bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved molecular chaperone PrsA stimulates protective immunity against group A Streptococcus
Authors: Lai Chien-Yu , Xie Jia-Xun , Lai Meng-Chih , Wu Zhao-Yi , Lin Jr-Shiuan , Huang Yu-Tsung , Chi Chia-Yu , Chiang-Ni Chuan , Walker Mark J. , Chang Yung-Chi 
Published: February 2024

AbstractGroup A Streptococcus (GAS) is a significant human pathogen that poses a global health concern. However, the development of a GAS vaccine has been challenging due to the multitude of diverse M-types and the risk of triggering cross-reactive immune responses. Our previous research has identified a critical role of PrsA1 and PrsA2, surface post-translational molecular chaperone proteins, in maintaining GAS proteome homeostasis and virulence traits. In this study, we aimed to further explore the potential of PrsA1 and PrsA2 as vaccine candidates for preventing GAS infection. We found that PrsA1 and PrsA2 are highly conserved among GAS isolates, demonstrating minimal amino acid variation. Antibodies specifically targeting PrsA1/A2 showed no cross-reactivity with human heart proteins and effectively enhanced neutrophil opsonophagocytic killing of various GAS serotypes. Additionally, passive transfer of PrsA1/A2-specific antibodies conferred protective immunity in infected mice. Compared to alum, immunization with CFA-adjuvanted PrsA1/A2 induced higher levels of Th1-associated IgG isotypes and complement activation and provided approximately 70% protection against invasive GAS challenge. These findings highlight the potential of PrsA1 and PrsA2 as universal vaccine candidates for the development of an effective GAS vaccine.
Automated model building and protein identification in cryo-EM maps
Authors: Jamali Kiarash , Käll Lukas , Zhang Rui , Brown Alan , Kimanius Dari , Scheres Sjors H. W. 
Published: February 2024

AbstractInterpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality to those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy to those built by humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will therefore remove bottlenecks and increase objectivity in cryo-EM structure determination.
The Dresden in vivo OCT dataset for automatic middle ear segmentation
Authors: Liu Peng , Steuer Svea , Golde Jonas , Morgenstern Joseph , Hu Yujia , Schieffer Catherina , Ossmann Steffen , Kirsten Lars , Bodenstedt Sebastian , Pfeiffer Micha , Speidel Stefanie , Koch Edmund , Neudert Marcus 
Published: February 2024

AbstractEndoscopic optical coherence tomography (OCT) offers a non-invasive approach to perform the morphological and functional assessment of the middle ear in vivo. However, interpreting such OCT images is challenging and time-consuming due to the shadowing of preceding structures. Deep neural networks have emerged as a promising tool to enhance this process in multiple aspects, including segmentation, classification, and registration. Nevertheless, the scarcity of annotated datasets of OCT middle ear images poses a significant hurdle to the performance of neural networks. We introduce the Dresden in vivo OCT Dataset of the Middle Ear (DIOME) featuring 43 OCT volumes from both healthy and pathological middle ears of 29 subjects. DIOME provides semantic segmentations of five crucial anatomical structures (tympanic membrane, malleus, incus, stapes and promontory), and sparse landmarks delineating the salient features of the structures. The availability of these data facilitates the training and evaluation of algorithms regarding various analysis tasks with middle ear OCT images, e.g. diagnostics.
Comparison of online, offline, and hybrid hypotheses of motor sequence learning using a quantitative model that incorporate reactive inhibition
Authors: Gupta Mohan W. , Rickard Timothy C. 
Published: February 2024

