Miracle-dz/UniFAR-FTUs huggingface dataset:
Selenite Cystine Agar for Enumeration of Inoculated Salmonella Serovars Recovered from Stressful Conditions during Antimicrobial Validation Studies

Process validation studies often require the inoculation of select foodborne pathogens into targeted foods to determine the lethality of the process or antimicrobial ingredients, and quantitative recovery of surviving inoculum bacteria helps to make those assessments. Such processes introduce various stressors on the inoculated challenge microorganisms whereby traditional selective media are too harsh to enumerate the remaining viable and injured population quantitatively. Innate antibiotic resistance of challenge organisms has often been used to establish simple selective media (i.e., Tryptic Soy Agar/TSA + antibiotics) for recovering inoculated strains, but sometimes antibiotic resistant background microorganisms are higher than desired. Salmonella Thompson 120, Salmonella Heidelberg F5038BG1, Salmonella Hadar MF60404, Salmonella Enteritidis H3527, and Salmonella Typhimurium H3380 were characterized for antibiotic resistance and acid adaptation in Tryptic Soy Broth containing 0%, 0.25%, or 1.0% glucose. Sodium pyruvate was evaluated for recovery after stress but no enhancing effect was observed, possibly because the strains were acid-adapted. Selenite Cystine Broth, traditionally used as a selective enrichment broth, was used as the basis for Selenite Cystine Agar (SCA) in combination with three antibiotics to which our Salmonella are resistant. Serovars of Salmonella, both individually and in mixtures, were enumerated on TSA, SCA, Xylose Lysine Desoxycholate (XLD), and Hektoen Enteric (HE) selective agars (all containing the same antibiotics) after conditions of nutrient starvation, desiccation, acid stress, and thermal stress. The data show that quantitative enumeration of our Salmonella serovars on SCA was not significantly different (p > 0.05) than those achieved on TSA for all tested stress categories. Levels of Salmonella enumerated on XLD and/or HE were significantly different (p < 0.05) than on TSA and SCA and often more than 1–2-log lower, consistent with the inhibition of injured cells. These data confirm that SCA (+ antibiotics) is a suitable selective medium for enumeration of these acid-adapted Salmonella serovars as challenge organisms recovered from various conditions of stress.
Biomechanics of the Sacroiliac Joint: Anatomy, Function, Biomechanics, Sexual Dimorphism, and Causes of Pain

ABSTRACT Background: The sacroiliac joints (SIJs), the largest axial joints in the body, sit in between the sacrum and pelvic bones on either side. They connect the spine to the pelvis and thus facilitate load transfer from the lumbar spine to the lower extremities. The majority of low back pain (LBP) is perceived to originate from the lumbar spine; however, another likely source of LBP that is mostly overlooked is the SIJ. This study (Parts I and II) aims to evaluate the clinical and biomechanical literature to understand the anatomy, biomechanics, sexual dimorphism, and causes and mechanics of pain of the SIJ leading to conservative and surgical treatment options using instrumentation. Part II concludes with the mechanics of the devices used in minimal surgical procedures for the SIJ. Methods: A thorough review of the literature was performed to analyze studies related to normal SIJ mechanics, as well as the effects of sex and pain on SIJ mechanics. Results: A total of 65 studies were selected related to anatomy, biomechanical function of the SIJ, and structures that surround the joints. These studies discussed the effects of various parameters, gender, and existence of common physiological disorders on the biomechanics of the SIJ. Conclusions: The SIJ lies between the sacrum and the ilium and connects the spine to the pelvic bones. The SIJ transfers large bending moments and compression loads to lower extremities. However, the joint does not have as much stability of its own against the shear loads but resists shear due the tight wedging of the sacrum between hip bones on either side and the band of ligaments spanning the sacrum and the hip bones. Due to these, sacrum does not exhibit much motion with respect to the ilium. The SIJ range of motion in flexion-extension is about 3°, followed by axial rotation (about 1.5°), and lateral bending (about 0.8°). The sacrum of the female pelvis is wider, more uneven, less curved, and more backward tilted, compared to the male sacrum. Moreover, women exhibit higher mobility, stresses/loads, and pelvis ligament strains compared to male SIJs. Sacroiliac pain can be due to, but not limited to, hypo- or hypermobility, extraneous compression or shearing forces, micro- or macro-fractures, soft tissue injury, inflammation, pregnancy, adjacent segment disease, leg length discrepancy, and prior lumbar fusion. These effects are well discussed in this review. This review leads to Part II, in which the literature on mechanics of the treatment options is reviewed and synthesized.
The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

