.10) loin yield and loin muscle area when compared with CON pigs. The loin from pigs fed fat sources had greater (P < 0.05) oleic acid and eicosenoic acid concentration when compared with CON. When CWG was compared with HOSO, pigs fed CWG had a higher (P < 0.05) concentration of palmitic acid and stearic acid, while the HOSO pigs had a higher concentration of oleic acid and linolenic acid in the loin. In the belly, CON had a higher (P < 0.05) concentration of palmitic acid and stearic acid compared to HOSO, while pigs fed fat sources had a higher concentration of oleic acid and eicosenoic acid. Bellies from HOSO had higher (P < 0.05) oleic acid and α-linolenic acid methyl ester concentrations, while CWG had higher concentrations of g-linolenic acid. For the sensory evaluation, the palatability and acceptability of pork were not affected (P > 0.05) by dietary treatments. In conclusion, supplementation with HOSO not only improved performance but tended to improve some carcass characteristics and increased the concentration of oleic acid, and some other unsaturated FA with a concomitant decrease in the concentration of some saturated FA in pork.
Temperature effect on the efficacy of 3 entomopathogenic nematode isolates against larvae of the lesser mealworm, Alphitobius diaperinus (Coleoptera: Tenebrionidae)
Authors: Karanastasi Eirini , Nikorezou Anna , Stamouli Maria , Skourti Anna , Boukouvala Maria C , Kavallieratos Nickolas G
Published: December 2024

The lesser mealworm Alphitobius diaperinus Panzer (Coleoptera: Tenebrionidae), an important insect pest of stored-product commodities and poultry production systems, is regarded among the most difficult species to control. It has developed resistance to many chemical insecticides, and though various cultural and biological methods have been assessed and identified as possible factors for its control, none are currently implemented. Entomopathogenic nematodes are often successfully employed as alternative to chemicals biocontrol agents of various insect species, including pests of stored products; nevertheless, their evaluation as potential biocontrol factors of the lesser mealworm is not efficiently scrutinized. In the current study, single A. diaperinus larvae were exposed to six doses of Heterorhabditis bacteriophora Poinar (Rhabditida: Heterorhabditidae), Steinernema carpocapsae (Weiser) (Rhabditida: Steinernematidae), and Steinernema feltiae (Filipjev) (Rhabditida: Steinernematidae), for 4 and 8 d, and mortality was recorded at 3 different temperature regimes, i.e., 25 oC, 30 oC, and 35 oC. The study concludes that S. carpocapsae and S. feltiae are both highly virulent against A. diaperinus larvae and may be considered as promising biological control agents for reducing lesser mealworm infestations when applied at a rate of 70 IJs/cm2 at 25 oC. When assessed at 30 oC, both species were effective at the same rate though causing lower mortality of ~60% and ~50%, respectively, whereas their efficacy was low at 35 oC.
Meningiomas in Rubinstein-Taybi syndrome: A case report and comprehensive review
Authors: Chen Andrea , Hart Shannon Louise , Lannon Melissa , Hawkins Cynthia , Reddy Kesava K V , Lu Jian-Qiang
Published: December 2024

Rubinstein-Taybi syndrome (RTS) is a congenital disorder with characteristic clinical manifestations. In the vast majority of cases, it is caused by mutations of the gene encoding the transcriptional co-activator cAMP-response element binding protein (CBP)-binding protein (CREBBP). It has been thought to be a tumor predisposition syndrome as RTS patients have an increased risk of developing tumors including meningiomas. However, RTS-associated meningiomas are rarely reported. We report a unique RTS-associated meningioma in which an oncogenic CREBBP mutation is identified. We also comprehensively review the reported RTS-associated meningiomas, from epidemiology and pathogenesis to clinicopathological characteristics and treatment. All RTS patients with meningiomas are female and have the exclusive mutations of CREBBP. In population-based studies RTS-associated meningiomas seem to develop at younger ages. Their pathogenesis may be driven by the CREBBP/CBP alterations resulting in aberrant signal transduction in the CBP-mediated signaling pathways. Meningiomas in RTS patients have common clinicopathological characteristics including comorbidity with other tumors, radiologically intra-osseous growth, and uncommon histopathology such as ossifying and secretory features. Given the genetic nature and rarity of RTS-associated meningiomas, further investigation of their characteristics may define molecular targets for improved therapeutic options for RTS patients.
Simultaneous bilateral deep femoral artery aneurysms: case report of a rare peripheral arterial aneurysm
Authors: Assefa Rahel Abebayehu , Zeleke Henok T/Silassie , G/Giorgis Dawit
Published: December 2024

