Miracle-dz/UniFAR-FTUs huggingface dataset:
Obesity-Related Neuroinflammation: Magnetic Resonance and Microscopy Imaging of the Brain

Obesity is a major risk factor of Alzheimer’s disease and related dementias. The principal feature of dementia is a loss of neurons and brain atrophy. The mechanistic links between obesity and the neurodegenerative processes of dementias are not fully understood, but recent research suggests that obesity-related systemic inflammation and subsequent neuroinflammation may be involved. Adipose tissues release multiple proinflammatory molecules (fatty acids and cytokines) that impact blood and vessel cells, inducing low-grade systemic inflammation that can transition to tissues, including the brain. Inflammation in the brain—neuroinflammation—is one of key elements of the pathobiology of neurodegenerative disorders; it is characterized by the activation of microglia, the resident immune cells in the brain, and by the structural and functional changes of other cells forming the brain parenchyma, including neurons. Such cellular changes have been shown in animal models with direct methods, such as confocal microscopy. In humans, cellular changes are less tangible, as only indirect methods such as magnetic resonance (MR) imaging are usually used. In these studies, obesity and low-grade systemic inflammation have been associated with lower volumes of the cerebral gray matter, cortex, and hippocampus, as well as altered tissue MR properties (suggesting microstructural variations in cellular and molecular composition). How these structural variations in the human brain observed using MR imaging relate to the cellular variations in the animal brain seen with microscopy is not well understood. This review describes the current understanding of neuroinflammation in the context of obesity-induced systemic inflammation, and it highlights need for the bridge between animal microscopy and human MR imaging studies.
Directionality and Logical Form: On the Scope of Focusing Particles and Wh-in-situ

Preface. Abbreviations used in glosses. Introduction. Notes. 1. Selected earlier work on the syntax and semantics of focusing particles. 2. Movement to a scope position: quantificational and scalar interpretation. 3. Focusing particles and quantifiers in pre- and postpositional phrases. 4. Focusing particles and quantifiers in determiner and noun phrases. 5. Focusing particles and quantifiers in adjectival phrases. 6. The verb phrase, clausal complements and extraposition. 7. Complementation and the scope of Wh in Bengali.
Proof of the Refined Alternating Sign Matrix Conjecture

Mills, Robbins, and Rumsey conjectured, and Zeilberger proved, that the number of alternating sign matrices of order $n$ equals $A(n):={{1! 4! 7! (3n-2)! } \over {n! (n+1)! (2n-1)! }}$. Mills, Robbins, and Rumsey also made the stronger conjecture that the number of such matrices whose (unique) `1' of the first row is at the $r^{th}$ column, equals $A(n) {{n+r-2} \choose {n-1}}{{2n-1-r} \choose {n-1}}/ {{3n-2} \choose {n-1}}$. Standing on the shoulders of A.G. Izergin, V. E. Korepin, and G. Kuperberg, and using in addition orthogonal polynomials and $q$-calculus, this stronger conjecture is proved.
Intra-host quasispecies reconstructions resemble inter-host variability of transmitted chronic hepatitis B virus strains

The hepatitis B virus is a partially double stranded DNA virus in the Hepadnaviridae family of viruses that infect the liver cells of vertebrates including humans. The virus replicates through the reverse transcription of an RNA intermediate by a viral poly-merase, akin to retroviruses. The viral polymerase has high replication capacity but low fidelity and no proofreading activity resulting in a high mutation rate. This contributes to the emergence of a cloud of mutants or quasispecies within host systems during infection. Several host and viral factors have been identified that contribute to mutations and mutation frequency in shaping viral evolution, however, because the dynamics of viral evolution cannot be understood from the fittest strain alone, the need exists to sequence and reconstruct intra-host diversity, recently made possible through next generation sequencing. Due to the extensive pipeline of bioinformatic analyses associated with next generation sequencing studies are needed to ascertain if quasispecies reconstruction methods and diversity measures accurately model known diversity. Here, next generation sequencing and various quasispecies reconstruction methods are used to model the natural evolution of viral populations across the full genome of hepatitis B virus strains from South Africa. This study illustrates that (i) different methods of quasispecies reconstruction reconstruct the same amount of diversity, (ii) intra-host diversity derived from full quasispecies analyses re-sembles diversity measures obtained from previous methods, (iii) inter-host diversity resembles the diversity between closely related quasispecies variants, (iv) diversity is increased in HIV-negative individuals, and (v) corroborate that seroconversion of HBV biomarkers increases mutation rates.
Stem Cells used for Tissue Engineering of Articular Cartilage: Literature Review