Stress granules are cytoplasmic compartments, which serve as mRNA storage units during stress, therefore regulating translation. The Arabidopsis thaliana lectin ArathEULS3 has been widely described as a stress inducible gene. This study aimed to examine in detail the localization of ArathEULS3 lectin in normal and stressed cells. Colocalization experiments revealed that the nucleo-cytoplasmic lectin ArathEULS3 relocates to stress granules after stress. The ArathEULS3 sequence encodes a protein with a EUL lectin domain and an N-terminal domain with unknown structure and function. Bioinformatics analyses showed that the N-terminal domain sequence contains intrinsically disordered regions and likely does not exhibit a stable protein fold. Plasmolysis experiments indicated that ArathEULS3 also localizes to the apoplast, suggesting that this protein might follow an unconventional route for secretion. As part of our efforts we also investigated the interactome of ArathEULS3 and identified several putative interaction partners important for the protein translation process.
Familiarity Detection and Memory Consolidation in Cortical Assemblies

Abstract Humans have a large capacity of recognition memory (Dudai, 1997), a fundamental property of higher-order brain functions such as abstraction and generalization (Vogt and Magnussen, 2007). Familiarity is the first step towards recognition memory. We have previously demonstrated using unsupervised neural network simulations that familiarity detection of complex patterns emerges in generic cortical microcircuits with bidirectional synaptic plasticity. It is therefore meaningful to conduct similar experiments on biological neuronal networks to validate these results. Studies of learning and memory in dissociated rodent neuronal cultures remain inconclusive to date. Synchronized network bursts (SNBs) that occur spontaneously and periodically have been speculated to be an intervening factor. By optogenetically stimulating cultured cortical networks with random dot movies (RDMs), we were able to reduce the occurrence of SNBs, after which an ability for familiarity detection emerged: previously seen patterns elicited higher firing rates than novel ones. Differences in firing rate were distributed over the entire network, suggesting that familiarity detection is a system level property. We also studied the change in SNB patterns following familiarity encoding. Support vector machine (SVM) classification results indicate that SNBs may be facilitating memory consolidation of the learned pattern. In addition, using a novel network connectivity probing method, we were able to trace the change in synaptic efficacy induced by familiarity encoding, providing insights on the long-term impact of having SNBs in the cultures.
Synthesis of Three-Dimensional Carbon Nanostructure/Copper Nanowire for Additive Interface Layer of Ionic Polymer Metal Composite

Additive interface materials for improved ionic polymer metal composite (IPMC) actuator performance are being investigated. In this study, three-dimensional carbon nanostructure/copper nanowire (3DC Cu-NW) with a novel structure was synthesized via low-pressure chemical vapor deposition. An IPMC actuator with a 3DC Cu-NW interface layer was fabricated, which exhibited improved actuation performance, long-term stability, and electrochemical properties. The proposed 3DC consists of carbon nanotubes (CNTs) and graphene, grown using an Fe catalyst and CH4 gas, respectively. We optimized the growth conditions (Fe catalyst: 12.5 mg/L, CH4: 20 sccm) to achieve a 3DC with an appropriate thickness and a large specific surface area. The 3DC Cu-NW benefited from a Cu oxidation prevention property and a large specific surface area. The electrochemical properties and actuation performance of the IPMC actuator improved with an increased 3DC Cu-NW concentration. An IPMC actuator with a 0.6 wt% 3DC Cu-NW interface layer exhibited 1.3- and 5.6-fold electrochemical property and actuation performance improvement, respectively, over an IPMC actuator with no 3DC Cu-NW interface layer. These results show that the proposed 3DC Cu-NW has potential as an IPMC actuator interface material, and that 3DC Cu-NW synthesis and application technology can be applied to future research on sensor, actuator, and flexible devices.
HMB in DRAM-less NVMe SSDs: Their usage and effects on performance

