bluuebunny/crossref_metadata_2025 huggingface dataset:
Architecture and functional regulation of a plant PSII-LHCII megacomplex
Authors: Shan Jianyu , Niedzwiedzki Dariusz M. , Tomar Rupal S. , Liu Zhenfeng , Liu Haijun
Published: December 2024

Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the C
4
S
4
M
2
-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR-deletion mutant plants are studied through electron microscopy (EM), structural mass spectrometry, and ultrafast fluorescence spectroscopy [time-resolved fluorescence (TRF)]. The cryo-EM structure of a type I C
4
S
4
M
2
megacomplex demonstrates that the three domains of PsbR bind to the stromal side of D1, D2, and CP43; associate with the single transmembrane helix of the redox active Cyt
b
559
; and stabilize the luminal extrinsic PsbP, respectively. This megacomplex, with PsbR and PsbY centered around the narrow interface between two dimeric PSII cores, provides the supramolecular structural basis that regulates the plastoquinone occupancy in Q
B
site, excitation energy transfer, and oxygen evolution. PSII-LHCII megacomplexes (types I and II) and LHC aggregation levels in
Arabidopsis psbR
mutant were also interrogated and compared to wild-type plants through EM and picosecond TRF.
Predicting optimal mixotrophic metabolic strategies in the global ocean
Authors: Moeller Holly V. , Archibald Kevin M. , Leles Suzana G. , Pfab Ferdinand
Published: December 2024

Mixotrophic protists combine photosynthesis with the ingestion of prey to thrive in resource-limited conditions in the ocean. Yet, how they fine-tune resource investments between their two different metabolic strategies remains unclear. Here, we present a modeling framework (Mixotroph Optimal Contributions to Heterotrophy and Autotrophy) that predicts the optimal (growth-maximizing) investments of carbon and nitrogen as a function of environmental conditions. Our model captures a full spectrum of trophic modes, in which the optimal investments reflect zero-waste solutions (i.e., growth is colimited by carbon and nitrogen) and accurately reproduces experimental results. By fitting the model to data for
Ochromonas
, we were able to predict metabolic strategies at a global scale. We find that high phagotrophic investment is the dominant strategy across different oceanic biomes, used primarily for nitrogen acquisition. Our results therefore support empirical observations of the importance of mixotrophic grazers to upper ocean bacterivory.
The Ptch/SPOUT1 methyltransferase deposits an m
3
U modification on 28
S
rRNA for normal ribosomal function in flies and humans
Authors: Chen Jie , Bai Yaofu , Huang Yuantai , Cui Min , Wang Yiqing , Gu Zhenqi , Wu Xiaolong , Li Yubin , Rong Yikang S.
Published: December 2024

The ribosomal RNA (rRNA) is one of the most heavily modified RNA species in nature. Although we have advanced knowledge of the sites, functions, and the enzymology of many of the rRNA modifications from all kingdoms of life, we lack basic understanding of many of those that are not universally present. A single N
3
modified uridine base (m
3
U) was identified to be present on the 28
S
rRNA from humans and frogs but absent in bacteria or yeast. Here, we show that the equivalent m
3
U is present in
Drosophila
and that the Ptch/CG12128 enzyme and its human homolog SPOUT1 are both necessary and sufficient for carrying out the modification. The Ptch-modified U is at a functional center of the large ribosomal subunit, and, consistently,
ptch
-mutant cells suffer loss of ribosomal functions. SPOUT1, suggested to be the most druggable RNA methyltransferases in humans, represents a unique target where ribosomal functions could be specifically compromised in cancer cells.
Composition and in situ structure of the
Methanospirillum hungatei
cell envelope and surface layer
Authors: Wang Hui , Zhang Jiayan , Liao Shiqing , Henstra Anne M. , Leon Deborah , Erde Jonathan , Loo Joseph A. , Ogorzalek Loo Rachel R. , Zhou Z. Hong , Gunsalus Robert P.
Published: December 2024

Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo–electron tomography, we visualized the S-layer lattice surrounding
Methanospirillum hungatei
, a methanogenic archaeon. Though more compact than known structures,
M. hungatei
’s S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer’s cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment.
M. hungatei
cell’s end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.
Effect of pandemic influenza A virus PB1 genes of avian origin on viral RNA polymerase activity and pathogenicity
Authors: Williams Stephanie L. , Qi Li , Sheng Zong-Mei , Xiao Yongli , Freeman Ashley , Matthews Lex , Legaspi Sharon Fong , Fodor Ervin , Taubenberger Jeffery K.
Published: December 2024