AbstractTwo hypotheses have been advanced for when motor sequence learning occurs: offline between bouts of practice or online concurrently with practice. A third possibility is that learning occurs both online and offline. A complication for differentiating between those hypotheses is a process known as reactive inhibition, whereby performance worsens over consecutively executed sequences, but dissipates during breaks. We advance a new quantitative modeling framework that incorporates reactive inhibition and in which the three learning accounts can be implemented. Our results show that reactive inhibition plays a far larger role in performance than is appreciated in the literature. Across four groups of participants in which break times and correct sequences per trial were varied, the best overall fits were provided by a hybrid model. The version of the offline model that does not account for reactive inhibition, which is widely assumed in the literature, had the worst fits. We discuss implications for extant hypotheses and directions for future research.
First isolation and genotyping of pathogenic Leptospira spp. from Austria
Authors: Sohm Cynthia , Willixhofer Denise , Fasching Eva , Waldner Karoline , Deitzer Nicole , Steiner Janina , Jöbstl Julia , Schleicher Corina , Schwarz Marcel , Fuchs Reinhard , Bourhy Pascale , Käsbohrer Annemarie , Wittek Thomas , Firth Clair , Steinparzer Romana , Desvars-Larrive Amélie 
Published: February 2024

AbstractLeptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospira strains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2–6 h and a real-time PCR targeting the lipL32 gene was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.
Fully automated deep learning based auto-contouring of liver segments and spleen on contrast-enhanced CT images
Authors: Gupta Aashish C. , Cazoulat Guillaume , Al Taie Mais , Yedururi Sireesha , Rigaud Bastien , Castelo Austin , Wood John , Yu Cenji , O’Connor Caleb , Salem Usama , Silva Jessica Albuquerque Marques , Jones Aaron Kyle , McCulloch Molly , Odisio Bruno C. , Koay Eugene J. , Brock Kristy K. 
Published: February 2024

AbstractManual delineation of liver segments on computed tomography (CT) images for primary/secondary liver cancer (LC) patients is time-intensive and prone to inter/intra-observer variability. Therefore, we developed a deep-learning-based model to auto-contour liver segments and spleen on contrast-enhanced CT (CECT) images. We trained two models using 3d patch-based attention U-Net ($${{\text{M}}}_{{\text{paU}}-{\text{Net}}})$$

M

paU
-
Net

)

and 3d full resolution of nnU-Net ($${{\text{M}}}_{{\text{nnU}}-{\text{Net}}})$$

M

nnU
-
Net

)

to determine the best architecture ($${\text{BA}})$$

BA
)

. BA was used with vessels ($${{\text{M}}}_{{\text{Vess}}})$$

M
Vess

)

and spleen ($${{\text{M}}}_{{\text{seg}}+{\text{spleen}}})$$

M

seg
+
spleen

)

to assess the impact on segment contouring. Models were trained, validated, and tested on 160 ($${{\text{C}}}_{{\text{RTTrain}}}$$

C
RTTrain

), 40 ($${{\text{C}}}_{{\text{RTVal}}}$$

C
RTVal

), 33 ($${{\text{C}}}_{{\text{LS}}}$$

C
LS

), 25 (CCH) and 20 (CPVE) CECT of LC patients. $${{\text{M}}}_{{\text{nnU}}-{\text{Net}}}$$

M

nnU
-
Net

outperformed $${{\text{M}}}_{{\text{paU}}-{\text{Net}}}$$

M

paU
-
Net

across all segments with median differences in Dice similarity coefficients (DSC) ranging 0.03–0.05 (p < 0.05). $${{\text{M}}}_{{\text{seg}}+{\text{spleen}}}$$

M

seg
+
spleen

, and $${{\text{M}}}_{{\text{nnU}}-{\text{Net}}}$$

M

nnU
-
Net

were not statistically different (p > 0.05), however, both were slightly better than $${{\text{M}}}_{{\text{Vess}}}$$

M
Vess

by DSC up to 0.02. The final model, $${{\text{M}}}_{{\text{seg}}+{\text{spleen}}}$$

M

seg
+
spleen

, showed a mean DSC of 0.89, 0.82, 0.88, 0.87, 0.96, and 0.95 for segments 1, 2, 3, 4, 5–8, and spleen, respectively on entire test sets. Qualitatively, more than 85% of cases showed a Likert score $$\ge$$
≥
3 on test sets. Our final model provides clinically acceptable contours of liver segments and spleen which are usable in treatment planning.
Odor identification score as an alternative method for early identification of amyloidogenesis in Alzheimer’s disease
Authors: Igeta Yukifusa , Hemmi Isao , Yuyama Kohei , Ouchi Yasuyoshi 
Published: February 2024

