bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Evolution and Genotype Shift of Porcine Circoviruses Type 2 in Vietnam
Authors: Lai Danh Cong , Le Dung Khanh Thi , Nguyen Trung Huu , Thach Manh , Hue Vo Thi , Le Phan , Ngo Tram Ngoc Thi , Nguyen Nam Minh , Do Duy Tien 
Published: July 2024

Abstract

Porcine Circovirus Type 2 (PCV2), a significant pathogen in the global swine industry, causes Porcine Circovirus Associated Diseases (PCVAD), contributing to substantial economic losses. This study investigates the genetic diversity and evolutionary dynamics of PCV2 in Vietnam from 2022 to 2023. We sequenced and analyzed 47 PCV2 genomes isolated from swine farms across Vietnam, revealing predominant circulation of PCV2d (80.85%) followed by PCV2b (19.15%). Phylogenetic analysis identified PCV2 genotypes PCV2a, PCV2b, PCV2d, PCV2g, and PCV2h circulating in Vietnam, with PCV2d emerging as the most prevalent genotype. Comparison with historical data highlighted genotype shifts from PCV2b to PCV2h in 2008 and then to PCV2d in 2014. Regional analysis indicated varied PCV2 epidemiological patterns between northern and southern Vietnam. Amino acid substitutions within the capsid protein were identified, predominantly in antigenic regions critical for immune recognition, suggesting implications for vaccine efficacy. Positive selection analysis identified multiple sites under evolutionary pressure, indicating ongoing adaptation of Vietnamese PCV2 strains. These findings enhance understanding of PCV2 dynamics in Vietnam and underscore the importance of continuous surveillance and adaptive management strategies in controlling PCV2-associated diseases in swine populations.
Detection and enhancement of latent fingerprint by powder method using bio-synthesized spherical-shaped Bismuth Oxychloride nanoparticles
Authors: Choudhary Nityanand 
Published: July 2024

Abstract

Green fluorescent nanoparticles Bi0.95Tb3+0.5Li0.3OCl were successfully synthesized through the solution combustion method using Mimosa pudica as a biofuel. The nanoparticles, annealed at 10000C for three hours, were characterized by X-ray diffraction, revealing a Body Centered Cubic structure. When excited with a 980 nm diode laser, the phosphor emitted a green color. The energy gap of the nanophosphor was estimated to be 3.64eV using diffuse reflectance spectra. High contrast latent fingerprints were developed on porous and semi-porous surfaces by exciting the phosphors with a 980nm diode laser. These fingerprints were compared with a commercially available green luminescent fingerprint. The synthesized nano phosphor proved to be a viable alternative to traditional luminescent powders for forensic applications, offering a simple, fast, highly sensitive, and eco-friendly method for detecting and enhancing fingermarks related to forensic materials.
Transcriptomic analysis identifies enrichment of cAMP/PKA/CREB signaling in Invasive Lobular Breast Cancer
Authors: Narayanan Susrutha Puthanmadhom , Wedn Abdalla , Shah Osama Shiraz , Chen Jian , Brown Daniel D , McAuliffe Priscilla , Steffi Oesterreich , Lee Adrian V. 
Published: July 2024