Zoonotic influenza A virus (IAV) infections pose a substantial threat to global health. The influenza RNA-dependent RNA polymerase (RdRp) comprises the PB2, PB1, and PA proteins. Of the last four pandemic IAVs, three featured avian-origin PB1 genes. Prior research linked these avian PB1 genes to increased viral fitness when reassorted with human IAV genes. This study evaluated chimeric RdRps with PB1 genes from the 1918, 1957, and 1968 pandemic IAVs in a low pathogenic avian influenza (LPAI) virus background to assess polymerase activity and pathogenicity. Substituting in the pandemic PB1 genes reduced polymerase activity, virulence, and altered lung pathology, while the native LPAI PB1 showed the highest pathogenicity and polymerase activity. The native LPAI PB1 virus caused severe pneumonia and high early viral RNA levels, correlating with elevated host cytokine signaling. Increased genetic distance from the LPAI PB1 sequence correlated with reduced polymerase activity, IFN-β expression, viral replication, and pathogenicity.
Assembly and biological functions of metal-biomolecule network nanoparticles formed by metal-phosphonate coordination
Authors: Xu Wanjun , Lin Zhixing , Kim Chan-Jin , Wang Zhaoran , Wang Tianzheng , Cortez-Jugo Christina , Caruso Frank
Published: December 2024

Metal-organic networks have attracted widespread interest owing to their hybrid physicochemical properties. Natural biomolecules represent attractive building blocks for these materials because of their inherent biological function and high biocompatibility; however, assembling them into coordination network materials, especially nanoparticles (NPs), is challenging. Herein, we exploit the coordination between metal ions and phosphonate groups, which are present in many biomolecules, to form metal-biomolecule network (MBN) NPs in aqueous solution at room temperature. Various phosphonate-containing biomolecules, including plant phytate, DNA, and proteins, were used to assemble MBN NPs with tunable physicochemical properties (e.g., size). In addition to excellent biocompatibility and high cargo-loading efficiency (>95%), these two-component MBN NPs have various biological functionalities, including endosomal escape, immune regulation, and molecular recognition, thus offering advantages over nonbiomolecular-based coordination materials. This work expands our understanding of metal-organic chemistry with the emerging class of metal-biomolecule systems and provides a pathway for incorporating biofunctionalities into advanced coordination materials for diverse fields.
RSV explorations: using a case series focused on a single microbe to connect concepts across an undergraduate microbiology course
Authors: Tremaglio Chadene , Dube Derek
Published: December 2024

The ASM Curriculum Guidelines recommend that undergraduate microbiology courses should cover a wide variety of content ideally utilizing active learning approaches, which promote participation and enhance student success. However, in content-heavy courses, it can be easier to revert to traditional lecture-based teaching. Here, we describe a case series designed to increase student engagement and connect course concepts by exploring a single microbe in the context of different learning objectives. In this case series, respiratory syncytial virus (RSV) is used due to its fascinating history, well-described biology, and current clinical relevance, as well as recently described advances in creating a vaccine for RSV. This four-part case series can be embedded across several units of a general microbiology course as individual “explorations,” and employs multiple, evidence-based pedagogical approaches including case-based learning, engaging with primary literature, jigsaw strategy, analysis of real-world data sets, and whole-class discussion. Each exploration is designed to cover or expand on key concepts in microbiology, including milestones in the history of the field, Koch’s postulates and the germ theory of disease, the discovery of viruses, virus structure and replication, clinical epidemiology, and vaccines. Throughout the course, students work individually, in pairs, and in small groups to complete the activities, which take place predominantly during class. Student feedback indicates that they enjoy these activities as an alternative to traditional lecturing. This case series enables students to build connections between course concepts, assemble higher-order thinking about diverse topics in Microbiology, and apply their learning to real-world examples and scenarios.
Aquatic circoviruses: emerging pathogens in global aquaculture — from discovery to disease management
Authors: Wang Yuanyuan , Guo Changjun , He Jianguo
Published: December 2024

The expansion of global aquaculture has brought challenges from emerging pathogens, resulting in disease-related production losses across various regions. Among these pathogens, aquatic circoviruses—small, single-stranded DNA viruses initially detected in barbel (
Barbus barbus
)—have now been identified in multiple aquaculture species. These viruses have been associated with various clinical manifestations in economically important fish, crustacean, and mollusk species, including acute hemorrhage syndrome, which has shown mortality rates up to 95% in controlled laboratory infections of turbot. This review consolidates current knowledge on aquatic circoviruses, focusing on their genetic diversity, epidemiology, pathogenesis, and management strategies. The analysis encompasses observed host range patterns, documented instances of cross-species transmission, and evolutionary characteristics, such as host-specific clustering and recombination events. Research gaps are highlighted, particularly in understanding viral pathogenic mechanisms, host–pathogen interactions, and their ecological roles within aquatic ecosystems. We evaluate recent advances in diagnostic methods, including targeted vaccine design and RNA interference technology. The review outlines future research priorities, including elucidating cross-species transmission potential, developing effective treatments, and assessing the full economic impact of these viruses on aquaculture. By providing a comprehensive overview, this review aims to guide future research efforts and inform strategies to mitigate the impact of circoviruses on aquaculture sustainability.
FSTL1 and TLR4 interact with PEDV structural proteins to promote virus adsorption to host cells
Authors: Liu Chunyun , Kong Ning , Liu Hailong , Zhang Yu , Qin Wenzhen , Zhao Wenli , Yang Xinyu , Wang Yahe , Cao Xinyu , Liu Tian , Liu Yuchang , Sun He , Tong Wu , Yu Hai , Zheng Hao , Lan Daoliang , Xie Shengsong , Tong Guangzhi , Shan Tongling
Published: December 2024

