Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations between lipids and subclinical coronary atherosclerosis.

OBJECTIVE Whether HIV modifies the relationship of serum lipids with coronary atherosclerosis and coronary plaque subtypes is uncertain. We examined the associations between traditional lipids and coronary atherosclerosis among HIV-infected (HIV+) and HIV-uninfected (HIV-) men. DESIGN The Multicenter AIDS Cohort Study (MACS) is an observational cohort with a total of 429 HIV+ and 303 HIV- men who had non-contrast cardiac computed tomography (CT) performed to measure coronary artery calcium (CAC) and coronary CT angiography to measure coronary stenosis, coronary plaque presence, and composition. METHODS We used multivariable adjusted prevalence ratios (PR) to examine the relationship between the standard deviation (SD) difference in each lipid parameter and coronary atherosclerosis. RESULTS Total cholesterol (TC) / HDL-C had the strongest associations with coronary atherosclerosis regardless of HIV status. Overall, lipid parameters were most strongly associated with the presence of mixed plaque, stenosis >50%, and CAC for both HIV+ and HIV- men. HIV+ men had similar, but weaker associations, between lipid parameters and coronary atherosclerosis compared to HIV- men. The strongest association was between the TC/HDL-C and stenosis >50% for both HIV+ [PR 1.25 per SD (95% CI 1.07-1.43)] and HIV- men [PR 1.46 per SD (95% CI 1.08-1.85)]. CONCLUSION The associations between lipids and coronary atherosclerosis tended to be weaker for HIV+ compared to HIV- men, although TC/HDL had the strongest association for both HIV+ and HIV- men. A weaker association between lipid levels and coronary atherosclerosis for HIV+ men may contribute to the decreased discrimination of CVD risk observed in HIV+ individuals.
Magnetic Resonance Imaging Observations of the Conus Medullaris in a Korean Population

Study Design Retrospective study (level of evidence: level 3). Purpose To study the anatomy of the conus medullaris in Koreans. Overview of Literature The anatomical position of the conus medullaris is well-documented in anatomy textbooks; however, the shape of the conus in the canal rarely described. Furthermore, to our knowledge, no study in Korea has not yet assessed the shape of the conus as well as its position in the canal via cadavaric dissection and/or magnetic resonance imaging (MRI). Methods MRI findings of 189 Korean patients aged 2–94 years (93 men and 94 women) were assessed. No subjects from other ethnicities were included. The method proposed by Arai and colleagues was used to assess the termination point and shape of the conus in the canal. The position of the intervertebral disc trisection of the vertebral body closest to the tip of the conus was recorded at the canal level. Results The tip of the conus medullaris was positioned from the upper T12 body to the L2–L3 disc, mostly in L1 bodies (52.4%), followed by the L2 bodies (22.5%), the L1–L2 disc, and the L2–L3 disc (1.1%). The shape of the conus was classified as type A in 74 (39.6%), type B in 58 (31%), and type C in 55 patients (29.4%). The conus did not terminate at the L3 body in any patient. In the first decade ones (five children) conus positioned rather lowly from L1 bodies to L2–L3 disc, and no type A conus shape, and mostly type B (80%). Conclusions The conus medullaris was positioned mostly in the lower one-third of L1 and it in the first decades terminated lowly. No type A in the first decade one, and type B was mostly frequently formed which was followed by type C.
Parallel Particle Swarm Optimization and Large Swarms