AbstractA simple screening test to identify the early stages of Alzheimer’s disease (AD) is urgently needed. We investigated whether odor identification impairment can be used to differentiate between stages of the A/T/N classification (amyloid, tau, neurodegeneration) in individuals with amnestic mild cognitive impairment or AD and in healthy controls. We collected data from 132 Japanese participants visiting the Toranomon Hospital dementia outpatient clinic. The odor identification scores correlated significantly with major neuropsychological scores, regardless of apolipoprotein E4 status, and with effective cerebrospinal fluid (CSF) biomarkers [amyloid β 42 (Aβ42) and the Aβ42/40 and phosphorylated Tau (p-Tau)/Aβ42 ratios] but not with ineffective biomarkers [Aβ40 and the p-Tau/total Tau ratio]. A weak positive correlation was observed between the corrected odor identification score (adjusted for age, sex, ApoE4 and MMSE), CSF Aβ42, and the Aβ42/40 ratio. The odor identification score demonstrated excellent discriminative power for the amyloidogenesis stage , according to the A/T/N classification, but was unsuitable for differentiating between the p-Tau accumulation and the neurodegeneration stages. After twelve odor species were analyzed, a version of the score comprising only four odors—India ink, wood, curry, and sweaty socks—proved highly effective in identifying AD amyloidogenesis, showing promise for the screening of preclinical AD.
Microplastic separation and enrichment in microchannels under derivative electric field gradient by bipolar electrode reactions
Authors: Sun Zhenrong , Ma Chicheng , Yu Chengjiao , Li Zirui 
Published: February 2024

AbstractThe decomposed plastic products in the natural environment evolve into tiny plastic particles with characteristics such as small size, lightweight, and difficulty in removal, resulting in a significant pollution issue in aquatic environments. Significant progress has been made in microplastic separation technology benefiting from microfluidic chips in recent years. Based on the mechanisms of microfluidic control technology, this study investigates the enrichment and separation mechanisms of polystyrene particles in an unbuffered solution. The Faraday reaction caused by the bipolar electrodes changes the electric field gradient and improves the separation efficiency. We also propose an evaluation scheme to measure the separation efficiency. Finite element simulations are conducted to parametrically analyze the influence of applied voltages, channel geometry, and size of electrodes on plastic particle separation. The numerical cases indicate that the electrode-installed microfluidic channels separate microplastic particles effectively and precisely. The electrodes play an important role in local electric field distribution and trigger violent chemical reactions. By optimizing the microchannel structure, applied voltages, and separation channel angle, an optimal solution for separating microplastic particles can be found. This study could supply some references to control microplastic pollution in the future.
Combinatorial characterization of metastable luminous silver cations
Authors: Masai Hirokazu , Koshimizu Masanori , Kawamoto Hiroki , Setoyama Hiroyuki , Onodera Yohei , Ikeda Kazutaka , Maruyama Shingo , Haruta Naoki , Sato Tohru , Matsumoto Yuji , Takahashi Chika , Mizoguchi Teruyasu 
Published: February 2024