Infection with porcine epidemic diarrhea virus (PEDV) results in enormous economic damage to the global swine industry. PEDV starts its life cycle by binding to the receptors of host cells and adsorbing onto the cellular surfaces. However, it is still unknown how PEDV adsorbs onto the surface of host cells and the mechanism beneath the interplay of host cell transmembrane protein with PEDV proteins. FSTL1, which is a secreted glycoprotein, participates in diverse pathological and physiological processes, including immune modulation and cell proliferation and differentiation. The transmembrane protein, TLR4, serves as a pattern recognition receptor recognizing a broad spectrum of pathogens, which exerts a crucial effect on the host immune system. In this study, we identified that FSTL1 promoted PEDV infection. Further studies demonstrated the interactive relationship between FSTL1 and PEDV structural proteins (N and S2). In addition, we also confirmed that TLR4 interacted with FSTL1 and PEDV N, S1, and S2 proteins on the cell surface. Moreover, FSTL1 promoted the interaction of TLR4 and PEDV and induced viral adsorption to host cells. This study offers explicit evidence that FSTL1 and TLR4 act as mediators for host cell adsorption of PEDV by interacting with PEDV N/S proteins.

IMPORTANCE

As a highly infectious porcine epidemic diarrhea virus (PEDV)-induced intestinal condition of swine, porcine epidemic diarrhea (PED) results in a 100% death rate among suckling piglets and poses a serious economic burden to global swine farming. Therefore, it is essential to investigate the mechanism of virus infection, replication, and proliferation. Virus begins its life cycle by binding to the receptor of host cells and adsorbing onto the cellular surfaces. However, it remains unclear how PEDV adsorbs onto the host cell surfaces. This study revealed that host protein FSTL1 interacted with the PEDV N and S2 proteins, while TLR4 interacted with the FSTL1 and PEDV proteins (N, S1, and S2). Moreover, we thoroughly and methodically demonstrated that FSTL1 was engaged in the PEDV internalization and attachment processes by promoting the recognition of PEDV N\S proteins by TLR4 and induced the viral adsorption to host cells.
Exploring the functional diversity and metabolic activities of the human gut microbiome in Thai adults in response to a prebiotic diet
Authors: Kingkaw Amornthep , Patumcharoenpol Preecha , Suratannon Narissara , Nakphaichit Massalin , Roytrakul Sittiruk , Vongsangnak Wanwipa
Published: December 2024

Exploring dietary methods to alter microbial communities and metabolic functions is becoming an increasingly fascinating strategy for improving health. Copra meal hydrolysate (CMH) is alternatively used as a gut health supplement. However, the functional diversity and metabolic activities in gut microbiome in relation to CMH treatment remain largely unknown. Therefore, this study aimed to identify key predominant groups of bacterial species toward diversified metabolic functions, activities, and routes using metaproteomics. As a result, the integrative analysis of metaproteomic data revealed that seven key families across 11 dominant gut bacterial species were concerted. Consistently, across 76,206 proteins assigned to the metabolism of the 255,964 annotated proteins, short-chain fatty acid (SCFA) biosynthesis, lipopolysaccharide (LPS) biosynthesis, and bile acid (BA) metabolism were positively associated with CMH. Further identification of cooperative metabolic routes promisingly highlighted the importance of glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, inositol phosphate metabolism, steroid hormone biosynthesis, O-antigen repeat unit biosynthesis, and chloroalkane and chloroalkene degradation. This work presents an initial study of metaproteomics associated with prebiotic diet in a Thai population-based cohort in a developing Southeast Asian country.

IMPORTANCE

Studies primarily focused on the impact of CMH on gastrointestinal symptoms and gut microbial compositions. However, as the field moves toward understanding the relationship between microbiome and diet in relation to gut health, it is critical to evaluate how changes in metabolic activities relate to cooperative metabolic routes in the gut microbiome for promoting human health. Through the use of metaproteomics, our findings highlighted the key predominant groups of bacterial species, potential proteins, and their metabolic routes involved in gut metabolism. This study provides comprehensive insights into the fundamental relationship between microbiome and dietary supplements and suggests that metaproteomics is a powerful method for monitoring metabolic functions, activities, and routes in the gut microbiome.
Supplemental Material: Devonian–Permian sedimentation in the Central Yunnan basin, SW Yangtze block (South China): Insights into provenance and paleogeography of Li-rich bauxitic claystone
Authors: Yan Zhen , al. et
Published: December 2024

Table S1: Geochemical data. Table S2: LA-ICP-MS zircon U-Pb age data.
Managing preschool wheeze: a qualitative study of parents’ views and experiences
Authors: Mohammed Abdul Wajid Lubna , Saglani Sejal , Nagakumar Prasad , Heath Gemma
Published: December 2024

Objective

The aim of this study was to explore parents’ views and experiences of managing preschool wheeze, including opinions on the use of investigations to inform treatment pathways.

Design

Purposive sampling was used to recruit 16 participants from 14 families across England and Wales. Qualitative data were collected via semi-structured interviews with parents of children aged 1–5 years with preschool wheeze, conducted on Microsoft (MS) Teams. Data were transcribed and analysed using thematic analysis, facilitated by NVivo software package.