Parallel Particle Swarm Optimization and Large Swarms Andrew McNabb Department of Computer Science Master of Science Optimization is the search for the maximum or minimum of a given objective function. Particle Swarm Optimization (PSO) is a simple and effective evolutionary algorithm, but it may take hours or days to optimize difficult objective functions which are deceptive or expensive. Deceptive functions may be highly multimodal and multidimensional, and PSO requires extensive exploration to avoid being trapped in local optima. Expensive functions, whose computational complexity may arise from dependence on detailed simulations or large datasets, take a long time to evaluate. For deceptive or expensive objective functions, PSO must be parallelized to use multiprocessor systems and clusters efficiently. This thesis investigates the implications of parallelizing PSO and in particular, the details of parallelization and the effects of large swarms. PSO can be expressed naturally in Google’s MapReduce framework to develop a simple and robust parallel implementation that automatically includes communication, load balancing, and fault tolerance. This flexible implementation makes it easy to apply modifications to the algorithm, such as those that improve optimization of difficult objective functions and improve parallel performance. Results show that larger swarms help with both of these goals, but they are most effective if arranged into sparse topologies with lower overhead from communication. Additionally, PSO must be modified to use communication more efficiently in a large sparse swarm for objective functions where information ideally flows quickly through a large swarm. Swarm size is usually fixed at a modest number around 50, but particularly in a parallel computational environment, much larger swarms are much more effective for deceptive objective functions. Likewise, swarms much smaller than 50 are more effective for expensive but less deceptive functions. In general, swarm size should be carefully chosen using all available information about the objective function and computational environment.
Redundancy of human ATG4 protease isoforms in autophagy and LC3/GABARAP processing revealed in cells

ABSTRACT Macroautophagy/autophagy is a cellular degradation pathway that delivers cytoplasmic material to lysosomes via double-membrane organelles called autophagosomes. Lipidation of ubiquitin-like LC3/GABARAP proteins on the autophagosome membrane is important for autophagy. The cysteine protease ATG4 executes 2 LC3/GABARAP processing events: priming of newly synthesized pro-LC3/GABARAP to enable subsequent lipidation, and delipidation/deconjugation of lipidated LC3/GABARAP (the exact purpose of which is unclear in mammals). Four ATG4 isoforms (ATG4A to ATG4D) exist in mammals; however, the functional redundancy of these proteins in cells is poorly understood. Here we show that human HAP1 and HeLa cells lacking ATG4B exhibit a severe but incomplete defect in LC3/GABARAP processing and autophagy. By further genetic depletion of ATG4 isoforms using CRISPR-Cas9 and siRNA we uncover that ATG4A, ATG4C and ATGD all contribute to residual priming activity, which is sufficient to enable lipidation of endogenous GABARAPL1 on autophagic structures. We also demonstrate that expressing high levels of pre-primed LC3B in ATG4-deficient cells can rescue a defect in autophagic degradation of the cargo receptor SQSTM1/p62, suggesting that delipidation by human ATG4 is not essential for autophagosome formation and fusion with lysosomes. Overall, our study provides a comprehensive characterization of ATG4 isoform function during autophagy in human cells. Abbreviations: Atg: autophagy-related; baf A1: bafilomycin A1; CASP3: caspase 3; CLEM: correlative light and electron microscopy; CMV: cytomegalovirus; CRISPR: clustered regularly interspaced short palindromic repeats; DKO: double knockout; EGFP: enhanced green fluorescent protein; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor-associated protein like 1; GABARAPL2: GABA type A receptor-associated protein like 2; GFP: green fluorescent protein; HB: homogenization buffer; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LIR: LC3 interacting region; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MFN2: mitofusin 2; N.A. : numerical aperture; NEM: N-ethylmaleimide; PDHA1: pyruvate dehydrogenase E1 alpha 1 subunit; PLD: phospholipase D; PE: phosphatidylethanolamine; RLUC: Renilla luciferase; SQSTM1: sequestosome 1; TEM: transmission electron microscopy; TKO: triple knockout; ULK1: unc-51 like autophagy activating kinase 1; VCL: vinculin; WT: wild-type
SINGLE-SHOT SEMANTIC MATCHER FOR UNSEEN OBJECT DETECTION

Abstract. In this paper we combine the ideas of image matching, object detection, image retrieval and zero-shot learning for stating and solving the semantic matching problem. Semantic matcher takes two images (test and request) as input and returns detected objects (bounding boxes) on test image corresponding to semantic class represented by request (sample) image. We implement our single-shot semantic matcher CNN architecture based on GoogleNet and YOLO/DetectNet architectures. We propose the detection-by-request training and testing protocols for semantic matching algorithms. We train and test our CNN on the ILSVRC 2014 with 200 seen and 90 unseen classes and provide the real-time object detection with mAP 23 for seen and mAP 21 for unseen classes.
A Study on Parametric Amplification in a Piezoelectric MEMS Device

