bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunoinformatics, molecular docking and dynamics simulation approaches unveil a multi epitope-based potent peptide vaccine candidate against avian leukosis virus
Authors: Elshafei Siham O. , Mahmoud Nuha A. , Almofti Yassir A. 
Published: February 2024

AbstractLymphoid leukosis is a poultry neoplastic disease caused by avian leukosis virus (ALV) and is characterized by high morbidity and variable mortality rates in chicks. Currently, no effective treatment and vaccination is the only means to control it. This study exploited the immunoinformatics approaches to construct multi-epitope vaccine against ALV. ABCpred and IEDB servers were used to predict B and T lymphocytes epitopes from the viral proteins, respectively. Antigenicity, allergenicity and toxicity of the epitopes were assessed and used to construct the vaccine with suitable adjuvant and linkers. Secondary and tertiary structures of the vaccine were predicted, refined and validated. Structural errors, solubility, stability, immune simulation, dynamic simulation, docking and in silico cloning were also evaluated.The constructed vaccine was hydrophilic, antigenic and non-allergenic. Ramchandran plot showed most of the residues in the favored and additional allowed regions. ProsA server showed no errors in the vaccine structure. Immune simulation showed significant immunoglobulins and cytokines levels. Stability was enhanced by disulfide engineering and molecular dynamic simulation. Docking of the vaccine with chicken’s TLR7 revealed competent binding energies.The vaccine was cloned in pET-30a(+) vector and efficiently expressed in Escherichia coli. This study provided a potent peptide vaccine that could assist in tailoring a rapid and cost-effective vaccine that helps to combat ALV. However, experimental validation is required to assess the vaccine efficiency.
Spin resolved topological bulk state in acoustics
Authors: Indaleeb Mustahseen M. , Banerjee Sourav 
Published: February 2024

AbstractExtremely rare topologically protected acoustic energy sink is presented in this article. Acoustic topological phenomena are generally described using quantum anomalous hall effects (QAHE), quantum valley hall effects (QVHE), and quantum spin hall effects (QSHE) where spin orbit coupling is predominant. Topological edge states are demonstrated by bulk-boundary distinction when the bulk is insulated. In this article topological acoustic conductor and its phenomena are theoretically demonstrated where the boundaries are insulated. This is exactly opposite to the behavior of a topological acoustic insulator. Phenomena presented in this article could not be explained by any of the trio Quantum Hall effects. To explain the phenomenon phononic crystals or PnCs were designed to obtain accidental triple degeneracies, resulting a Dirac-like cone at the Γ point ($$\overrightarrow{k}=0$$

k
→

=
0

). The phenomenon is microarchitecture and microrotation field independent. Here time reversal symmetry or the space inversion symmetry is not broken, and the degenerated ‘Deaf band’ dominates the local dispersion with a syncline top band. This scenario results in continuously changing ‘up spin’ and ‘down spin’ of the wave energy in the media and remain trapped without specific preferential direction of wave transport. The spin was found to generate the spin angular momentum, causing the switching in geometric phase from $$0-2\pi$$

0
-
2
π

in cyclic pattern, keeping the energy trapped inside the bulk media.
Morphological and biomechanical characterization of long bones and peri-implant bone repair in type 2 diabetic rats treated with resveratrol
Authors: Wajima Carolina Sayuri , Pitol-Palin Letícia , de Souza Batista Fábio Roberto , dos Santos Paulo Henrique , Matsushita Doris Hissako , Okamoto Roberta 
Published: February 2024

AbstractType 2 diabetes interferes with bone remodeling mechanisms, requiring studies to reverse this damage, and resveratrol is a polyphenol with rich properties. This study aimed to characterize the long bone morphology and peri-implant biomechanics of normoglycemic and type 2 diabetic animals treated with resveratrol. Thirty-two male Wistar rats were used and divided into normoglycemic and diabetic with or without treatment. They had the installation of implants in the tibia and treatment with oral resveratrol within 45 days. Resveratrol was responsible for weight homeostasis and decreased glycemic levels in rats with type 2 diabetes. The three-point bending testing, resveratrol showed positive effects on the biomechanics of long bones, corroborating a more resistant bone in comparison to untreated diabetics. Micro-ct revealed how bone metabolism is affected by systemic disease, decreasing bone quality. The counter-torque of normoglycemic animals showed superior osseointegration to diabetes, with no differences in the administration of the polyphenol, showing the sovereignty of the deleterious effects of the disease when there is a tissue lesion and an inflammatory picture installed. Overall, resveratrol acted positively in the etiopathogenesis of type 2 diabetes and revealed positive effects on the strength of long bones.
A novel nomogram and recursive partitioning analysis for predicting cancer-specific survival of patients with subcutaneous leiomyosarcoma
Authors: Ji Qiang , Hu Hua , Li Shulian , Tang Jun 
Published: February 2024