Deep femoral artery aneurysms are very rare; particularly when isolated and occur simultaneously in both limbs. We report such a case of a misdiagnosed 16-year-old male presenting after hematoma evacuation was attempted for painful swelling in the left groin. Once the diagnosis was confirmed by computed tomography angiography (CTA), an emergency aneurysmectomy with deep femoral artery (DFA) ligation was performed on the left limb. Subsequently, an elective aneurysmectomy with DFA ligation was done for the contralateral limb during the same admission, with no postoperative complications. Echocardiography, performed with suspicion for infective endocarditis as the cause for possible mycotic aneurysm, revealed Chronic Rheumatic Valvular Heart Disease, without evidence of vegetations, abscesses, or intracardiac thrombi. This case report seeks to discuss the patient’s clinical presentation, CTA findings, and surgical management in a low-resource setting, underscoring the risks of this rare condition if misdiagnosed.
Phylogenomic Insights into the Evolution and Origin of Nematoda
Authors: Qing Xue , Zhang Yuanmeng Miles , Sun Sidi , Ahmed Mohammed , Lo Wen-Sui , Bert Wim , Holovachov Oleksandr , Li Hongmei
Published: December 2024

The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to 8 nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is well-resolved across most clades, with topologies remaining consistent across various reconstruction parameters. The subclass Enoplia is placed as a sister group to the rest of Nematoda, agreeing with previously published phylogenies. While the order Triplonchida is monophyletic, it is not well-supported, and the order Enoplida is paraphyletic. Taxa possessing a stomatostylet form a monophyletic group; however, the superfamily Aphelenchoidea does not constitute a monophyletic clade. The genera Trichinella and Trichuris are inferred to have shared a common ancestor approximately 202 millions of years ago (Ma), a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated ~305 Ma, corresponding to the transition from the Devonian to the Permian period. The genus Thornia is placed outside of Dorylaimina and Nygolaimina, disagreeing with its position in previous studies. In addition, we tested the whole genome amplification method and demonstrated that it is a promising strategy for obtaining sufficient DNA for phylogenomic studies of microscopic eukaryotes. This study significantly expanded the current nematode genome dataset, and the well-resolved phylogeny enhances our understanding of the evolution of Nematoda.
Cold-related Mortality in US State and Private Prisons: A Case–Crossover Analysis
Authors: Skarha Julianne , Spangler Keith , Dosa David , Rich Josiah D. , Savitz David A. , Zanobetti Antonella
Published: December 2024

Background:

Cold temperatures are associated with increased risk for cardiovascular and respiratory disease mortality. Due to limited temperature regulation in prisons, incarcerated populations may be particularly vulnerable to cold-related mortality.

Methods:

We analyzed mortality data in US prisons from 2001 to 2019. Using a case–crossover approach, we estimated the association of a 10 °F decrease in cold temperature and extreme cold (days below the 10th percentile) with the risk of total mortality and deaths from heart disease, respiratory disease, and suicide. We assessed effect modification by personal, facility, and regional characteristics.

Results:

There were 18,578 deaths during cold months. The majority were male (96%) and housed in a state-operated prison (96%). We found a delayed association with mortality peaking 3 days after and remaining positive until 6 days after cold exposure. A 10 °F decrease in temperature averaged over 6 days was associated with a 5.1% (95% confidence interval [CI]: 2.1%, 8.0%) increase in total mortality. The 10-day cumulative effect of an extreme cold day was associated with an 11% (95% CI: 2.2%, 20%) increase in total mortality and a 55% (95% CI: 11%, 114%) increase in suicides. We found the greatest increase in total mortality for prisons built before 1980, located in the South or West, and operating as a dedicated medical facility.