Results

Analysis generated four themes: (1) pathway to diagnosis, (2) medication management, (3) living with preschool wheeze and (4) improving preschool wheeze healthcare. Findings suggest a negative impact of preschool wheeze on families’ lives, including high levels of worry and limiting capacity for work and travel. Barriers to effective management of preschool wheeze included inconsistent terminologies and diagnostic uncertainty alongside limited education and management support. Other barriers included parental concerns about medications, delayed investigations and challenges with accessing specialist care. Parents were in favour of performing investigations to guide treatment pathways.

Conclusion

Parents’ views highlight the problem of diagnosing and treating preschool wheeze at multiple system levels. To improve management and ensure that services for children with preschool wheeze are effective, there is an urgent need for consistent terminology, a unified approach to guide investigations and treatments and for upskilling healthcare professionals in primary and secondary care.
Number of macula optical coherence tomography scans needed to detect glaucoma progression
Authors: Mahmoudinezhad Golnoush , Moghimi Sasan , Latif Kareem , Brye Nicole , Walker Evan , Nishida Takashi , Du Kelvin H , Gunasegaran Gopikasree , Wu Jo-Hsuan , Liebmann Jeffrey M , Fazio Massimo A , Girkin Christopher A , Zangwill Linda M , Weinreb Robert N
Published: December 2024

Background

To evaluate the impact of testing frequency on the time required to detect statistically significant glaucoma progression for ganglion cell complex (GCC) with optical coherence tomography (OCT).

Materials and methods

From multicentre glaucoma registries, 332 eyes of 201 glaucoma patients were enrolled over an average of 4.4 years. Patients with 4 or more OCT tests were selected to calculate the longitudinal rates of GCC thickness change over time by linear regression. A computer simulation was then used to generate real-world GCC data and assess the time required to detect progression at different loss rates and testing frequencies based on variability estimates. Time and accuracy to detect worsening of progression were calculated.

Results

As testing frequency increased, the time required to detect a statistically significant negative GCC slope decreased, but not proportionally. All eyes with a GCC loss of −1 µm/year progressed after 3.8, 2.6 and 2.2 years on average when testing was conducted one, two and three times per year, respectively. For eyes with a GCC loss of −1.5 µm/year, progression was identified after 3.3, 2.2, and 1.8 years on average, respectively.

Conclusion

Increasing the frequency of macular OCT testing to three times per year more sensitively detects progression compared with two times per year. However, two times per year testing may be sufficient in clinical settings to detect progression and also to reduce the healthcare burden.

Trial registration numbers

NCT00221897,NCT00221923.
Association between birth weight and chronic obstructive pulmonary disease in the UK Biobank: a prospective cohort study
Authors: Luo Pengfei , He Jialiu , Wan Xinglin , Li Mengxia , Zhu Zheng , Chen Lulu , Hang Dong , Su Jian , Tao Ran , Zhou Jinyi , Fan Xikang
Published: December 2024

Background

Birth weight has been reported to be associated with chronic obstructive pulmonary disease (COPD) in adulthood, but the results have not yet been determined. This study aims to analyse the potential association of birth weight with COPD risk in UK Biobank.

Methods

We conducted a prospective analysis for participants without baseline COPD in UK Biobank. The HRs and 95% CIs were calculated by multivariable Cox regression models, and dose-response relationship was evaluated by restricted cubic splines. Besides, we also calculated the interactions for covariates and further analysed the joint effects.

Results

A total of 251 172 participants with birth weight data were included in this study, and 5602 COPD cases were found during follow-up. According to Cox regression models, participants with the lowest quintile of birth weight (< 2.86 kg) had higher risk for COPD (HR=1.21, 95% CI 1.11 to 1.32). In addition, the dose‒response analysis showed a non-linear relationship between birth weight and COPD risk, which first decreased and then increased, and the interactions for age, passive smoking and maternal smoking were also found by stratified analysis. Furthermore, we also found the joint effects between COPD risk and maternal smoking in the lowest quintile group.

Conclusions

This study indicated that lower birth weight may increase the risk of COPD. The non-linear associations between birth weight and COPD risk for prospective cohort; as birth weight increased, the risk showed a trend of decreasing first and then increasing. Moreover, maternal smoking had a joint effect with low birth weight for COPD risk.
Ultrasound-guided transbronchial cryobiopsy of mediastinal and hilar lesions: a multicenter pragmatic cohort study with real-world evidence
Authors: Mangold Melanie Scarlett , Franzen Daniel P , Hetzel Jürgen , Latshang Tsogyal D , Roeder Maurice , Vesenbeckh Silvan M , Ulrich Silvia , Gaisl Thomas , Steinack Carolin
Published: December 2024

Background

Limited data exist on the reliability, efficacy and safety of ultrasound-guided transbronchial cryobiopsy for suspicious mediastinal and hilar lesions. This study shares findings from implementing this method and compares the results with those of the standard endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA).

Methods

Patients undergoing diagnostic bronchoscopy for mediastinal or hilar lesions in four Swiss centres were included. The study aims to assess the diagnostic yield and safety of EBUS-guided cryobiopsy compared with EBUS-TBNA. Tunnelling to the target lesion was performed using an electric needle knife (70.8%), a 19 G- (12.4%) or a 22 G needle (16.8%). Cryobiopsies were obtained with a freezing time of 4–7 s (18.2% with a 1.7 mm probe) or 6–10 s (81.8% with a 1.1 mm probe).