Solid-state drives (SSDs) that do not have internal dynamic random-access memory (DRAM) are being widely spread for client SSD and embedded SSD markets in recent years because they are cheap and consume less power. Obviously, their performance is lower than conventional SSDs because they cannot exploit advantages of DRAM in the controller. However, this problem can be alleviated by using host memory buffer (HMB) feature of Non-Volatile Memory Express (NVMe), which allows SSDs to utilize the DRAM of host. In this paper, we show that commercial DRAM-less SSDs clearly exhibit worse I/O performance than SSDs with internal DRAM, but this can be improved by using the HMB feature. We also present methods that reveal how the host memory buffer is used in commercial DRAM-less SSDs to improve I/O performance. Through extensive experiments, we conclude that DRAM-less SSDs evaluated in this study mainly exploit the host memory buffer as an address mapping table cache rather than a read cache or write buffer to improve I/O performance.
A Two-Stage Framework for Automated Malignant Pulmonary Nodule Detection in CT Scans

This research is concerned with malignant pulmonary nodule detection (PND) in low-dose CT scans. Due to its crucial role in the early diagnosis of lung cancer, PND has considerable potential in improving the survival rate of patients. We propose a two-stage framework that exploits the ever-growing advances in deep neural network models, and that is comprised of a semantic segmentation stage followed by localization and classification. We employ the recently published DeepLab model for semantic segmentation, and we show that it significantly improves the accuracy of nodule detection compared to the classical U-Net model and its most recent variants. Using the widely adopted Lung Nodule Analysis dataset (LUNA16), we evaluate the performance of the semantic segmentation stage by adopting two network backbones, namely, MobileNet-V2 and Xception. We present the impact of various model training parameters and the computational time on the detection accuracy, featuring a 79.1% mean intersection-over-union (mIoU) and an 88.34% dice coefficient. This represents a mIoU increase of 60% and a dice coefficient increase of 30% compared to U-Net. The second stage involves feeding the output of the DeepLab-based semantic segmentation to a localization-then-classification stage. The second stage is realized using Faster RCNN and SSD, with an Inception-V2 as a backbone. On LUNA16, the two-stage framework attained a sensitivity of 96.4%, outperforming other recent models in the literature, including deep models. Finally, we show that adopting a transfer learning approach, particularly, the DeepLab model weights of the first stage of the framework, to infer binary (malignant-benign) labels on the Kaggle dataset for pulmonary nodules achieves a classification accuracy of 95.66%, which represents approximately 4% improvement over the recent literature.
Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam

Significance The acid dissociation constant (pKa) and protonation state of active-site residues plays a critical role in enzyme catalysis. Elucidating how these properties may be influenced by substrate/inhibitor binding is crucial to a deep understanding of enzyme function and inhibition. In this study, we focus on class A β-lactamases, one of the most common mediators of β-lactam antibiotic resistance in gram-negative bacteria. Through a series of high-resolution crystal structures of the class A β-lactamase CTX-M-14 in complex with the β-lactamase inhibitor avibactam at varying pHs, combined with pKa calculations and NMR, we examine how this inhibitor affects active-site residues’ pKa values and proton transfer. The results offer important insights into the mechanism of avibactam inhibition and the substrate influence on β-lactamase catalysis. Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The acyl–enzyme intermediate is a central milestone in the hydrolysis reaction catalyzed by these enzymes. However, the protonation states of the catalytic residues in this complex have never been fully analyzed experimentally due to inherent difficulties. To help unravel the ambiguity surrounding class A β-lactamase catalysis, we have used ultrahigh-resolution X-ray crystallography and the recently approved β-lactamase inhibitor avibactam to trap the acyl–enzyme complex of class A β-lactamase CTX-M-14 at varying pHs. A 0.83-Å-resolution CTX-M-14 complex structure at pH 7.9 revealed a neutral state for both Lys73 and Glu166. Furthermore, the avibactam hydroxylamine-O-sulfonate group conformation varied according to pH, and this conformational switch appeared to correspond to a change in the Lys73 protonation state at low pH. In conjunction with computational analyses, our structures suggest that Lys73 has a perturbed acid dissociation constant (pKa) compared with acyl–enzyme complexes with β-lactams, hindering its function to deprotonate Glu166 and the initiation of the deacylation reaction. Further NMR analysis demonstrated Lys73 pKa to be ∼5.2 to 5.6. Together with previous ultrahigh-resolution crystal structures, these findings enable us to follow the proton transfer process of the entire acylation reaction and reveal the critical role of Lys73. They also shed light on the stability and reversibility of the avibactam carbamoyl acyl–enzyme complex, highlighting the effect of substrate functional groups in influencing the protonation states of catalytic residues and subsequently the progression of the reaction.
Solubilization of Hexyl Aminolevulinate by Surfactants for Tumor Fluorescence Detection