Conclusions:

Cold temperatures were associated with an increased risk of mortality in prisons, with marked increases in suicides. This study contributes to the growing evidence that the physical environment of prisons affects the health of the incarcerated population.
The Association Between Ambient Particulate Matter Exposure and Anemia in HIV/AIDS Patients
Authors: Liang Wei , Han Aojing , Hou Dong , Li Ruihan , Hu Qilin , Shen Huanfeng , Jin Yalei , Xiang Hao
Published: December 2024

Background:

Anemia is common among HIV/AIDS patients, impacting prognosis. Particulate matter (PM) exposure is an understudied, potentially modifiable risk factor in this group.

Methods:

We gathered 36,266 hemoglobin (Hb) measurements from 6808 HIV/AIDS patients from the HIV/AIDS Comprehensive Response Information Management System from 1 January 2004 to 31 December 2021. We evaluated the relationship between Hb levels and short-term PM exposure using linear mixed-effects models. We used logistic regression to estimate the association of long-term PM exposure with baseline anemia prevalence and time-varying Cox models to estimate the association of long-term PM exposure with follow-up incidence of anemia. Mediation analysis explored the role of chronic kidney disease (CKD) in the association between PM exposure and anemia.

Results:

For every 5 µg/m³ increase in 28-day average PM1, Hb levels decreased by 0.43 g/l. For a 10 µg/m³ increase in PM2.5, Hb decreased by 0.55 g/l; for the same increase in PM10, Hb decreased by 0.35 g/l. A 5 µg/m³ increase in 1-year average PM1 corresponded to a 7% higher prevalence of anemia at baseline, a 10 µg/m³ increase in PM2.5 to 8% higher prevalence, and a 10 µg/m³ increase in PM10 to 6% higher prevalence. These rises in average PM concentrations during follow-up were associated with increased incident anemia by 54% (PM1), 72% (PM2.5), and 51% (PM10). CKD partially mediated the positive associations between PM exposure and the incidence of anemia.

Conclusion:

PM exposure was associated with lower Hb levels and higher incidence of anemia in HIV/AIDS patients and CKD with mediating estimated effects in PM-induced anemia.
Predicting vulnerability status of carotid plaques using CTA-based quantitative analysis
Authors: Lao Qun , Zhou Rongzhen , Wu Yitian , Feng ChangFeng , Pang Jianxin , Ma Ling , Yang Yunjun , Ji Wenbin
Published: December 2024

The study aimed to develop a radiomics model to assess carotid artery plaque vulnerability using CTA images. It retrospectively included 107 patients with carotid artery stenosis who underwent carotid artery stenting (CAS) from 2017 to 2022. Patients were categorized into stable and vulnerable plaque groups based on pathology. A training group and a testing group were formed in a 7:3 ratio. Clinical data, including demographics and lipid profiles, were collected alongside pre-treatment CTA images. Radiomics features were extracted and reduced using the LASSO method to minimize redundancy. A radiomics model was then constructed, utilizing 13 features with a minimum penalty coefficient logλ=0.047. Significant differences were found between stable and vulnerable plaques in terms of stenosis degree. The radiomics model showed high accuracy (AUC of 0.959 in training and 0.942 in testing) for identifying vulnerable plaques. When combined with clinical parameters stenosis degree, the model's diagnostic efficacy improved further, with AUC values of 0.985 and 0.961 in the training and testing groups, respectively. Decision curve analysis (DCA) indicated that the combined model offered superior clinical benefits over the clinical model and radiomics model alone. The study concludes that the combined radiomics model, incorporating stenosis degree, presents a promising tool for differentiating vulnerable from stable plaques.
Assessing Trauma and Training Needs of Sexual Assault Nurse Examiners Across the United States
Authors: Dawson Haley R. , Compo Nadja Schreiber , Thomas Tami , Nobrega Juan Lopez
Published: December 2024

Background

Much of the research on sexual assault nurse examiners (SANEs) focuses on program outcomes rather than the individual experiences of SANEs. The present research therefore sought to examine the individual experiences of SANEs regarding trauma, support, training needs, and challenges.

Methods

A national sample of SANEs participated in an online survey. In addition to a series of questions on work-related challenges and training needs, participants also completed the Secondary Traumatic Stress Scale (Bride et al., 2004) and the Professional Quality of Life Scale Stamm, 2009). Written survey responses were analyzed for themes regarding support services and training needs.