Results

Altogether, 137 patients were enrolled with a median follow-up of 89 days. The overall diagnostic yield was 56.2% for EBUS-TBNA and 91.2% for cryobiopsies (p<0.001). Cryobiopsies increased the diagnostic yield for benign disorders (+28.5%), uncommon tumours (+5.9%) and other metastatic cancer (+0.6%), but not for lung cancer (+0%). For lung cancer (n=27), immunohistochemistry was obtainable in 40.7% of EBUS-TBNA (median of 3 probes [IQR 3 to 3]), significantly lower than cryobiopsy’s 88.9% yield (median of 4 probes [IQR 3 to 5]) (p<0.001). Adverse events were found in 23.4% of participants; 10.2% had mild to moderate bleeding, 0.7% had pneumonia, and 0.7% (one) of patients had pneumothorax following pneumomediastinum. No deaths or mediastinum infections were observed.

Conclusion

Cryobiopsy of mediastinal and hilar lesions improves the diagnostic yield compared with EBUS-TBNA while maintaining a favourable safety profile.
Assessing the impact of information on patient attitudes toward artificial intelligence-based clinical decision support (AI/CDS): a pilot web-based SMART vignette study
Authors: Kim Bohye , Ryan Katie , Kim Jane Paik
Published: December 2024

Background

It is increasingly recognised that the success of artificial intelligence-based clinical decision support (AI/CDS) tools will depend on physician and patient trust, but factors impacting patients’ views on clinical care reliant on AI have been less explored.

Objective

This pilot study explores whether, and in what contexts, detail of explanation provided about AI/CDS tools impacts patients’ attitudes toward the tools and their clinical care.

Methods

We designed a Sequential Multiple Assignment Randomized Trial vignette web-based survey. Participants recruited through Amazon Mechanical Turk were presented with hypothetical vignettes describing health concerns and were sequentially randomised along three factors: (1) the level of detail of explanation regarding an AI/CDS tool; (2) the AI/CDS result; and (3) the physician’s level of agreement with the AI/CDS result. We compared mean ratings of comfort and confidence by the level of detail of explanation using t-tests. Regression models were fit to confirm conditional effects of detail of explanation.

Results

The detail of explanation provided regarding the AI/CDS tools was positively related to respondents’ comfort and confidence in the usage of the tools and their perception of the physician’s final decision. The effects of detail of explanation on their perception of the physician’s final decision were different given the AI/CDS result and the physician’s agreement or disagreement with the result.

Conclusions

More information provided by physicians regarding the use of AI/CDS tools may improve patient attitudes toward healthcare involving AI/CDS tools in general and in certain contexts of the AI/CDS result and physician agreement.
Object naming after epilepsy surgery in the dominant left temporal lobe: risk factors, time course and long-term outcome
Authors: Walther Katrin , Reindl Caroline , Schwarz Michael , Gollwitzer Stephanie , Kasper Burkhard S , Lang Johannes Dominik , Stritzelberger Jenny , Brandner Sebastian , Rössler Karl , Zhao Yining , Dörfler Arnd , Hamer Hajo M
Published: December 2024

Background

Deterioration in naming function is a common sequelae after epilepsy surgery in the language-dominant temporal lobe but information on recovery and long-term outcome is scarce. We, therefore, assessed short-term and long-term outcome of object naming in patients undergoing surgery in the temporal lobe and determined factors affecting deterioration and recovery of naming function.

Method

Object naming (Boston naming test) before surgery, at early follow-up (FU, 6–12 months) and late FU (≥2 years) was assessed in people with epilepsy (PWE) undergoing resections in the language-dominant left and non-dominant right temporal lobe.

Results

Sixty-six patients with left temporal lobe epilepsy (LTLE) and 87 control patients with right temporal lobe epilepsy (RLTE) were included. At early FU, 28 patients with LTLE (42%) and three patients with RTLE (3%) showed a significant naming decline. In patients with LTLE, risk for deterioration increased with lower verbal memory before surgery, older age at seizure onset and was particularly high with posterior temporal resections (≥40 mm from the temporal pole) and seizure onset >16 years. Of the patients with LTLE with early naming decline, 11 patients (39%) recovered fully in their naming abilities at late FU, averaging almost 10 years. Recovery was associated with the degree of postoperative naming decline at early FU. PWE with a decline of less than 10 items (<20%) had a good prognosis of recovery at late FU. Postoperative seizure control had no significant effect on recovery.