In various applications, damping from the surrounding fluid severely degrades the performance of micro-electro-mechanical systems (MEMS). In this paper, mechanical amplification through parametric resonance was investigated in a piezoelectrically actuated MEMS to overcome the effects of damping. The device was fabricated using the PiezoMUMPS process, which is based on a Silicon-on-Insulator (SOI) process with an additional aluminum nitride (AlN) layer. Here, a double-clamped cantilever beam with a concentrated mass at the center was excited at its first resonance mode (out-of-plane motion) in air and at atmospheric conditions. A parametric signal modulating the stiffness of the beam was added at twice the frequency of the excitation signal, which was swept through the resonance frequency of the mode. The displacement at the center of the device was detected optically. A four-fold increase in the quality-factor, Q, of the resonator was obtained at the highest values in amplitude used for the parametric excitation. The spring modulation constant was obtained from the effective quality-factor, Qeff, versus parametric excitation voltage curve. This study demonstrates that through these methods, significant improvements in performance of MEMS in fluids can be obtained, even for devices fabricated using standard commercial processes.
Emerging Trends and New Developments in Disaster Research after the 2008 Wenchuan Earthquake

On the tenth anniversary of the 2008 Wenchuan Earthquake, investigating the evolution of disaster science is worthwhile and can be used to improve the future execution of disaster risk management. Based on more than 55,786 articles on the relative topic of "Disaster" derived from the Web of Science Core Collection from 1999⁻2017, this study employs CiteSpace and Google Earth to identify and visualize the spatial distribution of publications, bursts of keywords and categories, highly cited references, and interdisciplinary levels and then identify the emerging trends of disaster research over the past 20 years. The results show that the earthquake indeed jumpstarted a massive wave of disaster research around the world and increased international cooperation over the last decade. However, in terms of both the quantity and quality of publications in disaster research fields, China is lagging behind the U.S. and European countries. Moreover, although designing disaster prevention and mitigation strategies is a new popular field of disaster science, geological environment changes and geologic hazards triggered by earthquakes are more popular research topics than disaster emergency and recovery. In addition, the transdisciplinary level of disaster science increased after the earthquake. This interdisciplinary characteristic of disaster science gradually increased in popularity, which demonstrates that people can learn from catastrophes. These emerging trends could serve as a scientific basis to clearly understand disaster science progress over the last 20 years and provide a reference for rapidly identifying frontier issues in disaster science.
Don't Sit So Close to Me: Restaurant Table Characteristics and Guest Satisfaction

Managing restaurant capacity effectively includes making sure that the dining room is equipped with sufficient tables of the appropriate size and type to meet expected demand. Restaurateurs usually make a point of seating parties at the right-size table to maximize seat utilization, and some restaurants set tables fairly close together to make the best use of the available floor space. We examined whether providing guests at a fullservice restaurant in New York City with extra personal space improved their satisfaction and meant increased spending or longer lengths of stay. Guests seated at tables that were larger than necessary (that is, parties of two seated at four-tops) did not have significantly different perceptions of satisfaction or spending behavior from those seated at right-size tables (that is, at deuces). However, parties at closely spaced tables reported significantly reduced satisfaction, as well as lower spending per minute when compared with widely spaced tables. Patrons dining at this New York restaurant seemed uncomfortable when tables were set as close as seventeen inches apart, and were more satisfied when the distance was closer to a yard apart. These findings, which apply to the dinner period at a fine-dining restaurant, offer support for the practice of seating parties at appropriately sized tables, and suggest that restaurant operators give careful consideration to the spacing of tables in the dining room.
The roles of αCaMKII and Ras-GRF2 in the establishment of drug addiction

5 Table of contents . 7 Chapter 1: General Introduction . 15 1. Addiction and substance abuse disorders . 16 1.1. Alcohol abuse . 16 1.2. Cocaine abuse . 19 2. Are our genes to blame? 22 Figure 1.1: The heritability of ten addictive disorders . 25 3. The learning of addictive behaviours . 26 4. Novel targets in the study of addiction . 29 4.1. alpha Ca/Calmodulin Dependent Protein Kinase II (αCaMKII) . 29 Figure 1.2: The αCaMKII autophosphorylation mechanism. 31 4.2. Ras-specific guanine nucleotide releasing factor 2 (Ras-GRF2) . 35 Figure 1.3: The MAPK/ERK signal transduction pathway. 36 Figure 1.4: The Ca2+/CaM/Ras-GRF2 complex. 38 5. The importance of genetically manipulated animals in behavioural pharmacology research . 40 6. Main research questions, aims and hypotheses . 43 Chapter 2: αCaMKII autophosphorylation controls exploratory activity to threatening novel stimuli . 47 Abstract: . 48 . 48
Differential Zika Virus Infection of Testicular Cell Lines