Results

One hundred twelve SANEs from 24 U.S. states participated in our survey. Of these, 74 SANEs completed the Secondary Traumatic Stress Scale, and 69 SANEs completed the Professional Quality of Life Scale. Overall, SANEs reported little secondary trauma or burnout. Furthermore, SANEs identified key areas in which additional training would be beneficial, including trial preparation, photography, and hands-on training.

Discussion

Self-reported trauma and burnout findings are discussed in light of the high use of support services such as therapy, decompressing with other SANEs, and leisure activities. Our findings provide valuable information for supervisors and training providers of SANEs and have important implications for future SANE research.
Workday Habits and Fatigue of American Jockeys
Authors: Keener Michaela M. , Vice Gavin C. , Tumlin Kimberly I. , Heebner Nicholas R.
Published: December 2024

Objective

1) Characterize the workday habits of American jockeys, and 2) Evaluate the relationship between workday habits and fatigue through changes in postural stability (balance) across their workday.

Methods

Thirty-seven jockeys participated in pre- and post-race day testing. Jockeys completed questionnaires on workday habits and a two-minute balance test with tri-axial accelerometers on the unstable surface and sacrum.

Results

The median caloric intake during their workday was 263.8 kcal. Wilcoxon-signed rank tests reported no significant changes in balance across the workday. Statistically significant (p < 0.05) correlations existed between sleep (τ = -0.41) and number of races ridden (τ = 0.37) with balance variables.

Conclusions

American jockeys exhibit weight-cycling behaviors, primarily restricted caloric and fluid intake. No changes were evaluated in balance across the workday. Future research should focus on evaluating other fatigue mechanisms involving abdominal muscle fatigue and cognitive fatigue.
Patient-Physician Communication Experience Modifies Racial/Ethnic Health Care Disparities Among Surveillance, Epidemiology, and End Results-Consumer Assessment of Healthcare Providers and Systems Participants With Colorectal Cancer and Multiple Chronic Conditions
Authors: Navarro Stephanie , Le Jessica , Tsui Jennifer , Barzi Afsaneh , Stern Mariana C. , Pickering Trevor , Farias Albert J.
Published: December 2024

Purpose:

After cancer diagnosis, non-White patients and those with multimorbidity use less primary care and more acute care than non-Hispanic White (NHW) patients and those lacking comorbidities. Yet, positive patient experiences with physician communication (PC) are associated with more appropriate health care use. In a multimorbid cohort, we measured associations between PC experience, race and ethnicity, and health care use following colorectal cancer (CRC) diagnosis.

Participants and Methods:

We identified 2606 participants using Surveillance, Epidemiology, and End Results (SEER)-Consumer Assessment of Health Care Providers and Systems (CAHPS) data who were diagnosed with CRC from 2001 to 2017 with pre-existing chronic conditions. Self-reported PC experiences were derived from Medicare CAHPS surveys. Chronic condition care, emergency department, and hospital use following CRC diagnosis were identified from Medicare claims. Simple survey-weighted multivariable logistic regression stratified by experiences with care analyzed associations between race and ethnicity and health care use.

Results:

Among patients reporting excellent PC experience, non-Hispanic Black (NHB), Hispanic, and non-Hispanic Asian (NHA) patients were more likely to use sufficient chronic condition care than NHW patients (NHB: OR=1.48, 99.38% CI=1.38–1.58; Hispanic: OR=1.34, 99.38% CI=1.26–1.42; NHA: OR=2.31, 99.38% CI=2.12–2.51). NHB and NHA patients were less likely than NHW patients to visit the emergency department when reporting excellent PC experience (NHB: OR=0.66, 99.38% CI=0.63–0.69; NHA: OR=0.67, 99.38% CI=0.64–0.71). Among patients reporting excellent PC, NHB, Hispanic, and NHA patients were less likely than NHW patients to be hospitalized (NHB: OR=0.93, 99.38% CI=0.87–0.99; Hispanic: OR=0.93, 99.38% CI=0.87–0.99; NHA: OR=0.20, 99.38% CI=0.19–0.22).

