Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of Human Leukocyte Antigen and Immune Escape in Head and Neck Cancer

Cancer cells evade recognition by the immune system to survive. Head and neck squamous cell carcinoma (HNSCC) is characterized by high levels of immune infiltration and mutation‐associated neoantigens; therefore, immune evasion is likely to be an important mechanism in HNSCC tumorigenesis and progression. A commonly employed mechanism of immune evasion is downregulation of human leukocyte antigen (HLA) or loss of heterozygosity (LOH) in tumor cells. The objective of this study was to integrate multi‐dimensional genomic and transcriptomic data from HNSCC tumors to better understand the clinical and immunologic implications of HLA LOH.
Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds

Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. ABSTRACT Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.
Bayesian conformity assessment in presence of systematic measurement errors

Conformity assessment of the distribution of the values of a quantity is investigated by using a Bayesian approach. The effect of systematic, non-negligible measurement errors is taken into account. The analysis is general, in the sense that the probability distribution of the quantity can be of any kind, that is even different from the ubiquitous normal distribution, and the measurement model function, linking the measurand with the observable and non-observable influence quantities, can be non-linear. Further, any joint probability density function can be used to model the available knowledge about the systematic errors. It is demonstrated that the result of the Bayesian analysis here developed reduces to the standard result (obtained through a frequentistic approach) when the systematic measurement errors are negligible. A consolidated frequentistic extension of such standard result, aimed at including the effect of a systematic measurement error, is directly compared with the Bayesian result, whose superiority is demonstrated. Application of the results here obtained to the derivation of the operating characteristic curves used for sampling plans for inspection by variables is also introduced.
Dissecting cell‐type‐specific pathways in medial entorhinal cortical‐hippocampal network for episodic memory

Episodic memory, which refers to our ability to encode and recall past events, is essential to our daily lives. Previous research has established that both the entorhinal cortex (EC) and hippocampus (HPC) play a crucial role in the formation and retrieval of episodic memories. However, to understand neural circuit mechanisms behind these processes, it has become necessary to monitor and manipulate the neural activity in a cell‐type‐specific manner with high temporal precision during memory formation, consolidation, and retrieval in the EC‐HPC networks. Recent studies using cell‐type‐specific labeling, monitoring, and manipulation have demonstrated that medial EC (MEC) contains multiple excitatory neurons that have differential molecular markers, physiological properties, and anatomical features. In this review, we will comprehensively examine the complementary roles of superficial layers of neurons (II and III) and the roles of deeper layers (V and VI) in episodic memory formation and recall based on these recent findings.
TP53 (rs1042522, rs28934571) and TP21 (rs1801270, rs1059234) Polymorphisms and Risk of Breast Cancer among Rural Women of Maharashtra: Findings from a Hospital Based Case- Control Study

Background: Various studies all around the world depicted the relationship of polymorphisms in tumor suppressor genes with risk of various cancers, but there are unambiguous conclusions on this association. A hospital based case-control study was designed to review the association of polymorphism of tumor suppressor genes p21 and p53 with breast cancer risk in women residing in rural Maharashtra. Methods: Two single nucleotide polymorphisms (SNPs) a C>A transversion (Ser>Arg) at codon 31 of exon 2 (rs1801270), C>T transition occurring 20bp upstream from stop codon of exon 3 (rs1059234) in p21 gene and G>C (Arg>Pro) transition at codon 72 of exon 4 (rs1042522), G>T (Arg>Ser) transition at codon 249 in exon 7 (rs28934571) in p53 gene were studied. To precise the quantitative assessment, we enrolled 800 subjects sorted into 400 clinically confirmed breast cancer patients and 400 healthy women from a tertiary care hospital (Krishna Hospital and Medical Research Centre) of south-western Maharashtra. The genetic polymorphisms in p21 and p53 genes was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method using blood genomic DNA isolated from breast cancer patients and controls. The level of association of polymorphisms was assessed using Odds ratio (OR) with 95% confidence interval and p-value identified using logistic regression model. Results: After the analysis of SNPs (rs1801270, rs1059234) of p21 and (rs1042522, rs28934571) in p53 gene our analysis suggested that heterozygote Ser/Arg genotype with OR=0.66; 95% CI: 0.47- 0.91; p=0.0003 and homozygote variant Arg/Arg genotype with OR=0.23; 95% CI: 0.13- 0.40; p<0.0001of rs1801270 of p21 was negatively associated with risk of breast cancer in studied population. Conclusion: The findings from this study supported that rs1801270 SNP of p21 was inversely associated with breast cancer risk in the studied rural women population.
Increasing transmission of dengue virus across ecologically diverse regions of Ecuador and associated risk factors