Abstract

OBJECTIVE
Invasive lobular breast cancer (ILC) is the most common special type of breast cancer and has unique clinicopathological and molecular hallmarks that differentiate it from the more common invasive carcinoma – no special type (NST). Despite these differences, ILC and NST are treated as a single entity and there is a lack of ILC-targeted therapies. To fill this gap, we sought to identify novel molecular alterations in ILC that could be exploited for targeted therapies.
METHODS
Differential gene expression and Geneset Enrichment and Variation analyses were performed on RNA-seq data from three large public breast cancer databases – the Sweden Cancerome Analysis Network-Breast (SCAN-B; luminal A ILC N = 263, luminal A NST N = 1162), The Cancer Genome Atlas (TCGA; luminal A ILC N = 157, luminal A NST N = 307) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC; luminal A ILC N = 65, luminal A NST N = 533). Pathways enriched in overlapping differentially expressed genes from these datasets were clustered using Jaccard similarity to identify pathways enriched in ILC. The cAMP/PKA/CREB signaling was studied in ILC, ILC-like and NST cell lines and patient-derived organoids (PDOs) using forskolin, an activator of the pathway.
RESULTS
Clinicopathological features of patients with ILC and NST in SCAN-B were similar to prior population-based studies. There was a consistent pattern of up-regulation of cAMP/PKA/CREB related signaling in ILC compared to NST in SCAN-B, TCGA and METABRIC. Treatment with forskolin resulted in a greater increase in phospho-CREB in ILC cell lines and organoids than NST. CRISPR deletion of CDH1 in NST cell lines did not alter response of cells to forskolin as measured by phospho-CREB. Forskolin treatment caused growth inhibition in ILC and NST, with ILC cell lines being more sensitive to forskolin-mediated growth inhibition.
CONCLUSION
In three separate datasets, cAMP/PKA/CREB signaling was identified to be higher in ILC than NST. This in silico finding was validated in cell line and organoid models. Loss of CDH1 was not sufficient to mediate this phenotype. Future studies should investigate the mechanisms for differential cAMP/PKA/CREB signaling and the potential for therapeutic targeting in patients with ILC.
A Comprehensive Survey of Scoring Functions for Protein Docking Models
Authors: Shirali Azam , Stebliankin Vitalii , Kark Ukesh , Shi Jimeng , Chapagain Prem , Narasimhan GIri 
Published: July 2024

Abstract

Background: While protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. Without accurate and efficient scoring functions to differentiate between native and non-native binding complexes, the accuracy of current docking tools cannot be guaranteed. Although many innovative scoring functions have been proposed, a good scoring function for docking remains elusive. Deep learning models offer alternatives to using explicit empirical or mathematical functions for scoring protein-protein complexes.
Results: In this study, we perform a comprehensive survey of the state-of-the-art scoring functions by considering the most popular and highly performant approaches, both classical and deep learning-based, for scoring protein-protein complexes.
Conclusions: We evaluate the strengths and weaknesses of classical and deep learning-based approaches across seven public and popular datasets to aid researchers in understanding the progress made in this field. Keywords: Computational structural biology, Protein-protein interactions, Scoring functions, Molecular docking, Deep learning, Protein surface properties
Introducing AIDx, The Physician's AI Copilot
Authors: Alwakeel Alan 
Published: July 2024

Abstract

The dynamic environment of medicine, like the Emergency Department, challenges physicians with an influx of patient data and the need for swift diagnosis and treatment under high-pressure situations. Furthermore, there are numerous AI models developed for medical applications that, despite their potential, rarely see hospital implementation because they fail to integrate into pre-existing clinical workflows. Addressing these challenges, I developed AIDx, a state-of-the-art AI-powered system designed to streamline clinical decision-making, provide accurate disease prediction and treatment planning, offer novel approaches for personalized patient healthcare, and serve as a hub for AI-assisted medical analysis. Unlike standalone systems, AIDx integrates seamlessly with a hospital's pre-existing electronic health records and automatically leverages supplemental tools (like an up-to-date medical knowledge database and capability-enhancing AI models), offering physicians a unified platform for comprehensive AI assistance. I trained AIDx on 400,000 de-identified patient charts and evaluated it on 7,000 medical exam questions, achieving a remarkable accuracy of 83.61% that rivals the performance of industry-leading models like Google's Med-PaLM 2 and OpenAI's GPT-4 with significantly fewer parameters (a model size metric), using only 46.7 billion compared to their 340 billion and 1.7 trillion. This parameter efficiency translates into feasible on-premises deployment, high-speed processing, and adaptability across clinical settings. AIDx also significantly enhances patient-physician communication, simplifying medical terminology and facilitating multilingual translation. Ultimately, AIDx represents a transformative integration of AI in medicine, establishing an unprecedented standard for personalized, reliable, and streamlined patient care, elevating the quality of healthcare, and enhancing the lives of patients and physicians alike.
Digging deeper into the impacts of different soil water systems on the date palm root architecture and associated fungal communities
Authors: Robin-Soriano Alexandre , Vincent Bryan , Maurice Kenji , Battesti Vincent , Boukcim Hassan , Ducousso Marc , Gros-Balthazard Muriel 
Published: July 2024

