Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of the JC Virus in Central Nervous System Tumorigenesis

Cancer is the second leading cause of mortality worldwide. The study of DNA tumor-inducing viruses and their oncoproteins as a causative agent in cancer initiation and tumor progression has greatly enhanced our understanding of cancer cell biology. The initiation of oncogenesis is a complex process. Specific gene mutations cause functional changes in the cell that ultimately result in the inability to regulate cell differentiation and proliferation effectively. The human neurotropic Polyomavirus JC (JCV) belongs to the family Polyomaviridae and it is the causative agent of progressive multifocal leukoencephalopathy (PML), which is a fatal neurodegenerative disease in an immunosuppressed state. Sero-epidemiological studies have indicated JCV infection is prevalent in the population (85%) and that initial infection usually occurs during childhood. The JC virus has small circular, double-stranded DNA that includes coding sequences for viral early and late proteins. Persistence of the virus in the brain and other tissues, as well as its potential to transform cells, has made it a subject of study for its role in brain tumor development. Earlier observation of malignant astrocytes and oligodendrocytes in PML, as well as glioblastoma formation in non-human primates inoculated with JCV, led to the hypothesis that JCV plays a role in central nervous system (CNS) tumorigenesis. Some studies have reported the presence of both JC viral DNA and its proteins in several primary brain tumor specimens. The discovery of new Polyomaviruses such as the Merkel cell Polyomavirus, which is associated with Merkel cell carcinomas in humans, ignited our interest in the role of the JC virus in CNS tumors. The current evidence known about JCV and its effects, which are sufficient to produce tumors in animal models, suggest it can be a causative factor in central nervous system tumorigenesis. However, there is no clear association between JCV presence in CNS and its ability to initiate CNS cancer and tumor formation in humans. In this review, we will discuss the correlation between JCV and tumorigenesis of CNS in animal models, and we will give an overview of the current evidence for the JC virus’s role in brain tumor formation.
Effects of Aerobic and Anaerobic Fatigue Exercises on Postural Control and Recovery Time in Female Soccer Players

Sixteen female soccer players (age = 20.19 ± 1.52 years; body mass = 56.52 ± 4.95 kg; body height = 164.81 ± 4.21 cm) with no history of lower extremity injury participated in the study. The Biodex SD Balance system was used to determine the non-dominant single-leg stability. In anaerobic exercise, each subject performed four maximal cycling efforts against a resistance equivalent to 0.075 kg/body mass for 30 s with three-minute rest intervals. In aerobic exercise, subjects performed the Bruce protocol on a motorized treadmill. After each exercise, subjects subsequently performed a single-leg stability test and then repeated the same test for four times with five-minute passive rest periods. In accordance with the results, it was found that the impairment observed right after the aerobic loading was higher (p < 0.001) compared to the anaerobic one. However, the time-related deterioration in both aerobic and anaerobic loadings was similar. The B-pre value was lower than Bpost and B5 (p < 0.01) and B10 (p < 0.05) in both conditions. Subjects could reach the initial balance level at B15 after aerobic and anaerobic loadings. The lactate level did not reach resting value even after 20 min of both fatigue protocols. Although the fatigue after aerobic and aerobic exercise negatively affects a single-leg dynamic balance level, single leg balance ability returns to the baseline status after 10 min of passive recovery duration.
A Hybrid Approach for Turning Intention Prediction Based on Time Series Forecasting and Deep Learning

At an intersection with complex traffic flow, the early detection of the intention of drivers in surrounding vehicles can enable advanced driver assistance systems (ADAS) to warn the driver in advance or prompt its subsystems to assess the risk and intervene early. Although different drivers show various driving characteristics, the kinematic parameters of human-driven vehicles can be used as a predictor for predicting the driver’s intention within a short time. In this paper, we propose a new hybrid approach for vehicle behavior recognition at intersections based on time series prediction and deep learning networks. First, the lateral position, longitudinal position, speed, and acceleration of the vehicle are predicted using the online autoregressive integrated moving average (ARIMA) algorithm. Next, a variant of the long short-term memory network, called the bidirectional long short-term memory (Bi-LSTM) network, is used to detect the vehicle’s turning behavior using the predicted parameters, as well as the derived parameters, i.e., the lateral velocity, lateral acceleration, and heading angle. The validity of the proposed method is verified at real intersections using the public driving data of the next generation simulation (NGSIM) project. The results of the turning behavior detection show that the proposed hybrid approach exhibits significant improvement over a conventional algorithm; the average recognition rates are 94.2% and 93.5% at 2 s and 1 s, respectively, before initiating the turning maneuver.
Production of Porous Films Based on Biodegradable Polyesters by the Casting Solution Technique Using a Co-Soluble Porogen (Camphor)