Conclusions

In our cohort, less than 50% of PWE showed significantly deteriorated naming function after resection of the dominant temporal lobe. If a decline occurred, it appeared to recover to a certain degree and remained as a permanent deficit in 26% of the patients. Long-term outcome of visual object naming can be predicted by the degree of early postoperative decline.
Pneumococcal pneumonia trends in adults hospitalised with community-acquired pneumonia over 10 years (2013–2023) and the role of serotype 3
Authors: Lansbury Louise , McKeever Tricia M , Lawrence Hannah , Pick Harry , Baskaran Vadsala , Edwards-Pritchard Rochelle , Matthews Laura , Bailey Helen , Ashton Deborah , Bendall Lesley , Rodrigo Chamira , Daniel Priya , Litt David , Eletu Seyi , Parmar Hanshi , Sheppard Carmen , Ladhani Shamez N , Trotter Caroline , Lim Wei Shen
Published: December 2024

Background

With higher valency pneumococcal vaccines on the horizon and new adult immunisation strategies under discussion, we aimed to evaluate the contribution of individual pneumococcal serotypes to the burden of pneumococcal community-acquired pneumonia (CAP). Over 10 years, trends in pneumococcal pneumonia epidemiology in adults hospitalised with CAP were assessed. The risk factors and severity associated with serotype 3 were examined.

Methods

We conducted a prospective cohort study of adults hospitalised with CAP between September 2013 and May 2023. Pneumococcal serotypes were identified using a serotype-specific 24-valent urinary-antigen assay. Trends in the proportion of CAP due to pneumococcus and causative serotypes were compared prepandemic and postpandemic. Risk factors and severity of serotype 3 pneumonia were compared with other serotypes using logistic regression.

Results

Of 5186 patients with CAP, 2193 (42.2%) had pneumococcal pneumonia. The proportion of CAP due to pneumococcus increased across all ages between 2013 and 2023 (36.4%–66.9%, p<0.001). The proportion due to serotype 3 increased significantly from 13.4% (2013) to 48.8% (2023). Serotype 3 pneumonia in adults was associated with older age (p<0.001), male sex (adjusted OR (aOR) 2.22, 95% CI 1.64 to 3.01) and chronic renal disease (aOR 1.81, 95% CI 1.09 to 3.02). Serotype 3 pneumonia was not observed to be associated with severity, critical care requirement, mortality or readmission.

Interpretation

Serotype 3 is the predominant serotype in adult pneumococcal CAP and has been increasing despite a mature infant pneumococcal immunisation programme, consistent with a lack of herd protection for this serotype.
A systematic review on catalytic synthesis of heterocyclic compounds using cobalt oxide and nickel oxide nanomaterials
Authors: Kadam Vikas K. , Shinde Rushikesh , Patil Shubham , Shelke Vaibhav , Pingale Shirish S.
Published: December 2024

Magnetic Cobalt Oxide (CoO/Co2O3/Co3[Formula: see text] and Nickel Oxide (NiO) Nanoparticles have been widely reported as heterogeneous catalysts for the preparation of derivatives of heterocycles. These are abundant, eco-friendly, relatively nontoxic and inexpensive catalysts. This review consists of the previous 10-year publications on the catalytic applications of Cobalt Oxide and Nickel Oxide Nanoparticles for the synthesis of heterocycles and their derivatives. Among the various metal oxide nanomaterials reported in the literature as catalyst materials for the synthesis of varied heterocycles and their derivatives, we have kept our focus on the key materials viz. Cobalt Oxide and Nickel Oxide Nanoparticles. In the conclusion part, we have also commented on the better options for the catalyst selection among the reports covered in this paper. This paper will definitely be useful for new researchers in the metal oxide nanomaterials-based catalytic applications for synthetic heterocyclic compounds.
Lithospheric structure and seismic anisotropy of the northern Appalachian region
Authors: Darbyshire Fiona A.
Published: December 2024

Over the course of more than 30 years, the seismic structure of the Appalachian Orogen of northern New England and Canada has been studied using several active- and passive-source methods. The resulting models shed light on present-day crust and upper-mantle wave speed structure, seismic anisotropy, and their relationship to the complex geological history of the region. Notable contributions were made by the Lithoprobe East project in the 1980s/1990s, and by the EarthScope USArray in the 2010s. Crustal studies revealed significant heterogeneity across the northern Appalachians. Variations in upper- and mid-crustal seismic wave speeds correlate with metamorphic grade and composition across the Appalachian domains, and the interaction between the Laurentian margin and accreted terranes varies along strike. Crustal thicknesses typically range from ∼30 to 46 km. Lithospheric thicknesses vary from ∼70 to 120 km beneath Maine and the Canadian Maritimes, preserving orogenic structures including a potential signature of flat-slab subduction. Anisotropic orientations are oblique to orogenic trends in New England, but sub-parallel in the Canadian Appalachians, with spatial variations that suggest a significant contribution from lithospheric deformational fabric associated with Palaeozoic orogenesis and later rifting processes.
Editorial: TOSEM Journal in 2025 and Beyond
Authors: Roychoudhury Abhik
Published: December 2024

TOSEM is ACM’s flagship journal for publishing
software engineering (SE)
research. TOSEM stays true to the foundations of the discipline while meaningfully engaging with the wave of disruptive innovations in the field. In this light, we discuss the plans for TOSEM in 2025. We discuss how we plan to continue to engage broadly with authors as well as the community as a whole.
Distributed Machine Learning in Edge Computing: Challenges, Solutions and Future Directions
Authors: Tu Jingke , Yang Lei , Cao Jiannong
Published: December 2024