Conclusion:

Improving patient experiences with PC, particularly among older racial and ethnic minority cancer survivors with chronic conditions, may help reduce disparities in adverse healthcare use following CRC diagnosis.
Threads of Care
Authors: Pradhan Rohit , Ghiasi Akbar , Davlyatov Ganisher , Gupta Shivani , Weech-Maldonado Robert
Published: December 2024

Objective:

To assess the association of agency nursing staff utilization with nursing home (NH) quality.

Background:

Nursing staff are the primary caregivers in NHs, where high-quality care is contingent upon their adequacy and expertise. Long-standing staffing challenges, exacerbated by the COVID-19 pandemic, have led NHs to rely on agency/contract labor to alleviate staffing shortages.

Methods:

This study used the following secondary datasets: Payroll-Based Journal, Care Compare: 5-Star Quality Rating System, LTCFocus.org, Area Health Resource Files, and Rural-Urban Commuting Area codes for 2017–2022. Multivariable ordinal logistic regression with 2-way (facility and year-level) fixed effects was employed. The study included all Centers for Medicare and Medicaid Services certified U.S. NHs. Analytic data comprised 80,244 facilities, averaging 13,374 unique NHs per year. The study focused on the quality star rating (1–5 scale) from the 5-Star Quality Rating System as the dependent variable. Independent variables included the proportion of agency nursing staff hours per resident day for registered nurses, licensed practical nurses, and certified nursing assistants while controlling for facility and community characteristics that may affect NH quality.

Results:

A 10% increase in agency registered nurses, licensed practical nurses, and certified nursing assistants (logged) was associated with a decrease in the odds of achieving a higher star rating by 4%, 5%, and 4%, respectively (P < 0.001).

Conclusions:

The use of agency nursing staff can negatively impact NH quality. Efforts to better integrate agency nursing staff into NHs, combined with strategies to recruit and retain permanent nursing staff, could lead to improved outcomes for residents.
Insights intoDEPDC5-Related Epilepsy from 586 people: Variant Penetrance, Phenotypic Spectrum, and Treatment Outcomes
Authors: Ochoa-Urrea Manuela , Butler Elizabeth A. , Bruenger Tobias , Leu Costin , Bosselmann Christian M. , Najm Imad , Lhatoo Samden , Lal Dennis
Published: December 2024

Variants in the GATOR1 complex geneDEPDC5disrupt mTORC1 pathway regulation, driving cortical malformations and focal epilepsy.DEPDC5is the most common genetic cause of focal epilepsy, often linked to focal cortical dysplasia (FCD). However, reduced penetrance complicates genetic counselling and risk prediction.

This study analysed the largestDEPDC5-related epilepsy cohort, synthesising data from 170 families and 586 variant carriers. Epilepsy penetrance was estimated at 64.9% (n=380/586), with median seizure onset at 5 years. By age 10, 76.1% of individuals experienced seizures. Drug resistance occurred in 48.3% (n=101/209) of cases, and cortical malformations were present in 28% (n=49/175) of MRIs. SUDEP accounted for 16% (n=4/25) of deaths among affected individuals.

Early seizure onset correlated strongly with drug resistance, intellectual disability, and MRI abnormalities, underscoring its role as a severity marker. Surgical intervention in drug-resistant cases (34.7% [n=35/101]) achieved favourable outcomes (Engel I or II) in 88% (n=29/33) of individuals, with pathology confirming cortical malformations in 92.6% (n=25/27) of those with abnormal MRIs.

This study advances the understanding ofDEPDC5-related epilepsy, providing critical insights into penetrance, phenotype, and treatment outcomes to inform precision care and genetic counselling.
Characterizing Tyrosine Ring Flips in Proteins by19F NMR
Authors: Lu Meng , Xu Guohua , Wu Qiong , Liu Xiaoli , Yang Mingjuan , Jiang Ling , Yang Minghui , Liu Maili , Li Conggang
Published: December 2024