AbstractAccurately predicting prognosis subcutaneous leiomyosarcoma (LMS) is crucial for guiding treatment decisions in patients. The objective of this study was to develop prediction models for cancer-specific survival (CSS) in patients with subcutaneous LMS. The collected cases of diagnosed subcutaneous LMS were randomly divided into a training cohort and a validation cohort at a 6:4 ratio based on tumor location and histological code. The X-tile program was utilized to determine the optimal cutoff points for age index. Univariate and Cox multivariate regression analyses were conducted to identify independent risk factors for subcutaneous LMS patients. Nomograms were constructed to predict CSS, and their performance was assessed using C-index and calibration plots. Additionally, a decision tree model was established using recursive partitioning analysis to determine the total score for CSS prediction in subcutaneous LMS patients based on the nomogram model. A total of 1793 patients with subcutaneous LMS were found. X-tile software divides all patients into ≤ 61 years old, 61–82 years old, and ≥ 82 years old. The most important anatomical sites were the limbs (including the upper and lower limbs, 48.0%). Only 6.2% of patients received chemotherapy, while 44% had a history of radiotherapy and 92.9% underwent surgery. The independent risk factors for patients with subcutaneous LMS were age, summary stage, grade, and surgery. CSS was significantly decreased in patients with distant metastases, which showed the highest independent risk predictor (HR 4.325, 95% CI 3.010–6.214, p < 0.001). The nomogram prediction model of LMS was constructed based on four risk factors. The C-index for this model was 0.802 [95% CI 0.781–0.823] and 0.798 [95% CI 0.768–0.829]. The training cohort's 3-, 5-, and 10-year AUCs for CSS in patients with subcutaneous LMS were 0.833, 0.830, and 0.859, and the validation cohort's AUC for predicting CSS rate were 0.849, 0.830, and 0.803, respectively. Recursive segmentation analysis divided patients into 4 risk subgroups according to the total score in the nomogram, including low-risk group < 145, intermediate-low-risk group ≥ 145 < 176, intermediate-high-risk group ≥ 176 < 196, and high-risk group ≥ 196; The probability of the four risk subgroups is 9.1%, 34%, 49%, and 79% respectively. In this retrospective study, a novel nomogram or corresponding risk classification system for patients with subcutaneous LMS were developed, which may assist clinicians in identifying high-risk patients and in guiding the clinical decision.
Waveform shaping in photonic time-crystals
Authors: Hwang Ruey-Bing 
Published: February 2024

AbstractThis paper reports on the waveform shaped by a finite duration photonic time-crystal with its permittivity and permeability periodically varying in time. A Gaussian-modulated sinusoidal pulse is incident onto this photonic time-crystal to evaluate the backward- and forward-scattering waveforms. An analytical formulation, utilizing a cascade of temporal transfer matrices and the inverse fast Fourier transform, was employed to conduct time-domain waveform computations. Interestingly, the dispersion diagram of the temporal unit cell, which displays a momentum gap characterized by a complex effective angular frequency, plays a crucial role in shaping the incident waveform. Specifically, the presence of momentum gaps in the spectrum of the incident pulse determines the frequencies of the generated oscillation modes.
Parent–child couples display shared neural fingerprints while listening to stories
Authors: Habouba Nir , Talmon Ronen , Kraus Dror , Farah Rola , Apter Alan , Steinberg Tamar , Radhakrishnan Rupa , Barazany Daniel , Horowitz-Kraus Tzipi 
Published: February 2024