Adult articular cartilage (AC) has a limited self-healing capacity. Cartilage defects lead to osteoarthritis (OA) characterized by severe pain and impaired mobility. Currently, there are no approved treatments for OA that successfully reverse or heal structural defects permanently. Although techniques such as microfracture, arthroplasty and subchondral drilling have been effective at treating small to intermediate sized AC defects over the short term, a long-term solution for OA is still necessary. In recent years, research has focused on tissue engineering of articular cartilage (TEAC) as a potential treatment option for OA. TEAC therapies utilizing chondrocytes such as autologous chondrocyte implantation (ACI) are promising but are limited by their complexity, high cost and inability to promote the formation of healthy hyaline AC. Due to the limitations of ACI, stem cells have been investigated as an alternative cell source for TEAC. To engineer AC, stem cells are allowed to differentiate on/in a scaffold in a bioreactor that controls chemical, physical and biological cues to support the chondrogenic potential of the stem cells. The use of stem cells provides numerous advantages as treatment costs can be lowered, the number of required surgeries can be reduced and high-quality AC can be formed. Mesenchymal stem cells (MSC) in particular are advantageous in that they are easily available and can be extracted from a diverse range of tissues including, bone marrow, adipose, and synovium. Each type of MSC have their own advantages and disadvantages but generally each of them possess high chondrogenic potential and immunosuppressive capacities. Induced pluripotent stem cells (iPSC) have also been recognized as a promising cell type for TEAC due to their unlimited proliferation and self-renewal capacities. Ultimately, each cell source has potential for use in TEAC therapies but further studies comparing cell sources are required before a gold standard can be determined. This review summarizes the pros and cons for potential use of each stem cell source in TEAC. The review is not meant to be comprehensive of the current literature.
A Memory-Augmented Multi-Task Collaborative Framework for Unsupervised Traffic Accident Detection in Driving Videos

Identifying traffic accidents in driving videos is crucial to ensuring the safety of autonomous driving and driver assistance systems. To address the potential danger caused by the long-tailed distribution of driving events, existing traffic accident detection (TAD) methods mainly rely on unsupervised learning. However, TAD is still challenging due to the rapid movement of cameras and dynamic scenes in driving scenarios. Existing unsupervised TAD methods mainly rely on a single pretext task, i.e., an appearance-based or future object localization task, to detect accidents. However, appearance-based approaches are easily disturbed by the rapid movement of the camera and changes in illumination, which significantly reduce the performance of traffic accident detection. Methods based on future object localization may fail to capture appearance changes in video frames, making it difficult to detect ego-involved accidents (e.g., out of control of the ego-vehicle). In this paper, we propose a novel memory-augmented multi-task collaborative framework (MAMTCF) for unsupervised traffic accident detection in driving videos. Different from previous approaches, our method can more accurately detect both ego-involved and non-ego accidents by simultaneously modeling appearance changes and object motions in video frames through the collaboration of optical flow reconstruction and future object localization tasks. Further, we introduce a memory-augmented motion representation mechanism to fully explore the interrelation between different types of motion representations and exploit the high-level features of normal traffic patterns stored in memory to augment motion representations, thus enlarging the difference from anomalies. Experimental results on recently published large-scale dataset demonstrate that our method achieves better performance compared to previous state-of-the-art approaches.
BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at \url{https://github.com/PharMolix/OpenBioMed}.
Analisis Runtun Waktu dalam Pengujian Pengaruh TIK terhadap Penurunan Laju Kemiskinan di Indonesia