Abstract

In arid regions, excessive water use threatens agricultural sustainability and overall livelihoods. It is essential to minimize water consumption to address these issues. Date palm (Phoenix dactylifera L.) is an emblematic crop of arid regions and a major water consumer. Tailoring current irrigation systems into new, water-efficient systems could help cope with the water consumption of this crop. Microbial communities associated with plants are essential for agricultural sustainability and could improve the water use efficiency in regions threatened by water scarcity. These communities should thus be seriously taken into account when adapting agrosystems to the current global change setting. However, no information is presently available on the effects of these modifications on date palm microbial communities. This study highlights the impact of different soil water systems (flooding and drip irrigation, natural conditions and abandoned farms) on date palm root fungal communities at different soil depths. The findings revealed that the soil water systems had a marked impact on fungal communities and that drip irrigation reduced the fungal diversity but increased the abundance of arbuscular mycorrhizal fungi. We showed that these effects were similar at all sampling depths. Finally, as the root architecture is a major determinant of water uptake, we reveal different behaviors of the root architecture under these different soil water systems to 160 cm depth. The findings of this study give new insights into the date palm root architecture and associated fungal communities, particularly in the context of the water availability crisis, which drives the adaptation of agricultural systems.
Diagnostic Accuracy of Ultrasound in Intensive Care Patients with Undifferentiated Shock: A Systematic Review and Meta-analysis.
Authors: Karigowda Lohith , Gupta Bhavna , Deshpande Kush , Elkady Hatem 
Published: July 2024

Abstract

Background:
Shock is a common condition in intensive care, affecting approximately one-third of patients in the intensive care unit (ICU).1 The standard method to diagnose shock in the ICU is based on clinical, hemodynamic, and biochemical signs. In the last decade, ultrasound has become the preferred tool for shock identification and treatment. Therefore, we performed a systematic review and meta-analysis to determine the diagnostic accuracy of ultrasound in patients with undifferentiated shock in the Intensive Care Department.
Method:
We searched PubMed, Embase, Scopus, Cochrane Central Register and Google scholar for Controlled trials published until June 2023. Two intensivists independently screened the articles for full-text reviews and assessed the quality of the selected studies using the Quadas-2 tool. We included a prospective study involving critically ill patients with undifferentiated shock which utilise ultrasound to diagnose the type of shock. The objective was to determine the accuracy of ultrasound in identifying shock type.
Results:
Of the 7287 articles, four met the study inclusion criteria for the meta-analysis. Pooled positive likelihood ratio values ranged from 8.8 (95% CI 2.4 to 32.37) for distributive shock to 137.56.54 (95% CI 27.76 to 681.64) for obstructive shock. The summary receiver operating characteristic (SROC) for cardiogenic and obstructive shock had an AUC (area under the curve) of 0.99, for hypovolemic and mixed shock was 0.5, and for distributive shock was 0.76, Pooled negative likelihood ratio values ranged from 0.05 (95% CI 0.010 to 0.24) for cardiogenic shock to 0.22 (95% CI 0.127 to 0.38) for mixed-etiology shock.
Conclusion:
Our meta-analysis showed that ultrasound in intensive care patients with undifferentiated shock can help diagnose obstructive and cardiogenic shock. However, this may not be helpful for other types of shocks.
Development Modul Guided Inquiry Integrated Augmented Reality (M-GIIAR) to Improve Student’s Science Process Skills on Mechanical Wave Material
Authors: Nindyatami Zulfi , Rochman Chaerul , Chusni Muhammad Minan 
Published: July 2024

Science learning skills need to be applied at every stage of learning. However, students do not have good science process skills (SPS). Learning media is also needed to support modern and engaging science learning skills. Research using the ADDIE model, a sample of 30 students in class XI MIPA at SMAN 1 Wanayasa. The average validity test results are 82.40%. The results of implementing Authentic assessment based on Teaching and Learning Trajectory with Student Activity Sheets increased from each meeting; the average value was 85.58% with good effectiveness. The results of the N-Gain pretest and posttest based on the science process skills indicator obtained an average N-Gain result of 0.57 with a moderate interpretation. The researcher used a nonparametric hypothesis test with the Wilcoxon sign rank type. The results of the hypothesis test obtained acceptance of the alternative hypothesis (Ha), meaning that there was an increase experienced by students in SPS in mechanical wave material. Based on several aspects, student responses obtained an average of 70.07% in the good and positive category.
Search for Novel Therapeutic Targets of Type 2 Diabetes Mellitus
Authors: Kumar Yadav Nitesh , Mazumder Rupa , Rani Anjna , Kumar Arvind , Kaur Jaskiran 
Published: July 2024