AbstractNeural fingerprinting is a method to identify individuals from a group of people. Here, we established a new connectome-based identification model and used diffusion maps to show that biological parent–child couples share functional connectivity patterns while listening to stories. These shared fingerprints enabled the identification of children and their biological parents from a group of parents and children. Functional patterns were evident in both cognitive and sensory brain networks. Defining “typical” shared biological parent–child brain patterns may enable predicting or even preventing impaired parent–child connections that develop due to genetic or environmental causes. Finally, we argue that the proposed framework opens new opportunities to link similarities in connectivity patterns to behavioral, psychological, and medical phenomena among other populations. To our knowledge, this is the first study to reveal the neural fingerprint that represents distinct biological parent–child couples.
Improving diagnostic accuracy of blood culture-positive cases in a cancer center via an antimicrobial stewardship program and infectious disease consultations
Authors: Itoh Naoya , Akazawa Nana , Kawabata Takanori , Yamaguchi Makoto , Kodama Eiichi N. , Ohmagari Norio 
Published: February 2024

AbstractThe direct impact of antimicrobial stewardship programs (ASP) and infectious disease (ID) consultations on patients' clinical diagnoses remains unknown. We assessed their influence on improving the diagnostic accuracy of blood culture-positive inpatients at a Japanese cancer center. Our single-center, retrospective observational study was conducted from April 1, 2018 to March 31, 2022 to evaluate two phases: pre-intervention (notification of antimicrobials by the infection control team) and post-intervention (ASP implementation and ID consultation service establishment). There were 42,514 inpatients: 22,096 during the pre-intervention and 20,418 during the intervention periods. A total of 939 blood culture-positive episodes (pre-intervention, n = 434; post-intervention, n = 505) were analyzed. During the pre-intervention period, 28.1% of the patients had an unknown diagnosis, which decreased significantly to 1.2% post-intervention. Furthermore, hepatobiliary tract and other infections increased significantly post-intervention, and the mortality rate due to Staphylococcus aureus infection decreased from 28.6% pre-intervention to 10.4% post-intervention. The trend and level of the total number of culture specimens submitted per 1000 patient days for all culture specimens increased significantly post-intervention. Notably, the two-set rate of monthly blood cultures increased significantly. In conclusion, improving the overall diagnostic process with ASP and ID consultations at cancer centers could lead to the optimization of patient care.
Using symbolic machine learning to assess and model substance transport and decay in water distribution networks
Authors: Laucelli Daniele Biagio , Enríquez Laura , Saldarriaga Juan , Giustolisi Orazio 
Published: February 2024

AbstractDrinking water infrastructures are systems of pipes which are generally networked. They play a crucial role in transporting and delivering clean water to people. The water quality analysis refers to the evaluation of the advective diffusion of any substance in drinking water infrastructures from source nodes. Such substances could be a contamination for the system or planned for the disinfection, e.g., chlorine. The water quality analysis is performed by integrating the differential equation in the pipes network domain using the kinetics of the substance decay and the Lagrangian scheme. The kinetics can be formulated using a specific reaction order depending on the substance characteristics. The basis for the integration is the pipes velocity field calculated by means of hydraulic analysis. The aim of the present work is to discover the intrinsic mechanism of the substance transport in drinking water infrastructures, i.e., their pipes network domain, using the symbolic machine learning, named Evolutionary Polynomial Regression, which provides “synthetic” models (symbolic formulas) from data. We demonstrated, using one real network and two test networks, that the concentration at each node of the network can be predicted using the travel time along the shortest path(s) between the source and each node. Additionally, the formula models provided by symbolic machine learning allowed discovering that a unique formula based on kinetic reaction model structure allows predicting the residual substance concentration at each node, given the source node concentration, surrogating with a good accuracy the integration of the differential equations.
Effectiveness, safety and indications of acute normovolemic haemodilution in total knee arthroplasty
Authors: Li Yucong , Chen Jingle , Xie Hao , Wu Hangxing , Zuo Zhijie , Hu Wanyan , Xie Chao , Lin Lijun 
Published: February 2024