Background: Zika virus is a mosquito-borne flavivirus responsible for recent outbreaks of epidemic proportions in Latin America. Sexual transmission of the virus has been reported in 13 countries and may be an important route of infection. Sexual transmission of ZIKV has mostly been male-to-female, and persistence of viral RNA in semen for up to 370 days has been recorded. The susceptibility to ZIKV of different testicular cell types merits investigation. Methods: We infected primary Sertoli cells, a primary testicular fibroblast Hs1.Tes, and 2 seminoma cell lines SEM-1 and TCam-2 cells with ZIKV Paraiba and the prototype ZIKV MR766 to evaluate their susceptibility and to look for viral persistence. A human neuroblastoma cell line SK-N-SH served as a control cell type. Results: Both virus strains were able to replicate in all cell lines tested, but ZIKV MR766 attained higher titers. Initiation of viral persistence by ZIKV Paraiba was observed in Sertoli, Hs1.Tes, SEM-1 and TCam-2 cells, but was of limited duration due to delayed cell death. ZIKV MR766 persisted only in Hs1.Tes and Sertoli cells, and persistence was also limited. In contrast, SK-N-SH cells were killed by both ZIKV MR766 and ZIKV Paraiba and persistence could not be established in these cells. Conclusions: ZIKV prototype strain MR766 and the clinically relevant Paraiba strain replicated in several testicular cell types. Persistence of ZIKV MR766 was only observed in Hs1.Tes and Sertoli cells, but the persistence did not last more than 3 or 4 passages, respectively. ZIKV Paraiba persisted in TCam-2, Hs1.Tes, Sertoli and SEM-1 cells for up to 5 passages, depending on cell type. TCam-2 cells appeared to clear persistent infection by ZIKV Paraiba.
Adherence to the mediterranean diet and lymphoma risk in the european prospective investigation into cancer and nutrition

There is a growing evidence of the protective role of the Mediterranean diet (MD) on cancer. However, no prospective study has yet investigated its influence on lymphoma. We evaluated the association between adherence to the MD and risk of lymphoma and its subtypes in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. The analysis included 476,160 participants, recruited from 10 European countries between 1991 and 2001. Adherence to the MD was estimated through the adapted relative MD (arMED) score excluding alcohol. Cox proportional hazards regression models were used while adjusting for potential confounders. During an average follow‐up of 13.9 years, 3,136 lymphomas (135 Hodgkin lymphoma [HL], 2,606 non‐HL and 395 lymphoma not otherwise specified) were identified. Overall, a 1‐unit increase in the arMED score was associated with a 2% lower risk of lymphoma (95% CI: 0.97; 1.00, p‐trend = 0.03) while a statistically nonsignificant inverse association between a high versus low arMED score and risk of lymphoma was observed (hazard ratio [HR]: 0.91 [95% CI 0.80; 1.03], p‐trend = 0.12). Analyses by lymphoma subtype did not reveal any statistically significant associations. Albeit with small numbers of cases (N = 135), a suggestive inverse association was found for HL (HR 1‐unit increase = 0.93 [95% CI: 0.86; 1.01], p‐trend = 0.07). However, the study may have lacked statistical power to detect small effect sizes for lymphoma subtype. Our findings suggest that an increasing arMED score was inversely related to the risk of overall lymphoma in EPIC but not by subtypes. Further large prospective studies are warranted to confirm these findings.
Comparison of Reliable Reference Genes Following Different Hormone Treatments by Various Algorithms for qRT-PCR Analysis of Metasequoia

