Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase

Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here, we aim at deciphering a structural basis for the GDH allosteric activation using bovine GDH as a model. For the first time, we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion, resolved to 2.45 Å. An improved 2.4-angstrom resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.
Introductory Causal Dynamical Triangulation

This report aims to present the main ideas of Regge calculus necessary to understand the basic premise of CDT. Next, the main strategy of the CDT approach is introduced in general terms. The main focus of this report is the 2-D model of CDT. The section on the 2-D model closely follows a single paper (\cite{ambjorn98}). While the 4-D or even 3-D case will behave very differently from the 2-D model, 2-D CDT can be solved exactly, and as such offers a better introductory exposition of CDT's methods. Higher-dimensional CDT requires a lot of computer simulation, and lies outside the scope of this report. All derivations carried out explicitly are the result of the author's independent work in attempting to find and prove how the results presented were obtained by CDT authors. Because these derivations were made explicit by the author, this paper can act as a guide to those who are new to CDT.
The Effect of Action Observation Combined with Motor Imagery Training on Upper Extremity Function and Corticospinal Excitability in Stroke Patients: A Randomized Controlled Trial

This study aimed to investigate the effect of motor imagery (MI) intervention with action observation (AO) on upper extremity function and corticospinal activation in stroke patients. MI and AO are two forms of motion simulation that activate the motor system without physical activity. There are many studies that show the effect of AO and MI alone, but there are few studies in parallel. This study was conducted on 45 patients who were divided into an experimental group (n = 22) and a control group (n = 23) using a computer randomization program. The experimental group conducted AO with MI, and the control group only AO. All participants received interventions for twenty-five minutes per session, five times a week, for eight weeks. For the pre- and post-evaluation of all participants, motor evoked potential (MEP) amplitude was measured to compare corticospinal activation, and Fugl-Meyer Assessment Upper Extremity (FMA UE), Wolf Motor Function Test (WMFT) and Motor Activity Log (MAL) were evaluated for changes in upper extremity function. In comparing the amount of change before and after the intervention, a significant change was observed in the experimental group’s MEP amplitude. In the comparison between groups after the intervention and the amount of change before and after the intervention, the experimental group showed significant changes in FMA UE and MAL Amount of Use (MAL AOU) items. As a result of this study, AO with MI is effective in enhancing upper extremity function and increasing cortical spinal cord activation in patients with severe stroke with limited movement.
Ocean Wind Observation Based on the Mean Square Slope Using a Self-Developed Miniature Wave Buoy

Real-time, continuous, and long-term marine monitoring data benefits ocean research. This study developed a low-cost, multi-parameter, miniature wave buoy. High spatial and temporal resolution of sea surface parameters, including wind, waves, and current, can be obtained at low cost through the deployment of numerous buoys, thus forming an observation array. Tested in the laboratory water tank, the relative error of water surface slope measurement of the buoy was approximately 5.6% when the slope angle was less than 15°. For frequencies between 0.1 and 1.0 Hz, the measurement of slope spectrum was almost identical to that of the wave gauge. The buoy underestimated the slope spectrum between 1.0–1.56 Hz. A good relationship (r2 = 0.75) was obtained between wind speed at 10 m above sea surface (U10) and the low-pass-filtered mean square slope (LPMSS). After incorporating the wave age into the U10 inversion process, the root mean square error (RMSE) and BIAS were reduced to 1.15 m/s and 0.02 m/s, respectively. The 2D distribution of buoy-measured slope components was used to detect the wind direction, with an RMSE of 23.7°. The spectral tail slope steepened with increasing wind speed at low wind speeds (<7 m/s). A technical flow chart of the miniature wave buoy is proposed to observe the sea surface parameters. This miniature buoy will play an essential complementary role in the growing demand for sea state monitoring, especially in nearshore oceans.
Camouflage and Exploratory Avoidance of Newborn Cuttlefish under Warming and Acidification