AbstractTotal knee arthroplasty (TKA) is the most cost-effective, and potent method for the treatment of end-stage knee osteoarthritis. Acute normovolemic haemodilution (ANH) can effectively replace the need for allogeneic transfusions due to the high amount of bleeding during TKA. However, more studies are needed to prove the efficacy and safety of ANH and to clarify its indications in the field of knee replacement. Medical records from June 1, 2019 to June 1, 2021 were searched and grouped according to inclusion and exclusion criteria. PART I: 58 patients with ANH during TKA were selected as the ANH group (n = 58), and 58 patients with allogeneic transfusion were chosen as the control group (n = 58). PART II: Patients with anaemia were divided into the ANH group (n = 18) and the control group (n = 12). PART I: The postoperative inflammatory index and serum albumin in the ANH group were significantly lower than those in the control group. No significant difference was observed in the theoretical loss of red blood cells, postoperative renal function, liver function, cardiac function and biochemical ion index between the two groups. The effective rate of ANH in the normal haemoglobin group was significantly lower than that in the anaemia group. PART II: In patients with anaemia, the theoretical loss of red blood cells in patients with ANH was less than that in the control group. The postoperative inflammation, renal function, liver function and cardiac function in the ANH group were better than those in the control group, and no significant difference was noted in biochemical ions and nutritional status indicators. This paper shows that ANH not only can replace allogeneic transfusion in TKA, especially in patients with anaemia, but also has lower inflammatory indicators than allogeneic transfusion. From a security perspective, the body’s tolerance to ANH is within the body’s compensation range.
Stress related to wild canid predators near dairy sheep farms associated with increased somatic cell counts in bulk-tank milk
Authors: Katsarou Eleni I. , Reid Neil , Lianou Daphne T. , Fthenakis George C. 
Published: February 2024

AbstractWe investigated the association between wild canid predators reported near sheep farms throughout Greece and somatic cell counts in bulk-tank milk as a reflection of milk quality. The study included 325 dairy sheep flocks, where bulk-tank milk somatic cell counts and total bacterial counts were measured and staphylococci were isolated. Farms were divided into three groups: Cohort A (farms with no reports of wild canid predators nearby), B (farms with canid predators (golden jackal and grey wolf) nearby yet with no experience of livestock losses to predation) and C (farms with canid predators nearby and livestock losses to predation). Somatic cell counts in bulk-tank milk of Cohort C farms were significantly higher, + 43% and + 29%, compared to those for Cohorts A and B, respectively: 0.617 × 106 cells mL−1 versus 0.433 × 106 or 0.477 × 106 cells mL−1, respectively. The presence of wild canid predators near sheep farms was associated with lower quality milk potentially indicative of stress consistent with the potential effects of a landscape of fear. Increasing biosecurity measures at livestock farms, e.g., fencing, and presence of livestock guard dogs could minimise predation risk, whilst also improving livestock welfare by reducing predator-associated stress.
Improved diagnostic accuracy of readout-segmented echo-planar imaging for peripheral zone clinically significant prostate cancer: a retrospective 3T MRI study
Authors: Deforche M. , Lefebvre Y. , Diamand R. , Bali M. A. , Lemort M. , Coquelet N. 
Published: February 2024

AbstractThis study compares the readout-segmented echo-planar imaging (rsEPI) from the conventional single-shot EPI (ssEPI) diffusion-weighted imaging (DWI) for the discrimination of patients with clinically significant prostate cancer (csPCa) within the peripheral zone (PZ) using apparent diffusion coefficient (ADC) maps and pathology report from magnetic resonance imaging (MRI)-targeted biopsy. We queried a retrospective monocentric database of patients with targeted biopsy. csPCa patients were defined as an International Society of Urological Pathology grade group ≥ 2. Group-level analyses and diagnostic accuracy of mean ADC values (ADCmean) within the tumor volume were assessed from Kruskal–Wallis tests and receiving operating characteristic curves, respectively. Areas under the curve (AUC) and optimal cut-off values were calculated. 159 patients (105 rsEPI, 54 ssEPI; mean age ± standard deviation: 65 ± 8 years) with 3T DWI, PZ lesions and targeted biopsy were selected. Both DWI sequences showed significantly lower ADCmean values for patients with csPCa. The rsEPI sequence better discriminates patients with csPCa (AUCrsEPI = 0.84, AUCssEPI = 0.68, p < 0.05) with an optimal cut-off value of 1232 μm2/s associated with a sensitivity–specificity of 97%-63%. Our study showed that the rsEPI DWI sequence enhances the discrimination of patients with csPCa.
Xanthomonas immunity proteins protect against the cis-toxic effects of their cognate T4SS effectors
Authors: Oka Gabriel U , Souza Diorge P , Sgro Germán G , Guzzo Cristiane R , Dunger German , Farah Chuck S 
Published: February 2024