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes for normalizing target gene expression is important for verifying expression changes. Metasequoia is a high-quality and economically important wood species. However, few systematic studies have examined reference genes in Metasequoia. Here, the expression stability of 14 candidate reference genes in different tissues and following different hormone treatments were analyzed using six algorithms. Candidate reference genes were used to normalize the expression pattern of FLOWERING LOCUS T and pyrabactin resistance-like 8. Analysis using the GrayNorm algorithm showed that ACT2 (Actin 2), HIS (histone superfamily protein H3) and TATA (TATA binding protein) were stably expressed in different tissues. ACT2, EF1α (elongation factor-1 alpha) and HIS were optimal for leaves treated with the flowering induction hormone solution, while Cpn60β (60-kDa chaperonin β-subunit), GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HIS were the best reference genes for treated buds. EF1α, HIS and TATA were useful reference genes for accurate normalization in abscisic acid-response signaling. Our results emphasize the importance of validating reference genes for qRT-PCR analysis in Metasequoia. To avoid errors, suitable reference genes should be used for different tissues and hormone treatments to increase normalization accuracy. Our study provides a foundation for reference gene normalization when analyzing gene expression in Metasequoia.
Hand Grip and Load Force Coordination of the Ipsilesional Hand of Chronic Stroke Individuals

Abstract Object manipulation depends on a refined control of grip force (GF) and load force (LF). After a brain injury, the GF control is altered in the paretic hand but what happens with the non-paretic hand is still unclear. In this study, we compared the GF control and GF–LF coordination of the non-paretic hand of 10 stroke individuals who suffered right brain damage (RBD) and 10 who suffered left brain damage (LBD), with 20 healthy individuals during lifting and oscillation task, using an instrumented object. GF was recorded with a force transducer, and LF was estimated from the object weight and acceleration. Overall, the ipsilesional hand of stroke individuals, independent of the lesion side, presented similar GF control and GF–LF coordination. However, LBD individuals took longer to start lifting the object, which may be due to the need of more time to obtain somatosensory information from the contact with the object. The findings indicate that stroke individuals preserve their ability to control and coordinate GF and LF when using their ipsilesional hand for object manipulation and the left hemisphere may play an essential role in the processing of somatosensory information needed for the GF control.
A Three-Phase Model Characterizing the Low-Velocity Impact Response of SMA-Reinforced Composites under a Vibrating Boundary Condition

Structural vibration induced by dynamic load or natural vibration is a non-negligible factor in failure analysis. Based on a vibrating boundary condition, the impact resistance of shape memory alloy (SMA)-reinforced composites was investigated. In this investigation, a modified Hashin’s failure criterion, Brinson’s model, and a visco-hyperelastic model were implemented into a numerical model to characterize the mechanical behavior of glass fiber/epoxy resin laminates, SMAs, and interphase, respectively. First, a fixed boundary condition was maintained in the simulation to verify the accuracy of the material parameters and procedures by a comparison with experimental data. Then, a series of vibrating boundaries with different frequencies and amplitudes was applied during the simulation process to reveal the effect on impact resistances. The results indicate that the impact resistance of the composite under a higher frequency or a larger amplitude is lower than that under a lower frequency or a smaller amplitude.
Activation of the rat hypothalamic supramammillary nucleus by food anticipation, food restriction or ghrelin administration

The circulating orexigenic hormone ghrelin targets many brain areas involved in feeding control and signals via a dedicated receptor, the growth hormone secretagogue receptor 1A. One unexplored target area for ghrelin is the supramammillary nucleus (SuM), a hypothalamic area involved in motivation and reinforcement and also recently linked to metabolic control. Given that ghrelin binds to the SuM, we explored whether SuM cells respond to ghrelin and/or are activated when endogenous ghrelin levels are elevated. We found that peripheral ghrelin injection activates SuM cells in rats, reflected by an increase in the number of cells expressing c‐Fos protein in this area, as welll as by the predominantly excitatory response of single SuM cells recorded in in vivo electrophysiological studies. Further c‐Fos mapping studies reveal that this area is also activated in rats in situations when circulating ghrelin levels are known to be elevated: in food‐restricted rats anticipating the consumption of food and in fed rats anticipating the consumption of an energy‐dense food. We also show that intra‐SuM injection of ghrelin induces a feeding response in rats suggesting that, if peripheral ghrelin is able to access the SuM, it may have direct effects on this brain region. Collectively, our data demonstrate that the SuM is activated when peripheral ghrelin levels are high, further supporting the emerging role for this brain area in metabolic and feeding control.