Aromatic ring flip dynamics are essential for elucidating the catalytic mechanism of enzyme, protein binding, and the “breathing” motions of proteins. NMR is the primary method for measuring aromatic ring flip rates in proteins at the residue level, but it typically requires extreme conditions such as high pressure or low temperature to slow down the ring flips to a detectable rate on the NMR time scale. Consequently, ring flip rates have only been measured for a limited number of proteins due to the lack of simple method under mild conditions. Here we report a novel19F NMR method utilizing 2,6-difluoro-tyrosine (2,6-F2Y) substitution to measure the ring flip rate of tyrosine residuesin vitroand in living cells. We validated the effectiveness of method on three proteins, the B1 domain of protein G (GB1), ubiquitin (UBQ) and histidine-containing phosphocarrier protein (HPr). The results demonstrated that this19F NMR approach can quantify the ring flip on timescales from microseconds to seconds under mild experimental conditions. For the first time, we measured the tyrosine ring flip dynamics of HPr in three types of living cells:E. coli, A2780 cells andX. laevisoocytes. Our findings reveal that tyrosine ring flip dynamics are remarkably affected by cellular environment and are cell-type dependent. The strong interactions and the low activation enthalpy are associated with fast ring flipping. Our study provides a simple, convenient and efficient method for characterizing tyrosine ring flip in proteins bothin vitroand in cells, and it also opens a new avenue for measuring the ring flip rates in proteins in complex biological environments.

TOC
Data-driven clustering of mental health symptoms and brain functional connectivity signatures in transdiagnostic psychiatric inpatients
Authors: Aruldass Athina R. , Rubbani Shafi , Zhukovsky Peter , Sneider Jennifer T. , Cohen-Gilbert Julia , Osman Abdirahman , Tatham Jocelyn , Chen Joann , Howell Allyna-London , Irujo Carmen , Bronson Lilikoi , Rossvall Annah , Duffy Lucie , Wong Samantha , Layfield Savannah , Rodriguez-Villa Fernando , Gelda Steven , Gelwan Eliot , Leslie Michael , Eisen Jane , Coletti Joseph , Busch Alisa B. , Sugarman Dawn E. , Pizzagalli Diego A. , Yip Agustin , Ressler Kerry J. , Daskalakis Nikolaos P.
Published: December 2024

Background

Psychiatric disorders are notoriously heterogenous, often rendering diagnostic efforts challenging, and leading to poor therapeutic outcomes. The growing emphasis on ‘transdiagnostic’ approaches in psychiatry aligns well with the National Institute of Health-devised Research Domain Criteria (RDoc) framework that seeks to enable precision psychiatry. Here, we sought to identify transdiagnostic subgroups, which share behavioral and neural abnormalities, in a large population of psychiatric inpatients treated at a tertiary psychiatric hospital.

Methods

The sample included 1,571 patients across five units within the Depression & Anxiety Disorders Division at McLean Hospital who completed self-assessments as part of an ongoing quality-of-care improvement project. Self-assessments included validated measures of depression, anxiety, anhedonia, trauma, personality and substance misuse as well as broader screening questions. First, we identified naturally occurring transdiagnostic subgroups based on the self-reported questionnaires using consensus clustering to implement partition-around-medoids. In a subsample, we ascertained brain functional connectivity differences between the resultant subgroups using a multi-granular approach, i.e. whole-brain to connection-wise.

Results

In a k=2 partitioning solution, the first transdiagnostic cluster; C1 (N=809) had consistently higher means across all questionnaires compared to the second cluster; C2 (N=762). QIDS total score (P<0.0001, effect size = 0.54) and BASIS-24 derived total score (P<0.0001, effect size = 0.53) showed the largest difference between the groups. In follow-up imaging analysis (N=26) functional connectivity (FC) differences were observed connection-wise (P<0.0001) and between functional networks (P<0.0001), with C1 showing stronger FC than C2. Cluster-by-sex analyses revealed that females had higher BASIS-24 derived depression/functioning (C1|C2; P<0.0001 | P<0.0001), and QIDS (C1|C2; P<0.0001 | P<0.0001) scores compared to males. This was coupled with greater intermodular FC in males than females in C1 (P<0.0001) and C2 (P<0.0005).

Conclusions

These results suggest that inpatients with transdiagnostic symptoms show biobehavioral abnormalities, underpinned by sex differences. Behaviorally, this is a function of acuity, i.e., severity of psychopathological symptoms, and not diagnosis. Biologically, the dysfunction captured here may span across various brain networks, rather than a singular region.