AbstractMany bacteria kill rival species by translocating toxic effectors into target cells. Effectors are often encoded along with cognate immunity proteins that could (i) protect against “friendly-fire” (trans-intoxication) from neighboring sister cells and/or (ii) protect against internal cis-intoxication (suicide). Here, we distinguish between these two mechanisms in the case of the bactericidal Xanthomonas citri Type IV Secretion System (X-T4SS). We use a set of X. citri mutants lacking multiple effector/immunity protein (X-Tfe/X-Tfi) pairs to show that X-Tfis are not absolutely required to protect against trans-intoxication by wild-type cells. Our investigation then focused on the in vivo function of the lysozyme-like effector X-TfeXAC2609 and its cognate immunity protein X-TfiXAC2610. In the absence of X-TfiXAC2610, we observe X-TfeXAC2609-dependent and X-T4SS-independent accumulation of damage in the X. citri cell envelope, cell death, and inhibition of biofilm formation. While immunity proteins in other systems have been shown to protect against attacks by sister cells (trans-intoxication), this is an example of an antibacterial secretion system in which the immunity proteins are dedicated to protecting cells against cis-intoxication.
Sirt6 ablation in the liver causes fatty liver that increases cancer risk by upregulating Serpina12
Authors: Li Licen , Zeng Jianming , Zhang Xin , Feng Yangyang , Lei Josh Haipeng , Xu Xiaoling , Chen Qiang , Deng Chu-Xia 
Published: February 2024

AbstractNon-alcoholic fatty liver disease is a chronic liver abnormality that exhibits high variability and can lead to liver cancer in advanced stages. Hepatic ablation of SIRT6 results in fatty liver disease, yet the potential mechanism of SIRT6 deficiency, particularly in relation to downstream mediators for NAFLD, remains elusive. Here we identify Serpina12 as a key gene regulated by Sirt6 that plays a crucial function in energy homeostasis. Specifically, Sirt6 suppresses Serpina12 expression through histone deacetylation at its promoter region, after which the transcription factor, Cebpα, binds to and regulates its expression. Sirt6 deficiency results in an increased expression of Serpina12 in hepatocytes, which enhances insulin signaling and promotes lipid accumulation. Importantly, CRISPR-Cas9 mediated Serpina12 knockout in the liver ameliorated fatty liver disease caused by Sirt6 ablation. Finally, we demonstrate that Sirt6 functions as a tumor suppressor in the liver, and consequently, deletion of Sirt6 in the liver leads to not only the spontaneous development of tumors but also enhanced tumorigenesis in response to DEN treatment or under conditions of obesity.
TGFβ-induced long non-coding RNA LINC00313 activates Wnt signaling and promotes cholangiocarcinoma
Authors: Papoutsoglou Panagiotis , Pineau Raphaël , Leroux Raffaële , Louis Corentin , L’Haridon Anaïs , Foretek Dominika , Morillon Antonin , Banales Jesus M , Gilot David , Aubry Marc , Coulouarn Cédric 
Published: February 2024

AbstractCholangiocarcinoma is a devastating liver cancer characterized by high aggressiveness and therapy resistance, resulting in poor prognosis. Long non-coding RNAs and signals imposed by oncogenic pathways, such as transforming growth factor β (TGFβ), frequently contribute to cholangiocarcinogenesis. Here, we explore novel effectors of TGFβ signalling in cholangiocarcinoma. LINC00313 is identified as a novel TGFβ target gene. Gene expression and genome-wide chromatin accessibility profiling reveal that nuclear LINC00313 transcriptionally regulates genes involved in Wnt signalling, such as the transcriptional activator TCF7. LINC00313 gain-of-function enhances TCF/LEF-dependent transcription, promotes colony formation in vitro and accelerates tumour growth in vivo. Genes affected by LINC00313 over-expression in CCA tumours are associated with KRAS and TP53 mutations and reduce overall patient survival. Mechanistically, ACTL6A and BRG1, subunits of the SWI/SNF chromatin remodelling complex, interact with LINC00313 and affect TCF7 and SULF2 transcription. We propose a model whereby TGFβ induces LINC00313 in order to regulate the expression of hallmark Wnt pathway genes, in co-operation with SWI/SNF. By modulating key genes of the Wnt pathway, LINC00313 fine-tunes Wnt/TCF/LEF-dependent transcriptional responses and promotes cholangiocarcinogenesis.