AbstractThermodynamically metastable glasses that can contain metastable species are important functional materials. X-ray absorption near-edge structure (XANES) spectroscopy is an effective technique for determining the valence states of cations, especially for the doping element in phosphors. Herein, we first confirm the valence change of silver cations from monovalent to trivalent in aluminophosphate glasses by X-ray irradiation using a combination of Ag L3-edge XANES, electron spin resonance, and simulated XANES spectra based on first-principles calculations. The absorption edge of the experimental and simulated XANES spectra demonstrate the spectral features of Ag(III), confirming that AgO exists as Ag(I)Ag(III)O2. A part of Ag(I) changes to Ag(III) by X-ray irradiation, and the generation of Ag(III) is saturated after high irradiation doses, in good agreement with conventional radiophotoluminescence (RPL) behaviour. The structural modelling based on a combination of quantum beam analysis suggests that the local coordination of Ag cations is similar to that of Ag(III), which is confirmed by density functional theory calculations. This demonstration of Ag(III) in glass overturns the conventional understanding of the RPL mechanism of silver cations, redefining the science of silver-related materials.
The effect of glycosylated hemoglobin levels on the response to intravitreal dexamethasone implant for treating diabetic macular edema
Authors: Lee Hyuk Jun , Bae Kunho , Yoon Chang Ki , Park Un Chul , Park Kyu Hyung , Lee Eun Kyoung 
Published: February 2024

AbstractThis study investigates the impact of glycosylated hemoglobin (HbA1c) on the efficacy of intravitreal dexamethasone (DEX) implants in patients with diabetic macular edema (DME) over a 12-month period. We retrospectively reviewed 90 DME patients treated with DEX implants, categorizing them based on baseline HbA1c levels (≤ 7% and > 7%) and 12-month changes in HbA1c ("improved", "stable", "worsened"). At the 2-month mark, the mean central subfield thickness (CST) reduction in the HbA1c ≤ 7% group was − 147.22 ± 113.79 µm compared to -130.41 ± 124.50 µm in the > 7% group (p = 0.506). Notably, 12-month outcomes between these groups showed no significant difference. The "improved" HbA1c subgroup experienced a more pronounced CST reduction at 2 months (p = 0.042), with outcomes leveling off with other groups by 12 months. Conclusively, DEX implant outcomes in DME were not influenced by either baseline HbA1c levels or their changes over time. This suggests that local alterations in the inflammation milieu may have a potentially stronger impact on DME treatment outcomes, highlighting the importance of considering local factors in DME treatment.
Isolation and encapsulation of bacteriophage with chitosan nanoparticles for biocontrol of multidrug-resistant methicillin-resistant Staphylococcus aureus isolated from broiler poultry farms
Authors: Elsayed Mona M. , Elkenany Rasha M. , EL-Khateeb Ayman Y. , Nabil Nehal M. , Tawakol Maram M. , Hassan Heba M. 
Published: February 2024

AbstractThis study was divided into two parts. The first part, the determination of methicillin-resistant Staphylococcus aureus (MRSA) prevalence in 25 broiler chicken farms, with the detection of multidrug resistant MRSA strains. The prevalence of MRSA was 31.8% (159 out of 500 samples) at the level of birds and it was 27% (27 out of 100) in the environmental samples. The highest antimicrobial resistance of the recovered MRSA strains was recorded to streptomycin (96%). All isolates (100%) had multidrug resistance (MDR) to four or more antibiotics with 16 distinct antibiotic resistant patterns, and multiple antibiotic resistance index (MARI) of 0.4–1. The second part, implementing novel biocontrol method for the isolated multidrug resistant MRSA strains through the isolation of its specific phage and detection of its survival rate at different pH and temperature degrees and lytic activity with and without encapsulation by chitosan nanoparticles (CS-NPs). Encapsulated and non-encapsulated MRSA phages were characterized using transmission electron microscope (TEM). Encapsulation of MRSA phage with CS-NPs increasing its lytic activity and its resistance to adverse conditions from pH and temperature. The findings of this study suggested that CS-NPs act as a protective barrier for MRSA phage for the control of multidrug resistant MRSA in broiler chicken farms.
Ciprofloxacin loaded PEG coated ZnO nanoparticles with enhanced antibacterial and wound healing effects
Authors: Ibne Shoukani Hussan , Nisa Sobia , Bibi Yamin , Zia Muhammad , Sajjad Anila , Ishfaq Afsheen , Ali Hussain 
Published: February 2024