Hexyl aminolevulinate (HAL) is a lipophilic derivative of 5‐aminolevulinic acid (5‐ALA) and can induce more protoporphyrin IX (PpIX) formation and stronger fluorescence intensity (FI) than 5‐ALA, which will greatly facilitate photodynamic diagnosis and therapy. The main drawback of HAL is its low solubility in neutral aqueous media. In this study, surfactants were used to increase HAL solubility in the cell culture medium and serum, followed by in vitro fluorescence formation measurement in human pancreatic cancer cells (SW1990) and in vivo fluorescence detection in tumor‐bearing mice. The results showed that Tween 80 (TW80) and Kolliphor® HS 15 (HS15) increased the solubility of HAL in the selected media. Although TW80 and HS15 exhibited in vitro cytotoxicity at high concentrations (5 mg mL−1), they facilitated fluorescent signal formation at the early stage of cell incubation. When surfactants were used, the FI should be determined without the routine washing process because surfactant‐containing culture medium caused the loss of synthesized PpIX during the washing process. When HAL dissolved in TW80 solution was injected intraperitoneally into pancreatic cancer‐bearing mice at a dose of 50 mg kg−1, the tumors exhibited red fluorescence, which indicated that systemic administration of surfactant‐solubilized HAL might be applicable for tumor fluorescence detection in vivo.
Towards PCB-Based Miniaturized Thermocyclers for DNA Amplification

In recent years, printed circuit board (PCB)-based microfluidics have been explored as a means to achieve standardization, seamless integration, and large-scale manufacturing of microfluidics, thus paving the way for widespread commercialization of developed prototypes. In this work, static micro polymerase chain reaction (microPCR) devices comprising resistive microheaters integrated on PCBs are introduced as miniaturized thermocyclers for efficient DNA amplification. Their performance is compared to that of conventional thermocyclers, in terms of amplification efficiency, power consumption and duration. Exhibiting similar efficiency to conventional thermocyclers, PCB-based miniaturized thermocycling achieves faster DNA amplification, with significantly smaller power consumption. Simulations guide the design of such devices and propose means for further improvement of their performance.
Genotoxicity of TiO2 Nanoparticles in Four Different Human Cell Lines (A549, HEPG2, A172 and SH-SY5Y)

Titanium dioxide nanoparticles (TiO2 NPs) have a wide variety of applications in many consumer products, including as food additives, increasing the concern about the possible hazards that TiO2 NPs may pose to human health. Although most previous studies have focused on the respiratory system, ingestion must also be considered as an important exposure route. Furthermore, after inhalation or ingestion, TiO2 NPs can reach several organs, such as the liver, brain or lungs. Taking this into consideration, the present study focuses on the uptake and potential genotoxicity (micronuclei induction) of TiO2 NPs on four human cell lines of diverse origin: lung cells (A549), liver cells (HepG2), glial cells (A172) and neurons (SH-SY5Y), using flow cytometry methods. Results showed a concentration-, time- and cell-type- dependent increase in TiO2 NPs uptake but no significant induction of micronuclei in any of the tested conditions. Data obtained reinforce the importance of cell model and testing protocols choice for toxicity assessment. However, some questions remain to be answered, namely on the role of cell culture media components on the agglomeration state and mitigation of TiO2 NPs toxic effects.
Clozapine Prevents Poly (I:C) Induced Inflammation by Modulating NLRP3 Pathway in Microglial Cells