Simple Summary Sub-lethal effects of climate change on organisms have received little attention to date. For instance, little is known concerning the ability of cuttlefish to camouflage and to explore under ocean acidification and warming. This study aimed to evaluate the physiology, camouflage performance, and exploratory avoidance behavior of cuttlefish hatchlings exposed to these stressors during embryogenesis. Hatchlings were placed in arenas with either sand or white and black gravel covering the bottom. Photographs were taken remotely to extract camouflage latency and pixel values in the cuttlefish body and the background. Mobility and proximity to the arena walls were recorded. Despite survival being lower under acidification and warming combined, our results indicate that camouflage was strengthened under warming, whilst no effect was found on spatial exploration. This study shows that cuttlefish mobility and exploratory avoidance behaviors are unlikely to be impacted by changes in climate. Moreover, camouflage, an anti-predator strategy essential to the survival of cuttlefish newborns, is not impeded and might be enhanced by future levels of ocean acidification and warming. Abstract Ocean warming and acidification have been shown to elicit deleterious effects on cephalopod mollusks, especially during early ontogeny, albeit effects on behavior remain largely unexplored. This study aimed to evaluate, for the first time, the effect of end-of-the-century projected levels of ocean warming (W; + 3 °C) and acidification (A; 980 µatm pCO2) on Sepia officinalis hatchlings’ exploratory behavior and ability to camouflage in different substrate complexities (sand and black and white gravel). Cuttlefish were recorded in open field tests, from which mobility and exploratory avoidance behavior data were obtained. Latency to camouflage was registered remotely, and pixel intensity of body planes and background gravel were extracted from photographs. Hatching success was lowered under A and W combined (AW; 72.7%) compared to control conditions (C; 98.8%). Motion-related behaviors were not affected by the treatments. AW delayed camouflage response in the gravel substrate compared to W alone. Moreover, cuttlefish exhibited a higher contrast and consequently a stronger disruptive pattern under W, with no changes in background matching. These findings suggest that, although climate change may elicit relevant physiological challenges to cuttlefish, camouflage and mobility of these mollusks are not undermined under the ocean of tomorrow.
Cross identification between X-ray and Optical Clusters of Galaxies in the SDSS DR7 Field

We use the ROSAT all sky survey X-ray cluster catalogs and the optical SDSS DR7 galaxy and group catalogs to cross-identify X-ray clusters with their optical counterparts, resulting in a sample of 201 X-ray clusters in the sky coverage of SDSS DR7. We investigate various correlations between the optical and X-ray properties of these X-ray clusters, and find that the following optical properties are correlated with the X-ray luminosity: the central galaxy luminosity, the central galaxy mass, the characteristic group luminosity ($\propto \Lx^{0.43}$), the group stellar mass ($\propto \Lx^{0.46}$), with typical 1-$\sigma$ scatter of $\sim 0.67$ in $\log \Lx$. Using the observed number distribution of X-ray clusters, we obtain an unbiased scaling relation between the X-ray luminosity, the central galaxy stellar mass and the characteristic satellite stellar mass as ${\log L_X} = -0.26 + 2.90 [\log (M_{\ast, c} + 0.26 M_{\rm sat}) -12.0]$ (and in terms of luminosities, as ${\log L_X} = -0.15 + 2.38 [\log (L_{c} + 0.72 L_{\rm sat}) -12.0]$). We find that the systematic difference between different halo mass estimations, e.g., using the ranking of characteristic group stellar mass or using the X-ray luminosity scaling relation can be used to constrain cosmology. Comparing the properties of groups of similar stellar mass (or optical luminosities) and redshift that are X-ray luminous or under-luminous, we find that X-ray luminous groups have more faint satellite galaxies and higher red fraction in their satellites. The cross-identified X-ray clusters together with their optical properties are provided in Appendix B.
Quality by Design of Pranoprofen Loaded Nanostructured Lipid Carriers and Their Ex Vivo Evaluation in Different Mucosae and Ocular Tissues

Transmucosal delivery is commonly used to prevent or treat local diseases. Pranoprofen is an anti-inflammatory drug prescribed in postoperative cataract surgery, intraocular lens implantation, chorioretinopathy, uveitis, age-related macular degeneration or cystoid macular edema. Pranoprofen can also be used for acute and chronic management of osteoarthritis and rheumatoid arthritis. Quality by Design (QbD) provides a systematic approach to drug development and maps the influence of the formulation components. The aim of this work was to develop and optimize a nanostructured lipid carrier by means of the QbD and factorial design suitable for the topical management of inflammatory processes on mucosal tissues. To this end, the nanoparticles loading pranoprofen were prepared by a high-pressure homogenization technique with Tween 80 as stabilizer and Lanette® 18 as the solid lipid. From, the factorial design results, the PF-NLCs-N6 formulation showed the most suitable characteristics, which was selected for further studies. The permeability capacity of pranoprofen loaded in the lipid-based nanoparticles was evaluated by ex vivo transmucosal permeation tests, including buccal, sublingual, nasal, vaginal, corneal and scleral mucosae. The results revealed high permeation and retention of pranoprofen in all the tissues tested. According to the predicted plasma concentration at the steady-state, no systemic effects would be expected, any neither were any signs of ocular irritancy observed from the optimized formulation when tested by the HET-CAM technique. Hence, the optimized formulation (PF-NLCs-N6) may offer a safe and attractive nanotechnological tool in topical treatment of local inflammation on mucosal diseases.
iCache: An Intelligent Caching Scheme for Dynamic Network Environments in ICN-Based IoT Networks