Kemiskinan di Indonesia dipandang sebagai ketidakmampuan dari sisi ekonomi dalam memenuhi kebutuhan pangan dan non pangan. Pandangan ini memicu penyelesaian masalah dengan pendekatan ekonomi pula. Hingga tahun 2012, jumlah penduduk miskin sebesar 11,37 persen. Meski telah mengalami penurunan, besarannya tidak signifikan. Hal ini disebabkan strategi pengentasan kemiskinan yang belum tepat. Di sisi lain, penetrasi teknologi informasi dan komunikasi tumbuh dengan pesatnya. Penelitian ini bertujuan untuk mengkaji pengaruh penetrasi telepon seluler, internet, dan pitalebar terhadap laju angka kemiskinan. Dengan pendekatan ekonometris runtun waktu selama 13 tahun, ditemukan bahwa penetrasi telepon seluler dan internet berpengaruh secara signifikan dalam menurunkan laju kemiskinan. Setiap kenaikan 1 persen penetrasi telepon seluler dapat menurunkan laju kemiskinan hingga 0,18 persen, sedangkan penetrasi internet berimpak pada penurunan laju kemiskinan hingga 0,27 persen. Di antara kedua penetrasi tersebut, penetrasi internet memiliki pengaruh yang dominan terhadap laju penurunan kemiskinan.
Accurate channel estimation based on Bayesian Compressive Sensing for next-generation wireless broadcasting systems

Digital television terrestrial broadcasting (DTTB) industry has achieved rapid development in recent years. It is now facing new development opportunities for next-generation wireless broadcasting systems. As one of the DTTB standards, digital terrestrial multimedia/television broadcasting (DTMB) uses the time domain synchronous OFDM (TDS-OFDM) as its basic core technology. TDS-OFDM has higher spectral efficiency and faster synchronization but it cannot support high-order modulation and high-definition television (HDTV) delivery in fast fading channels. Recently, compressive sensing (CS) methods have been used for the accurate channel estimation. However, the classical CS algorithms require the channel sparsity in prior and the signal recovery accuracy is unacceptable when the signal-to-noise ratio (SNR) is low. To solve this problem, in this paper we exploit the Bayesian Compressive Sensing (BCS) based on statistical learning theory (SLT) and relevance vector machines (RVM) to improve the sparse channel estimation accuracy. Besides, we propose to reduce the correlation of the measurement matrix columns for a further performance improvement. Simulation results demonstrate that the proposed BCS-based channel estimation has better performance than conventional solutions.
Hydrolysis of Enkepholins in Homogenotes of Anterior Segment Tissues of the Albino Robbit Eye

experimental allergic uveitis induced by rhodopsin and retinal rod outer segments. Ophthalmic Res 12:165, 1980. 5. Meyers-Elliott RH, Gammon RA, Somner HL, and Shimizu I: Experimental retinal autoimmunity (ERA) in strain 13 guinea pigs: Induction of ERA retinopathy with rhodopsin. Clin Immunol Immunopath 27:81, 1983. 6. Broekhuyse RM, Winkens HJ, Kuhlmann ED, and van Vugt AHM: Opsin-induced experimental autoimmune retinitis in rats. Curr Eye Res 3:1405, 1984. 7. Kalsow CM and Wacker WB: Pineal gland involvement in retinainduced experimental allergic uveitis. Invest Ophthalmol Vis Sci 17:774, 1978. 8. Mochizuki M, Charley J, Kuwabara T, Nussenblatt RB, and Gery I: Involvement of the pineal gland in rats with experimental autoimmune uveitis. Invest Ophthalmol Vis Sci 24:1333, 1983. 9. Redmond TM, Wiggert B, Robey FA, Ngoyen N, Lewis MS, Lee L, and Chader GJ: Isolation and characterization of monkey interphotoreceptor retinoid-binding protein, a unique extracellular matrix component of the retina. Biochemistry 24:787, 1985. 10. Rodrigues MM, Hackett J, Gaskins R, Wiggert B, Lee L, Redmond TM, and Chader GJ: Interphotoreceptor retinoid-binding protein in retinal rod cells and pineal gland. Invest Ophthalmol Vis Sci 27:844, 1986. 11. de Kozak Y, Sakai J, Thillaye B, and Faure J-P: S antigen-induced experimental autoimmune uveoretinitis in rats. Current Eye Res 1:327, 1981. 12. Mochizuki M, Kuwabara T, McAllister C, Nussenblatt RB, and Gery I: Adoptive transfer of experimental autoimmune uveoretinitis in rats: Immunopathogenic mechanisms and histological features. Invest Ophthalmol Vis Sci 26:1, 1985.
Selective predation by larval Agabus (Coleoptera: Dytiscidae) on mosquitoes: support for conservation- based mosquito suppression in constructed wetlands