The distribution and intensity of viral diseases transmitted by Aedes aegypti mosquitoes, including dengue, have rapidly increased over the last century. Ecuador is an interesting country to study drivers of dengue virus (DENV) transmission given it has multiple ecologically and demographically distinct regions. Here, we analyze province-level age-stratified dengue prevalence data from 2000-2019 using catalytic models to estimate the force of infection of DENV over eight decades and across provinces in Ecuador. We found that provinces established endemic DENV transmission at different time periods. Coastal provinces with the largest and most connected cities had the earliest and highest increase in DENV transmission, starting around 1980 and continuing to the present. In contrast, remote and rural areas with reduced access, like the northern coast and the Amazon regions, experienced a rise in DENV transmission and endemicity only in the last 10 to 20 years. The newly introduced chikungunya and Zika viruses have distinct age-specific prevalence distributions consistent with recent emergence across all provinces. We evaluated factors to the resolution of 1 hectare associated with geographic differences in vector suitability and arbovirus disease in the last 10 years by modeling 11,693 A aegypti presence points and 73,550 arbovirus cases. In total, 56% of the population of Ecuador lives in areas with high risk of Aedes aegypti. Most suitable provinces had hotspots for arbovirus disease risk, with population size, elevation, sewage connection, trash collection, and access to water as important determinants. Our investigation serves as a case study of the changes driving the expansion of DENV and other arboviruses globally and suggest that control efforts should be expanded to semi-urban and rural areas and to historically isolated regions to counteract increasing dengue outbreaks.
Hazard perception training effectiveness on experienced drivers: decay of improvement in the follow-up

Abstract A variety of road hazard perception training programmes have been proposed recently, based on the assumption that these skills contribute to lower crash rates across different countries. However, the long-term effectiveness of suggested programmes has been under-investigated. The main objective of this study is to explore the long-term effectiveness of online hazard perception training for experienced drivers and examine the moderating role of driving self-efficacy. Fifty-six experienced drivers (21 males and 35 females) were assigned to the experimental (n = 31) or the control (n = 25) group. The experimental group received two 45 min session interventions; the control group received no intervention. The effectiveness of the programme was tested by the change in scores of Lithuanian hazard prediction test (HPT) LHP12 that was conducted before training (pre-test), immediately after training (post-test) and six months after training (follow-up). The twelve-item Adelaide Driving Self–Efficacy Scale (ADSES; George et al., 2007) was used to measure self-reported driving self-efficacy at the pre-test. The results revealed a significant increase in hazard prediction scores immediately after training, but the short-term effect of training decayed at follow-up. Experienced drivers with higher self-efficacy developed better hazard prediction skills during training. The results confirmed short-term effectiveness of the programme.
O‐GlcNAcylation promotes topoisomerase IIα catalytic activity in breast cancer chemoresistance

DNA topoisomerase IIα (TOP2A) plays a vital role in replication and cell division by catalytically altering DNA topology. It is a prominent target for anticancer drugs, but clinical efficacy is often compromised due to chemoresistance. In this study, we investigate the role of TOP2A O‐GlcNAcylation in breast cancer cells and patient tumor tissues. Our results demonstrate that elevated TOP2A, especially its O‐GlcNAcylation, promotes breast cancer malignant progression and resistance to adriamycin (Adm). O‐GlcNAcylation at Ser1469 enhances TOP2A chromatin DNA binding and catalytic activity, leading to resistance to Adm in breast cancer cells and xenograft models. Mechanistically, O‐GlcNAcylation‐modulated interactions between TOP2A and cell cycle regulators influence downstream gene expression and contribute to breast cancer drug resistance. These results reveal a previously unrecognized mechanistic role for TOP2A O‐GlcNAcylation in breast cancer chemotherapy resistance and provide support for targeting TOP2A O‐GlcNAcylation in cancer therapy.
Safety and immunogenicity of rabies vaccine (PVRV-WIBP) in healthy Chinese aged 10–50 years old: Randomized, blinded, parallel controlled phase III clinical study