Advanced network technologies and ubiquitous connected devices are boosting the development of the Internet of Things (IoT) at an unprecedented pace. However, as most of the connected IoT devices are battery powered, the energy consumption issue has become the bottleneck of the IoT’s development. Caching is a promising approach to reducing the energy consumption of the battery-powered devices since the requested data packets can be retrieved from intermediate nodes in the network, e.g., routers, instead of from the remote battery-powered IoT devices, which allows the IoT devices to spend more time in the sleep mode. To realize in-network caching and overcome the IP-based networks’ inefficiency support for IoT, building IoT over information-centric networking (ICN) is a promising approach advocated by researchers. However, existing works in this area assume the network environments are static, which hinders the development of existing approaches in the real dynamic network environments. In this article, we leverage the deep $Q$ -networks (DQNs) to propose an intelligent caching scheme (named as iCache) that can automatically adjust the caching nodes’ caching parameters to make caching decisions for the dynamic network environments. Extensive evaluations were conducted and the results show that the proposed iCache outperforms the existing approaches in terms of the total energy consumption (e.g., more than 29% reduction compared to the caching transient data (CTD) caching scheme) and the average number of hops (e.g., more than 20% reduction compared to the CTD caching scheme).
Proviral ALV-LTR Sequence Is Essential for Continued Proliferation of the ALV-Transformed B Cell Line

Avian leukosis virus (ALV) induces B-cell lymphomas and other malignancies in chickens through insertional activation of oncogenes, and c-myc activation has been commonly identified in ALV-induced tumors. Using ALV-transformed B-lymphoma-derived HP45 cell line, we applied in situ CRISPR-Cas9 editing of integrated proviral long terminal repeat (LTR) to examine the effects on gene expression and cell proliferation. Targeted deletion of LTR resulted in significant reduction in expression of a number of LTR-regulated genes including c-myc. LTR deletion also induced apoptosis of HP45 cells, affecting their proliferation, demonstrating the significance of LTR-mediated regulation of critical genes. Compared to the global effects on expression and functions of multiple genes in LTR-deleted cells, deletion of c-myc had a major effect on the HP45 cells proliferation with the phenotype similar to the LTR deletion, demonstrating the significance of c-myc expression in ALV-induced lymphomagenesis. Overall, our studies have not only shown the potential of targeted editing of the LTR for the global inhibition of retrovirus-induced transformation, but also have provided insights into the roles of LTR-regulated genes in ALV-induced neoplastic transformation.
Stabilization Effects Induced by Trehalose on Creatine Aqueous Solutions Investigated by Infrared Spectroscopy

Creatine is a very popular amino acid widely utilized in the sports world due to its functions mainly related to muscle building and increasing performance. The present work investigates the behavior of creatine aqueous solutions and of creatine aqueous in the presence of trehalose as a function of time changes by means of Infrared spectroscopy. Infrared spectra have been gathered and studied over time for both the full spectrum and the intramolecular OH-stretching region for the two mixtures. This latter region was studied more specifically using a cutting-edge technique called Spectral Distance (SD). From this analysis of the spectral features of the investigated samples, it emerges that trehalose has a significant stabilizing effect on creatine aqueous solutions.
Image-guided transthoracic transpedicular microdiscectomy for a giant thoracic disc herniation: patient series

BACKGROUND This case series reports on five consecutive patients who underwent image-guided transpedicular transthoracic microdiscectomy. The authors retrospectively reviewed five patients who had undergone Stealth image-guided transpedicular transthoracic microdiscectomy between 2015 and 2021. OBSERVATIONS Image guidance with O-arm verified critical anatomical landmarks in the setting of large central calcified and/or soft tissue disc prolapse. This allowed limited rib head resection, pedicle removal, and corpectomy to give adequate access and not require interbody fusion. The authors performed a partial posterior corpectomy anterior to the affected disc prolapse and microsurgical delivery of the affected disc anteriorly into the corpectomy cave away from the thecal sac. Electronic and radiographic records were analyzed at their initial presentation and at follow-up. The median patient age was 51 years (range, 44–56 years), with 80% of the patients being males. Four of five patients had significant improvement of their presenting clinical symptoms. One patient had a complicated postoperative recovery with a pneumothorax and subsequent bilateral pneumonia requiring intensive care. Another patient developed delayed postoperative worsening of paraparesis. LESSONS The use of Stealth image guidance with O-arm for transthoracic microdiscectomy for complex calcified thoracic disc herniation is an effective operative technical adjunct to verify anatomical landmarks and limit the microsurgical procedure.
Extending the FLExible Network Tester (Flent) for IEEE 802.11s WLAN Mesh Networks