SUMMARY 1. Wetland insect predators can structure aquatic prey communities via selective predation, but receive considerably less attention than vertebrate predators. We conducted laboratory experiments to test selective predation by two species of larval dytiscid beetles (Agabus; Coleoptera: Dytiscidae) and the potential contribution of these beetles to suppression of mosquito populations in constructed wetlands. 2. Agabus consumed copepods, ostracods and mosquito larvae in no-choice tests. When offered a choice, 76% of all prey consumed were mosquito larvae, indicating selective predation. Subsequent experiments revealed this preference was due to ease of capture of mosquito larvae over alternative prey. 3. Cannibalism and intraguild predation were common within and between species of Agabus, which may reduce the overall impact of the observed selective predation. 4. Agabus larvae selectively preyed on mosquito larvae over alternative prey, which is not characteristic of some fish used as biological control agents for mosquitoes. Predator exclusion or similar experiments in the field could document how these results translate into a natural setting. 5. The findings of this study suggest developing mosquito suppression strategies focused on conservation of native wetland predators. These strategies are preferable to introducing non-native generalist predators, or applying pesticides.
Improved Murine MHC-Deficient HLA Transgenic NOD Mouse Models for Type 1 Diabetes Therapy Development

Improved mouse models for type 1 diabetes (T1D) therapy development are needed. T1D susceptibility is restored to normally resistant NOD. β2m−/− mice transgenically expressing human disease–associated HLA-A*02:01 or HLA-B*39:06 class I molecules in place of their murine counterparts. T1D is dependent on pathogenic CD8+ T-cell responses mediated by these human class I variants. NOD. β2m−/−-A2.1 mice were previously used to identify β-cell autoantigens presented by this human class I variant to pathogenic CD8+ T cells and for testing therapies to attenuate such effectors. However, NOD. β2m−/− mice also lack nonclassical MHC I family members, including FcRn, required for antigen presentation, and maintenance of serum IgG and albumin, precluding therapies dependent on these molecules. Hence, we used CRISPR/Cas9 to directly ablate the NOD H2-Kd and H2-Db classical class I variants either individually or in tandem (cMHCI−/−). Ablation of the H2-Ag7 class II variant in the latter stock created NOD mice totally lacking in classical murine MHC expression (cMHCI/II−/−). NOD-cMHCI−/− mice retained nonclassical MHC I molecule expression and FcRn activity. Transgenic expression of HLA-A2 or -B39 restored pathogenic CD8+ T-cell development and T1D susceptibility to NOD-cMHCI−/− mice. These next-generation HLA-humanized NOD models may provide improved platforms for T1D therapy development.
Line fiducial material and thickness considerations for ultrasound calibration