Background:
Type 2 Diabetes (T2D) is a chronic metabolic disease characterized by
hyperglycemia and carries a high risk of numerous complications. The rising prevalence of this
lifelong condition affects millions globally, demanding novel therapeutic strategies. Existing medications
targeting insulin and other pathways often pose limitations like suboptimal glycemic control,
side effects, and high costs. Novel therapeutic targets are crucial for developing better treatments
and potentially reducing side effects associated with previous drugs.

Objective:
This paper aims to comprehensively review and analyze potential targets for the treatment
of diabetes mellitus.

Method:
We conducted a comprehensive search of MEDLINE, Scopus, Science Direct, PubMed,
and Google Scholar databases. Search terms included “diabetes mellitus”, “novel targets”, “drug
discovery”, “gene expression” and “molecular pathways”. We identified over 175 published articles
exploring novel therapeutic targets for DM.

Results:
The review presented a detailed analysis of promising anti-diabetic targets. These targets
encompass various pathways and mechanisms, including insulin signaling, Glucose signaling, inflammation
and oxidative stress, gut microbiome, and epigenetic modifications. Several promising
candidates emerged, such as Glucokinase activators, GPCRs modifiers, Fructose-1,6-bisphosphatase
antagonists, Protein tyrosine phosphatase 1B antagonist, 11β-Hydroxysteroid, andDehydrogenase
antagonists. Potential therapeutic agents targeting these emerging targets will be discussed,
along with their mechanisms of action and preclinical/clinical evidence.

Conclusion:
By identifying and comprehensively analyzing new therapeutic targets, this review
intends to provide insights for the development of more effective and efficient diabetes management
strategies. The information presented can guide future research initiatives and drug development
efforts toward novel and promising anti-diabetic therapies.
Formulation and Characterization of Emulgel Lornoxicam Containing Lemon Grass Oil as Penetration Enhancer
Authors: Kumari Vibha , Bajpai Meenakshi 
Published: July 2024

Introduction:
Emulgel dosage form is an advanced form of transdermal drug de-livery. It is a combination of emulsion and gel in a definite ratio. Emulsions are incorporated into the gel with proper mixing. The emulsion present in emulgel can be either oil/water or water/oil, which is thickened by mixing it with a gelling agent.

Material and Methods:
On the basis of the solubility of lornoxicam in various oils, a surfactant and a co-surfactant were selected for further research. For the preparation of emulgel, the emulsion was prepared with Smix (surfactant and co-surfactant) in a ratio of 1:2. The prepared emulsion was incorporated into different concentrations of carbapol 934 in a 1:1 ratio to make a homogenous emulgel.

Results:
The emulgel was inspected visually to see if it had any phase behaviour, spreadabil-ity, or grittiness by applying it to a slide. All formulations were evaluated for pH, physical properties, drug content, spreadability, extrudability, swelling index, viscosity, and centrifu-gation. Franz diffusion cell was used to perform in-vitro release of formulation with the help of egg membrane. Among all formulations, F3 showed 83% release after 6 hours and showed acceptable physical properties like homogeneity, colour, consistency, pH value, spreadability, extrudability, and drug content.

Discussion:
Thus, emulgel can be regarded as a more feasible drug delivery system for hydrophobic drugs (lornoxicam) than the currently marketed formulation. Optimized emulgel formulation consists of a microemulsion of lornoxicam, 1% of carbopol 934, propylene glycol, sodium benzoate, lemon grass oil, glycerin, and distilled water. In the in-vitro release studies, pH 7.4 phosphate buffer emulgel formulation (F3) showed 83% after 6 hours. Emulgel was found to be stable under stable conditions.