ABSTRACT This phase III clinical trial aimed to assess the safety and demonstrate the immunogenicity of a candidate freeze-dried purified Vero cell-based rabies vaccine (PVRV-WIBP) developed for human use. A cohort of 40 participants in stage 1 and 1956 subjects in stage 2 with an age range of 10–50 years were recruited for the phase III clinical trial. For safety analysis in stage 1, 20 participants received either 4-dose or 5-dose regimen of PVRV-WIBP. In stage 2, 1956 subjects were randomly divided into the 5-dose PVRV-WIBP, 5-dose PVRV-LNCD, and 4-dose PVRV-WIBP groups. The serum neutralizing antibody titer against rabies was determined on day 7 or 14 and day 35 or 42. Adverse reactions were recorded for more than 6 months. Most adverse reactions, which were mild and moderate in severity, occurred and resolved within 1 week after each injection in the PVRV-WIBP (4 and 5 doses) and PVRV-LNCD (5 doses) groups. All three groups achieved complete seroconversion 14 days after the initial dose and 14 days after completing the full vaccination schedule, the susceptible subjects in the PVRV-WIBP group (4-dose or 5-dose regimen) displayed higher neutralizing antibody titers against the rabies virus compared to those in the PVRV-LNCD group (5-dose regimen). PVRV-WIBP induced non-inferior immune responses versus PVRV-LNCD as assessed by seroconversion rate. PVRV-WIBP was well tolerated and non-inferior to PVRV-LNCD in healthy individuals aged 10–50 years. The results indicated that PVRV-WIBP (both 4- and 5-dose schedules) could be an alternative to rabies post-exposure prophylaxis.
Cost savings through continuous vital sign monitoring in the medical-surgical unit

Abstract Objective This study aimed to determine the potential cost-savings for implementing continuous vital sign monitoring in a hospital’s medical-surgical units. Methods A cost-savings analysis was designed to calculate potential cost-savings for an average-sized U.S. community hospital (153 total beds) over a 1-year time horizon. Analysis parameters were extracted from national databases and previous studies that compared outcomes for patients receiving continuous vital sign monitoring (SpO2, HR, and RR) or standard of care (intermittent vital sign measurements) in medical-surgical units based on a targeted literature review. Clinical parameters and associated costs served as analysis inputs. The analysis outputs were costs and potential cost-savings using a 50% and 100% adoption rate of continuous monitoring technologies across the medical-surgical unit. Results Potential annual cost-savings for in-hospital medical-surgical stays were estimated at $3,414,709 (2022 USD) and $6,829,418 for a 50% and 100% adoption rate, respectively. The cost-savings for an adoption rate of 100% equated to a ∼14% reduction in the overall annual cost of medical-surgical unit stays for an average-sized hospital. The largest contribution to potential cost-savings came from patients that avoided serious adverse events that require transfer to the intensive care unit; this resulted in annual cost-savings from reduced average length of stay between $1,756,613 and $3,513,226 (50% and 100% adoption rate, respectively). Additional cost-savings can be attained from reductions in in-hospital cardiac arrest-associated hospitalizations and decreased rapid response team activation. Conclusions Our findings demonstrate that there is the potential for cost-savings of over $6.8 million dollars per year in an average-sized US community hospital by improving patient outcomes through implementation of continuous monitoring technologies in medical-surgical units. Continuous vital sign monitoring technologies that increase patient mobility and facilitate recovery may further contribute to cost-savings and should be considered for economic analyses. Future research is needed to explore these health-related outcomes.
Dosimetric Study to Estimate Deviations in Delivered Radiation Dose due to Occluded Air Spaces in Vaginal Vault Brachytherapy Applications

Background: To develop a dosimetric tool to estimate the dose delivered in the presence of air pockets with EBT3 film while simulating the conditions of vaginal vault brachytherapy (VVBT) with 3.0 diameter cylindrical applicator at a prescription dose distance of 5mm from the surface of it. Materials and Method: Six acrylic plates (10 cm x 10 cm, 0.5 cm thick) with four different types of slots were designed and produced locally. They can hold a cylindrical vaginal brachytherapy applicator in the centre, air equivalent material from the applicator’s surface [(sizes 4.5 mm (A), 3.0 mm (B), and 2.0 mm (C)], EBT3 film at the prescribed dose distance, and holder rods. Plates were layered together with acrylic rods and assembled in a holding box in a water phantom. Three treatment plans done in TPS with prescription doses of 2 Gy, 3 Gy, and 4 Gy at 5.0 mm with a treatment length of 6 cm, and were executed in Co-60-based HDR brachytherapy unit (M/s SagiNova, Germany) with & without the placement of air equivalent material, and the dose received at slot locations A, B, & C were noted. Results: The mean percentage deviation of measured dose without and with presence of air pocket at A, B and C was 13.9%, 11.0% and 6.4% respectively for all dose prescriptions. As the air pocket size expanded radially from 2.0 mm to 4.5 mm, the increase in dosage ranged from 6.4% to 13.9% which was due to the fact that the film was held at dosage prescription distance and the lack of attenuation of photons radially through air pocket. Conclusions: The present study can be carried out with a 3D printed phantom that simulates VVBT application having air pockets of different dimensions at different locations and also can be analyzed with Monte Carlo simulations.
Association of MTR A2756G and MTRR A66G Polymorphisms With Male Infertility: An Updated Meta-Analysis