Schizophrenia is a complex psychiatric disorder that exhibits an interconnection between the immune system and the brain. Experimental and clinical studies have suggested the presence of neuroinflammation in schizophrenia. In the present study, the effect of antipsychotic drugs, including clozapine, risperidone, and haloperidol (10, 20 and 20 μM, respectively), on the production of IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-10, IL-17, IL-18, INF-γ, and TNF-α was investigated in the unstimulated and polyriboinosinic-polyribocytidilic acid [poly (I:C)]-stimulated primary microglial cell cultures. In the unstimulated cultures, clozapine, risperidone, and haloperidol did not influence the cytokine levels. Nevertheless, in cell cultures under strong inflammatory activation by poly (I:C), clozapine reduced the levels of IL-1α, IL-1β, IL-2, and IL-17. Risperidone and haloperidol both reduced the levels of IL-1α, IL-1β, IL-2, and IL-17, and increased the levels of IL-6, IL-10, INF-γ, and TNF-α. Based on the results that were obtained with the antipsychotic drugs and observing that clozapine presented with a more significant anti-inflammatory effect, clozapine was selected for the subsequent experiments. We compared the profile of cytokine suppression obtained with the use of NLRP3 inflammasome inhibitor, CRID3 to that obtained with clozapine, to test our hypothesis that clozapine inhibits the NLRP3 inflammasome. Clozapine and CRID3 both reduced the IL-1α, IL-1β, IL-2, and IL-17 levels. Clozapine reduced the level of poly (I:C)-activated NLRP3 expression by 57%, which was higher than the reduction thay was seen with CRID3 treatment (45%). These results suggest that clozapine might exhibit anti-inflammatory effects by inhibiting NLRP3 inflammasome and this activity is not typical with the use of other antipsychotic drugs under the conditions of strong microglial activation.
Association between Food Preferences, Eating Behaviors and Socio-Demographic Factors, Physical Activity among Children and Adolescents: A Cross-Sectional Study

The prevalence of overweight and obesity is a serious health issue among children and adolescents worldwide. This study aimed to investigate factors influencing weight status-associated food preferences and eating behaviors. A cross-sectional study was conducted to collect data from 2578 pairs of Chinese children and parents in five cities from December 2018 to March 2019. There was an increase in consumptions of processed seafood, nuts and dried fruit/vegetables, and fruit/vegetable juice, but a reduction of consuming puffed and processed meat products, sugar/artificially sweetened beverages and milk tea, and picky eating. These food preferences differentiate between sexes. Picky eating behavior was greatly presented in children of lower educated mothers or heavy-smoking fathers. Children of the lower educated fathers consumed less processed seafood and dairy products, and those of the heavy-smoking fathers consumed more puffed products, but less fruit/vegetable juice, and had greater snack preference. The father’s body mass index(BMI)status was also positively associated with unhealthy behaviors. Those who exercised daily longer showed better eating behaviors, and picky eating and fast-food lovers likely occurred in higher-income families. Our study provides an insight into that fathers being educated for health-conscious advice and physical activity may be the potential strategies to foster their children’s healthy eating patterns. Their efficacy needs to be further investigated.
You Win Some, You Lose Some: How Demographic Factors Interact with the Ubiquity of the Framing Effect

The current literature review is a compilation of research that addresses the ubiquity of the framing effect and presents examples of demographic features that hinder or facilitate the susceptibility to it. The framing effect, which was initially empirically studied through the exploration of gain vs. loss frames (Tversky & Kahneman, 1981), is a phenomenon in which discrepancies in the phrasing of the same content can elicit significantly different responses. A variety of frames, contexts, and demographics are discussed to reveal examples where the framing effect is present. Although our susceptibility to the framing effect emerges from underlying cognitive processes, the purpose of the current literature review is to promote awareness of the framing effect by explaining how it is utilized so that we can consciously decrease our susceptibility to our own cognitive biases.