AbstractAntimicrobial resistance is a worldwide health problem that demands alternative antibacterial strategies. Modified nano-composites can be an effective strategy as compared to traditional medicine. The current study was designed to develop a biocompatible nano-drug delivery system with increased efficacy of current therapeutics for biomedical applications. Zinc oxide nanoparticles (ZnO-NPs) were synthesized by chemical and green methods by mediating with Moringa olifera root extract. The ZnO–NPs were further modified by drug conjugation and coating with PEG (CIP-PEG-ZnO-NPs) to enhance their therapeutic potential. PEGylated ZnO-ciprofloxacin nano-conjugates were characterized by Fourier Transform Infrared spectroscopy, X-ray diffractometry, and Scanning Electron Microscopy. During antibacterial screenings chemically and green synthesized CIP-PEG-ZnO-NPs revealed significant activity against clinically isolated Gram-positive and Gram-negative bacterial strains. The sustainable and prolonged release of antibiotics was noted from the CIP–PEG conjugated ZnO-NPs. The synthesized nanoparticles were found compatible with RBCs and Baby hamster kidney cell lines (BHK21) during hemolytic and MTT assays respectively. Based on initial findings a broad-spectrum nano-material was developed and tested for biomedical applications that eradicated Staphylococcus aureus from the infectious site and showed wound-healing effects during in vivo applications. ZnO-based nano-drug carrier can offer targeted drug delivery, and improved drug stability and efficacy resulting in better drug penetration.
When temporal attention interacts with expectation
Authors: Duyar Aysun , Ren Shiyang , Carrasco Marisa 
Published: February 2024

AbstractTemporal attention is voluntarily deployed at specific moments, whereas temporal expectation is deployed according to timing probabilities. When the target appears at an expected moment in a sequence, temporal attention improves performance at the attended moments, but the timing and the precision of the attentional window remain unknown. Here we independently and concurrently manipulated temporal attention–via behavioral relevance–and temporal expectation–via session-wise precision and trial-wise hazard rate–to investigate whether and how these mechanisms interact to improve perception. Our results reveal that temporal attention interacts with temporal expectation–the higher the precision, the stronger the attention benefit, but surprisingly this benefit decreased with delayed onset despite the increasing probability of stimulus appearance. When attention was suboptimally deployed to earlier than expected moments, it could not be reoriented to a later time point. These findings provide evidence that temporal attention and temporal expectation are different mechanisms, and highlight their interplay in optimizing visual performance.
Integrated transcriptomics and proteomics analysis reveals muscle metabolism effects of dietary Ulva lactuca and ulvan lyase supplementation in weaned piglets
Authors: Ribeiro David Miguel , Coelho Diogo , Costa Mónica , Carvalho Daniela Filipa Pires , Leclercq Céline C. , Renaut Jenny , Freire João Pedro Bengala , Almeida André Martinho , Mestre Prates José António 
Published: February 2024

AbstractSeaweeds, including the green Ulva lactuca, can potentially reduce competition between feed, food, and fuel. They can also contribute to the improved development of weaned piglets. However, their indigestible polysaccharides of the cell wall pose a challenge. This can be addressed through carbohydrase supplementation, such as the recombinant ulvan lyase. The objective of our study was to assess the muscle metabolism of weaned piglets fed with 7% U. lactuca and 0.01% ulvan lyase supplementation, using an integrated transcriptomics (RNA-seq) and proteomics (LC–MS) approach. Feeding piglets with seaweed and enzyme supplementation resulted in reduced macronutrient availability, leading to protein degradation through the proteasome (PSMD2), with resulting amino acids being utilized as an energy source (GOT2, IDH3B). Moreover, mineral element accumulation may have contributed to increased oxidative stress, evident from elevated levels of antioxidant proteins like catalase, as a response to maintaining tissue homeostasis. The upregulation of the gene AQP7, associated with the osmotic stress response, further supports these findings. Consequently, an increase in chaperone activity, including HSP90, was required to repair damaged proteins. Our results suggest that enzymatic supplementation may exacerbate the effects observed from feeding U. lactuca alone, potentially due to side effects of cell wall degradation during digestion.