The objective of the present study was to find out the association of folate genes MTR A2756G and MTRR A66G polymorphisms with the risk of male infertility. The databases of Google Scholar, PubMed, and Science Direct were searched to find relevant studies. Data were extracted from the eligible studies and were analyzed for pooled up odds ratio (OR) with 95% confidence interval (CI). Review Manager 5.4 was used for statistical analysis. Nineteen case-control studies were included in this meta-analysis which comprised 3621 cases and 3327 controls. Pooled analysis revealed that there is a significant association between MTR A2756G polymorphism with male infertility except for the dominant model. The ORs and 95% CI for each genetic model were as follows: 1.21 [1.03–1.42] for the allele model (G vs. A), 2.31 [1.38–3.96] for the additive model (GG vs. AA), 1.17 [0.98–1.38] for the dominant model (GG+AG vs. AA) and 2.10 [1.55–2.86] for the recessive model (GG vs. AG+AA). MTRR A66G has no noticeable association with male infertility. The current meta-analysis suggests that MTR A2756G polymorphism might be a potential risk factor for male infertility. In the future, the sample size should be increased to confirm the present results.
Application of phyto‐fabricated zinc oxide nanoparticles to diminish brown spot of pear whilst maintaining its quality

Pyrus communis is a common fruit of temperate region, its domestication and origin is at two different points, Asia and China. Pear fruits bearing brown spot symptoms were picked, and pathogen was isolated and poured on Potato Dextrose Agar (PDA) media. On basis of molecular and molecular analyses, this isolated pathogen was identified as Alternaria alternata. Zinc oxide nanoparticles (ZnO NPs) were prepared from Theveti peruviana leaf extract and were characterized through various techniques Fourier Transform Infrared Spectroscopy (FTIR) analysis of prepared ZnO NPs depicted the presence of agents responsible for stabilization and reduction such as alkenes, alkynes, nitro compounds, alkyl halides, aromatic compounds and aliphatic amines. X‐ray diffraction (XRD) analysis confirmed the size (27 nm) and crystalline nature of ZnO NPs. Scanning electron microscopy (SEM) depicted the irregular shape of the prepared ZnO NPs. Mass percentage of zinc (79.84%) and oxygen (20.16%) was depicted using Energy Dispersive X‐Ray (EDX) analysis. The in vitro and in vivo antifungal activity (A.F) of prepared NPs against A. alternata was confirmed by poisoned food technique and wound inoculation method. On the basis of which it was concluded that 1.0 mg/mL concentration of ZnO NPs could effectively inhibit A. alteranata growth and minimize the risk of brown spot of pear. SEM images of A. alternata under 1 mg/mL NPs showed the deformation in morphology of A. alternata. ZnO NPs also aided in the preservation of its various organoleptic and biochemical properties. The high percentage of soluble solids, firmness, ascorbic acid and sugars demonstrated its high quality. It has been concluded that 1 mg/mL ZnO NPs can effectively control brown spot of pear while maintaining its quality. In addition, the method might be applied to control emerging diseases in an ecofriendly way to meet the global food demand.
Hybrid imaging of prompt x-rays and induced positrons using a pinhole gamma camera during and after irradiation of protons

Objective. Prompt x-ray imaging using a low-energy x-ray camera is a promising method for observing a proton beam’s shape from outside the subject. Furthermore, imaging of positrons produced by nuclear reactions with protons is a possible method for observing the beam shape. However, it has not been possible to measure these two types of images with a single imaging system due to the limited imaging capability of existing systems. Imaging of both prompt x-rays and the distribution of positrons may compensate for the shortcomings of each method. Approach. We conducted imaging of the prompt x-ray using a pinhole x-ray camera during irradiation with protons in list mode. Then, after irradiation with protons, imaging of annihilation radiations from the produced positrons was conducted using the same pinhole x-ray camera in list mode. After this imaging, list-mode data were sorted to obtain prompt x-ray images and positron images. Main results. With the proposed procedure, we could measure both prompt x-ray images and induced positron images with a single irradiation by a proton beam. From the prompt x-ray images, ranges and widths of the proton beams could be estimated. The distributions of positrons were slightly wider than those of the prompt x-rays. From the time sequential positron images, we could derive the time activity curves of the produced positrons. Significance. Hybrid imaging of prompt x-rays and induced positrons using a pinhole x-ray camera was achieved. The proposed procedure would be useful for measuring prompt x-ray images during irradiation to estimate the beam structures as well as for measuring the induced positron images after irradiation to estimate the distributions and time activity curves of the induced positrons.