Ultrasound calibration is a necessary procedure in many image-guided interventions, relating the position of tools and anatomical structures in the ultrasound image to a common coordinate system. This is a necessary component of augmented reality environments in image-guided interventions as it allows for a 3D visualization where other surgical tools outside the imaging plane can be found. Accuracy of ultrasound calibration fundamentally affects the total accuracy of this interventional guidance system. Many ultrasound calibration procedures have been proposed based on a variety of phantom materials and geometries. These differences lead to differences in representation of the phantom on the ultrasound image which subsequently affect the ability to accurately and automatically segment the phantom. For example, taut wires are commonly used as line fiducials in ultrasound calibration. However, at large depths or oblique angles, the fiducials appear blurred and smeared in ultrasound images making it hard to localize their cross-section with the ultrasound image plane. Intuitively, larger diameter phantoms with lower echogenicity are more accurately segmented in ultrasound images in comparison to highly reflective thin phantoms. In this work, an evaluation of a variety of calibration phantoms with different geometrical and material properties for the phantomless calibration procedure was performed. The phantoms used in this study include braided wire, plastic straws, and polyvinyl alcohol cryogel tubes with different diameters. Conventional B-mode and synthetic aperture images of the phantoms at different positions were obtained. The phantoms were automatically segmented from the ultrasound images using an ellipse fitting algorithm, the centroid of which is subsequently used as a fiducial for calibration. Calibration accuracy was evaluated for these procedures based on the leave-one-out target registration error. It was shown that larger diameter phantoms with lower echogenicity are more accurately segmented in comparison to highly reflective thin phantoms. This improvement in segmentation accuracy leads to a lower fiducial localization error, which ultimately results in low target registration error. This would have a profound effect on calibration procedures and the feasibility of different calibration procedures in the context of image-guided procedures.
Perceived Control and Privacy in a Professional Cloud Environment

Cloud customers need to assess whether their cloud service provider offers high-quality services and handles sensitive information confidentially. Privacy protection is therefore a major challenge during cloud sourcing. Although cloud customers want control over their sensitive information, they have limited resources to do so. They therefore consider other control agents, such as certification authorities or collectives, but the effectiveness of these groups to ensure privacy protection is unknown. This study differentiates between three control agents (personal control, proxy control, and collective control) and investigates the influence of these agents on cloud customers’ perceived control over sensitive information to protect privacy during cloud sourcing. Results show that proxy and collective control influence cloud customers’ perceptions but personal control does not. Therefore, only external control agents, who can apply sanctions, are perceived as being able to effectively protect privacy.
Forensic Diagnosis of Acute Myocardial Infarction: Application of Mass Spectrometry

Although acute myocardial infarction (AMI) is one of the most common causes of sudden death outside hospital [1], its molecular pathogenesis is not sufficiently understood. Whereas chronic cardiac infarction lesions show gross fibrosis, and scarring in autopsy, AMI lesions rarely include such changes and it is often difficult to diagnosis on autopsy. For obvious reasons, diagnosis of myocardial infarction by chest pain, or other symptoms such as ST-elevation and/or Q-wave, is limited in autopsy cases, and macroscopic findings are limited and not sufficiently informative at the phase immediately after the onset of the infarction episode. In the autopsied heart, dark mottling is detectable within 4 h after the onset, but varies by case, and a yellow tan may be detectable on damaged tissue within a few days; scarring develops within 8–10 weeks, and is completed by 2 months after the onset. Coronary spasm of an artery in acute coronary syndrome [2] by thrombus formation is so transient that the coronary thrombi are frequently lost in most cases; a guideline for ECG has been recently suggested [3,4]. However, when the AMI is followed by sudden death in the absence of a physician or other trained witness at the scene, forensic diagnosis can be difficult. For this reason, diagnostic findings are guided by histologic examination. In fact, wavy fibers and contraction bands are a hallmark of injured myocardium [5]. However, these injuries take prior to in flammatory neutrophil infiltrates that are also detectable 4–6 h after onset [6]. CXCL8 chemotaxically attracts neutrophils into the myocardium [7]. Neutrophilic infiltrate coronary plaques and infarcted myocardium, and mediate tissue damage by releasing matrix-degrading enzymes and reactive oxygen species. Neutrophils are also involved in adverse post-infarction cardiac remodeling and neointima formation [8]. Thus, neutrophils are pivotal in damaging cardiac myocytes at acute infarction.