Mesh networks based on the wireless local area network (WLAN) technology, as specified by the standards amendment IEEE 802.11s, provide for a flexible and low-cost interconnection of devices and embedded systems for various use cases. To assess the real-world performance of WLAN mesh networks and potential optimization strategies, suitable testbeds and measurement tools are required. Designed for highly automated transport-layer throughput and latency measurements, the software FLExible Network Tester (Flent) is a promising candidate. However, so far Flent does not integrate information specific to IEEE 802.11s networks, such as peer link status data or mesh routing metrics. Consequently, we propose Flent extensions that allow to additionally capture IEEE 802.11s information as part of the automated performance tests. For the functional validation of our extensions, we conduct Flent measurements in a mesh mobility scenario using the network emulation framework Mininet-WiFi.
Drivers of Seafood Consumption at Different Geographical Scales

As an important source of essential amino acids and micronutrients, fish is critical in the fight against malnutrition, especially in low income and food deficient countries. However, because fish consumption is reportedly linked to overfishing and the generation of negative environmental consequences from fish farming. There have been calls to reduce fish consumption, which may have implications for fish intake and the drive to reduce childhood malnutrition in many developing countries. Here we assess the role of urbanization, income, fish prices, preferences, nutritional knowledge, and cultural attitudes in fish demand. We conducted analysis using the fixed effect model at three geographical scales: global—151 countries drawn from all continents that consume over 90% of global seafood supply; at the continental; and at the national scales, where we assessed seafood consumption in Nigeria, Portugal, Bangladesh and the United States. Our results suggest that at the global level, a 10% increase in disposable income leads to a 5% increase in fish consumption, although a 10% increase in domestic fish price leads to 8% decrease in fish consumption. In our continental level analysis, we found distinct drivers of seafood consumption across continents, for example, urbanization drives fish consumption in Africa, while domestic fish prices influence fish consumption in South America and Oceania regions. The estimates of the current study are broadly consistent with other earlier studies, showing a
Development of a Cooperative Localization System using a UWB Network and BLE Technology

This paper presents the development of a system able to estimate the 2D relative position of nodes in a wireless network, based on distance measurements between the nodes. The system uses ultra wide band ranging technology and the Bluetooth Low Energy protocol to acquire data. Furthermore, a nonlinear least squares problem is formulated and solved numerically for estimating the relative positions of the nodes. The localization performance of the system is validated by experimental tests, demonstrating the capability of measuring the relative position of a network comprised of 4 nodes with an accuracy of the order of 3 cm and an update rate of 10 Hz. This shows the feasibility of applying the proposed system for multi-robot cooperative localization and formation control scenarios.
Single-Event Upset in 3-D Charge-Trap NAND Flash Memories

The effects of single-event upset (SEU) on the threshold voltage (<inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula>) of a programmed cell in 3-D charge-trap (CT) NAND flash memory have been investigated using 3-D technology-computer-aided design (TCAD) simulations. After ion strikes, the surrounding electric field (<inline-formula> <tex-math notation="LaTeX">${E}$ </tex-math></inline-formula>-field) accelerates the generated holes into the CT layer (CTL), which lowers <inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula> of the programmed cell. The tunneling oxide (TOX) strike causes a more severe <inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula> shift than the blocking oxide (BOX) strike due to the higher <inline-formula> <tex-math notation="LaTeX">${E}$ </tex-math></inline-formula>-field in the TOX layer. As the strike angle increases from 0° (lateral) to 90° (vertical), the effective irradiation volume is reduced, resulting in the mitigation of the SEU influence. Scaling of cell dimensions becomes more vulnerable to SEU except for the thinner TOX.
Public relations strategy in rebuilding Airline Company reputation following aircraft crash

The issue discussed in this study is rebuilding Lion Air's reputation tarnished by aircraft accidents. This study aims to identify public relations strategies pursued by case study of Lion Air, Indonesia, to rebuild its reputation following air accidents it has been involved. The research method employed in this study is the qualitative method using single case studies on Lion Air Company. Data is collected through observation, interviews, and a review of news articles in the media. The output of the research takes the form of corporate strategies that are aimed at rebuilding the company's reputation using stakeholder approaches, including (1) alignment of internal perceptions within the organization; (2) "communication holding,"; (3) centralization of information issuance; (4) appointment of partners as "communicators"; (5) use of humanitarian approaches. The conclusion drawn from the research is that public relations strategies through a stakeholder approach would provide a basis for Lion Air's management to exercise control over information that brings positive value. The result also shapes stakeholders' perceptions to align with the company's expectation in restoring its reputation.