Distributed machine learning on edges is widely used in intelligent transportation, smart home, industrial manufacturing, and underground pipe network monitoring to achieve low latency and real time data processing and prediction. However, the presence of a large number of sensing and edge devices with limited computing, storage, and communication capabilities prevents the deployment of huge machine learning models and hinders its application. At the same time, although distributed machine learning on edges forms an emerging and rapidly growing research area, there has not been a systematic survey on this topic. The article begins by detailing the challenges of distributed machine learning in edge environments, such as limited node resources, data heterogeneity, privacy, security issues, and summarizes common metrics for model optimization. We then present a detailed analysis of parallelism patterns, distributed architectures, and model communication and aggregation schemes in edge computing. we subsequently present a comprehensive classification and intensive description of node resource-constrained processing, heterogeneous data processing, attacks and protection of privacy. The article ends by summarizing the applications of distributed machine learning in edge computing and presenting problems and challenges for further research.
Acceleration by Stepsize Hedging: Multi-Step Descent and the Silver Stepsize Schedule
Authors: Altschuler Jason , Parrilo Pablo
Published: December 2024

Can we accelerate the convergence of gradient descent without changing the algorithm—just by judiciously choosing stepsizes? Surprisingly, we show that the answer is yes. Our proposed
Silver Stepsize Schedule
optimizes strongly convex functions in

\(\kappa ^{\log _{\rho } 2} \approx \kappa ^{0.7864} \)

iterations, where

\(\rho =1+\sqrt {2} \)

is the silver ratio and
κ
is the condition number. This is intermediate between the textbook unaccelerated rate
κ
and the accelerated rate
κ
1/2
due to Nesterov in 1983. The non-strongly convex setting is conceptually identical, and standard black-box reductions imply an analogous partially accelerated rate

\(\varepsilon ^{-\log _{\rho } 2} \approx \varepsilon ^{-0.7864} \)

. We conjecture and provide partial evidence that these rates are optimal among all stepsize schedules.

The Silver Stepsize Schedule is constructed recursively in a fully explicit way. It is non-monotonic, fractal-like, and approximately periodic of period

\(\kappa ^{\log _{\rho } 2} \)

. This leads to a phase transition in the convergence rate: initially super-exponential (acceleration regime), then exponential (saturation regime).

The core algorithmic intuition is
hedging
between individually suboptimal strategies—short steps and long steps—since bad cases for the former are good cases for the latter, and vice versa. Properly combining these stepsizes yields faster convergence due to the misalignment of worst-case functions. The key challenge in proving this speedup is enforcing long-range consistency conditions along the algorithm’s trajectory. We do this by developing a technique that recursively glues constraints from different portions of the trajectory, thus removing a key stumbling block in previous analyses of optimization algorithms. More broadly, we believe that the concepts of hedging and multi-step descent have the potential to be powerful algorithmic paradigms in a variety of contexts in optimization and beyond.

This paper publishes and extends the first author’s 2018 Master’s Thesis (advised by the second author)—which established for the first time that judiciously choosing stepsizes can enable acceleration in convex optimization. Prior to this thesis, the only such result was for the special case of quadratic optimization, due to Young in 1953.
Supplementary Table 1 from SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors
Authors: Palmer Theron , Kessler Michael D. , Shao Xiaoshan M. , Balan Archana , Yarchoan Mark , Zaidi Neeha , Lopez-Vidal Tamara Y. , Saeed Ali M. , Gore Jessica , Azad Nilofer S. , Jaffee Elizabeth M. , Favorov Alexander V. , Anagnostou Valsamo , Karchin Rachel , Gaykalova Daria A. , Fertig Elana J. , Danilova Ludmila
Published: December 2024

Supplementary Table S1. TCGA cancer study abbreviations and names.
Figure 6 from SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors
Authors: Palmer Theron , Kessler Michael D. , Shao Xiaoshan M. , Balan Archana , Yarchoan Mark , Zaidi Neeha , Lopez-Vidal Tamara Y. , Saeed Ali M. , Gore Jessica , Azad Nilofer S. , Jaffee Elizabeth M. , Favorov Alexander V. , Anagnostou Valsamo , Karchin Rachel , Gaykalova Daria A. , Fertig Elana J. , Danilova Ludmila
Published: December 2024

Per splice junction normalized SA for responders compared with baseline samples. The SA averaged across samples for the subset of splice junctions derived from the top 20 genes with the highest SA per sample. The black horizontal line is the median SA for baseline samples. *, P value ≤ 0.05; **, P value ≤ 0.005; ***, P value ≤ 0.0005; ****, P value ≤ 0.00005. SA, splicing antigenicity.
Figure 3 from SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors
Authors: Palmer Theron , Kessler Michael D. , Shao Xiaoshan M. , Balan Archana , Yarchoan Mark , Zaidi Neeha , Lopez-Vidal Tamara Y. , Saeed Ali M. , Gore Jessica , Azad Nilofer S. , Jaffee Elizabeth M. , Favorov Alexander V. , Anagnostou Valsamo , Karchin Rachel , Gaykalova Daria A. , Fertig Elana J. , Danilova Ludmila
Published: December 2024