Conclusion:
The emulgel of the poorly water-soluble drug (lornoxicam) was formulated. The components and their optimum ratio for the formulation of microemulsion were obtained by solubility studies and droplet size analysis. Thus, microemulsion can be regarded as a more feasible dose delivery system for lornoxicam than the currently marketed tablet, capsule, and injection formulations. Optimized microemulsion of lornoxicam was incorporated into the gel base. Therefore, it may be concluded that emulgel of lornoxicam can be used as a controlled-release dosage form of the drug for local application in rheumatoid arthritis.
Transformasi tanah perdikan sebagai basis pengembangan budaya Islam Jawa (analisa pada tanah perdikan Majan Tulungagung)
Authors: Awalin Fatkur Rohman Nur 
Published: July 2024

Tanah perdikan sebagai tanah bebas pejak merupakan anugrah dari raja kepada rakyatnya. Pamor tanah perdikan saat ini meredup karena sudah dihapuskan melebur ke NKRI. Namun pada sisi lainnya kearifan-kearifan dalam tanah perdikan masih bisa diidentifikasi sampai saat ini. Sampelnya adalah tanah perdikan Majan Tulungagung Jawa Timur. Secara legal formal tanah perdikan Majan di berikan kepada KHR. Khasan Mimbar oleh Raja Mataram Islam Pakubuwana II tahun 1727 M. Pemberian tanah perdikan merupakan hak penuh KHR. Khasan Mimbar dalam mengelolanya untuk mendakwahkan Islam di kabupaten Ngrowo sekarang bertransformasi menjadi kabupaten Tulungagung. Dalam pengelolaanya KHR. Khasan Mimbar mendirikan Masjdi Al-Mimbar dan Pondok Pesantren Nggrenjol. Berdasarkan analisanya ditemukan kearifan-kearifan seperti jamasan pusaka kyai golok, nikah Majan dan grebeg Maulud. Kesimpulannya berdasarkan kasu tanah perdikan Majan merupakan kuasa Kyai dalam hal ini dikembangkan untuk mendakwahkan agama Islam yang rahmatan lil alamin. Indikatornya adalah tidak bertentangan budaya setempat dimana Islam itu tumbuh. Sehingga wajah Islam penuh dengan kedamaian yang mampu mengadvokasi budaya masyarakat setempat.
Examining the Role of Physician Characteristics in Web-Based Verified Primary Care Physician Reviews: Observational Study
Authors: Sehgal Neil K R , Rader Benjamin , Brownstein John S 
Published: July 2024

Background
Doctor review websites have become increasingly popular as a source of information for patients looking to select a primary care provider. Zocdoc is one such platform that allows patients to not only rate and review their experiences with doctors but also directly schedule appointments. This study examines how several physician characteristics including gender, age, race, languages spoken in a physician’s office, education, and facial attractiveness impact the average numerical rating of primary care doctors on Zocdoc.

Objective
The aim of this study was to investigate the association between physician characteristics and patient satisfaction ratings on Zocdoc.

Methods
A data set of 1455 primary care doctor profiles across 30 cities was scraped from Zocdoc. The profiles contained information on the physician’s gender, education, and languages spoken in their office. Age, facial attractiveness, and race were imputed from profile pictures using commercial facial analysis software. Each doctor profile listed an average overall satisfaction rating, bedside manner rating, and wait time rating from verified patients. Descriptive statistics, the Wilcoxon rank sum test, and multivariate logistic regression were used to analyze the data.

Results
The average overall rating on Zocdoc was highly positive, with older age, lower facial attractiveness, foreign degrees, allopathic degrees, and speaking more languages negatively associated with the average rating. However, the effect sizes of these factors were relatively small. For example, graduates of Latin American medical schools had a mean overall rating of 4.63 compared to a 4.77 rating for US graduates (P<.001), a difference roughly equivalent to a 2.8% decrease in appointments. On multivariate analysis, being Asian and having a doctor of osteopathic medicine degree were positively associated with higher overall ratings, while attending a South Asian medical school and speaking more European and Middle Eastern languages in the office were negatively associated with higher overall ratings.

Conclusions
Overall, the findings suggest that age, facial attractiveness, education, and multilingualism do have some impact on web-based doctor reviews, but the numerical effect is small. Notably, bias may play out in many forms. For example, a physician's appearance or accent may impact a patient's trust, confidence, or satisfaction with their physician, which could in turn influence their take-up of preventative services and lead to either better or worse health outcomes. The study highlights the need for further research in how physician characteristics influence patient ratings of care.