SA by tissue type and in relation to the tumor mutational burden. A, The SA averaged across genes per sample for tumor and normal samples for each tumor type analyzed (Wilcoxon test, Cohens d). B, The SA averaged across all genes per sample for TMB=high and TMB-low samples for all analyzed TCGA samples (linear regression, Cohens d). **, P value ≤ 0.005; ***, P value ≤ 0.0005; ****, P value ≤ 0.00005. See TCGA cancer-type abbreviations in Supplementary Table S1. SA, splicing antigenicity.
Allergen Sensitization in Allergic Skin Diseases in Suzhou, East China: A Retrospective Study from 2021 to 2023
Authors: Zheng Chunjiao , Dong Jiacheng , Li Peizhen , Li Yan , Wang Miaomiao , Zhu Yueqian , Wu Tingting , Zhou Naihui
Published: December 2024

Introduction: Allergen distribution varies geographically, and local epidemiological data can guide disease prevention and management. We investigated allergen sensitization among patients with three types of allergic skin disease in Suzhou, East China, from 2021 to 2023.
Methods: Serum-specific immunoglobulin-E levels were analyzed from 4,603 patients who visited The First Affiliated Hospital of Soochow University between January 2021 and December 2023. Sensitization prevalence to 20 allergen species was assessed, considering age, sex, year, and disease type.
Results: Common aeroallergens included Dermatophagoides farinae, Dermatophagoides pteronyssinus, and house dust, while major food allergens were soybean, egg, and crab. Children exhibited higher sensitization rates, with males more sensitized to D. farinae, D. pteronyssinus, Alternaria, and milk, and females more sensitized to Blattella germanica and egg. Compared with previous years, sensitization rates for soybean and milk decreased in 2023, whereas those for D. farinae and crab increased. Patients with atopic dermatitis had the highest overall sensitization rates.
Conclusion: Allergen sensitization patterns in Suzhou varied by age, sex, year, and disease type. Understanding these patterns can help improve the management of allergic skin diseases in this region.
Gender as a Contextual Factor in Quality of Life of Cancer Survivors: A Literature Review
Authors: Göttgens Irene , Oertelt-Prigione Sabine
Published: December 2024

Background: Cancer survivorship brings numerous challenges extending beyond physical health to include psychological, social, and functional aspects that define the quality of life (QoL) of survivors. Although recognizing that diverse gender experiences lead to different ways of coping with these challenges, many clinical trials fail to account for the distinct constructs of “sex” and “gender,” often conflating the two. This review highlights how gender-related aspects can manifest in core QoL domains for cancer survivors, emphasizing the importance of inclusive and effective support systems and interventions. Summary: While interest in the impact of gender is increasing in cancer survivor research, the terms “sex” and “gender” are still often conflated in research. Gender is a social concept consisting of multiple dimensions, such as gender identity, gender roles and norms, and gender relations. Each of these dimensions can have a distinct impact on the QoL domain of cancer survivors. Research indicates that not gender identity, but gender roles, norms, and relations can significantly influence coping behaviors that, subsequently, impact QoL domains such as physical, emotional, social, and role functioning. Understanding the interplay of gender roles, norms, and their relations with other contextual social factors is crucial for developing inclusive and effective support systems and interventions for cancer survivors. Key Messages: Gender roles and norms impact important QoL domains of cancer survivors. It is important to recognize that gendered behaviors, as a result of internalized or socially desired gender roles and norms, can both help and hinder effective coping with cancer, affecting QoL.
Pose analysis in free-swimming adult zebrafish, Danio rerio: “fishy” origins of movement design
Authors: Kanwal Jagmeet S. , Sanghera Bhavjeet S. , Dabbi Riya , Glasgow Eric
Published: December 2024

Introduction
Movement requires maneuvers that generate thrust to either make turns or move the body forward in physical space. The computational space for perpetually controlling the relative position of every point on the body surface can be vast. We hypothesize the evolution of efficient design for movement that minimizes active (neural) control by leveraging the passive (reactive) forces between the body and the surrounding medium at play. To test our hypothesis, we investigate the presence of stereotypical postures during free-swimming in adult zebrafish, Danio rerio.
Methods
We perform markerless tracking using DeepLabCut, a deep learning pose estimation toolkit, to track geometric relationships between body parts. To identify putative clusters of postural configurations obtained from twelve freely behaving zebrafish, we use unsupervised multivariate time-series analysis (B-SOiD machine learning software).
Results
When applied to single individuals, this method reveals a best-fit for 36 to 50 clusters in contrast to 86 clusters for data pooled from all 12 animals. The centroids of each cluster obtained over 14,000 sequential frames recorded for a single fish represent an apriori classification into relatively stable “target body postures” and inter-pose “transitional postures” that lead towards and away from a target pose. We use multidimensional scaling of mean parameter values for each cluster to map cluster-centroids within two dimensions of postural space. From a post-priori visual analysis, we condense neighboring postural variants into 15 superclusters or core body configurations. We develop a nomenclature specifying the anteroposterior level/s (upper, mid and lower) and degree of bending.
Conclusion
Our results suggest that constraining bends to mainly three levels in adult zebrafish preempts the neck, fore- and hindlimb design for maneuverability in land vertebrates.