Porous films have been prepared from degradable polymers—poly-3-hydroxybutyrate (PHB), poly-ε-caprolactone (PCL) and a blend of these polymers (1:3)—by adding porogen (camphor) to the polymer solution at 10%, 30% or 50% of the total mass of the polymer and porogen, and leaching it out afterwards. After the rinse, camphor content in films decreased to about 0.025%. The structure, physical/mechanical and biological properties of the films were investigated as dependent on their composition and porosity, which varied depending on the amount of camphor added. The surface of PHB films was porous, the PCL films were relatively smooth, and the PHB/PCL films had an intermediate structure. The addition of camphor increased the thickness (from 35 to 45 µm, from 40 to 80 µm and from 20 to 65 µm for PHB, PCL and PHB/PCL, respectively) and porosity (from 4.2(±3.6)% to 50.0(±12.8)%, from 6.4(±5.5)% to 54.5(±6.0)% and from 4.9(±4.8)% to 51.5(±5.8)%, respectively) of the films. The introduction (and removal) of 10% camphor into the PHB and PHB/PCL films led to an approximately twofold increase in the polar component of the free surface energy (from 5.4 ± 0.38 to 11.8 ± 1.33 and from 2.7 ± 0.13 to 5.2 ± 0.09 mN/m, respectively) but in other cases, on the contrary, a decrease in this indicator was registered. The increase of camphor addition from 0% to 50% gradually impaired mechanical properties of the films: so, Young’s modulus decreased from 3.6 to 1.8 GPa, from 0.30 to 0.12 GPa and from 0.50 to 0.20 GPa for PHB, PCL and PHB/PCL, respectively. At the same time, the water vapor transmission rate considerably increased from 197.37 ± 23.62 to 934.03 ± 114.34 g/m2/d for PHB films; from 1027.99 ± 154.10 to 7014.62 ± 280.81 g/m2/d for PCL films; and from 715.47 ± 50.08 to 4239.09 ± 275.54 g/m2/d for PHB/PCL films. Results of biocompatibility testing in the culture of NIH 3T3 mouse fibroblast cells showed that for the most of experimental samples cell adhesion and proliferation were comparable or superior to the corresponding parameters on the initial nonporous films. The best results were obtained for PHB films where at Day 3 of the experiment the registered cell density for experimental samples arrived at 2.66(±0.26) × 105 cells/cm2 versus 1.29(±0.33) × 105 cells/cm2 in the control. So, the proposed method can be used to construct highly porous cell scaffolds for cellular engineering.
Habitat loss and thermal tolerances influence the sensitivity of resident bird populations to winter weather at regional scales.

Climate change and habitat loss pose the greatest contemporary threats to biodiversity, but their impacts on populations largely vary across species. These differential responses could be caused by complex interactions between landscape and climate change and species-specific sensitivities. Understanding the factors that determine which species are most vulnerable to the synergistic effects of climate change and habitat loss is a high conservation priority. Here, we ask (a) whether and to what extent land cover moderates the impacts of winter weather on population dynamics of wintering birds, and (b) what role species' physiology might play in modifying their responses to changing weather conditions. To address these questions, we used thousands of observations collected by citizen scientists participating in Project FeederWatch to build dynamic occupancy models for 14 species of wintering birds. Populations of wintering birds were more dynamic, having higher rates of local extinction and colonization, in more forested landscapes during extreme cold - presumably enabling them to better track resources. However, urban areas appeared to provide refuge for some species, as demonstrated by increased local colonization during the harshest winter weather. Lastly, we found that species-specific differences in thermal tolerances strongly influenced occupancy dynamics such that species that are less cold-tolerant were more likely to go locally extinct at colder sites and during colder periods throughout winter. Together, our results suggest that species that are less cold-tolerant and populations occupying less forested landscapes are most vulnerable to extreme winter weather.
Retrospective Evaluation of NI-RADS for Detecting Post-Surgical Recurrence of Oral Squamous Cell Carcinoma on Surveillance CT or MRI.

Background: Imaging surveillance is important for the early diagnosis of recurrence following definitive treatment for oral squamous cell carcinoma (OSCC). The Neck Imaging Reporting and Data System (NI-RADS) provides a standardized template for surveillance imaging and categorizes probability of recurrence at the primary site and the neck (cervical lymph nodes) by assigning categories of 1 (no evidence of recurrence), 2 (low suspicion, subdivided into 2a and 2b for the primary site), 3 (high suspicion), or 4 (definite recurrence). Objectives: The aim of this study was to determine the rate of locoregional and nodal OSCC recurrence stratified by NI-RADS category in patients undergoing surveillance CT or MRI. Methods: This retrospective study included 158 patients enrolled in an institutional surveillance program after resection of OSCC with curative intent. A total of 503 contrast-enhanced CT or MRI examinations performed during surveillance were evaluated. Each examination was randomly assigned to one of four radiologists with expertise in head and neck imaging, who provided NI-RADS categories for the primary site and the neck (1006 assigned NI-RADS categories). NI-RADS performance in identifying recurrence was assessed using receiver operating characteristic (ROC) curve analysis. All four readers evaluated 50 randomly selected cases to determine interreader agreement using Kendall's W. Results: Cancer recurrence was confirmed in 7.6% (38/503) of cases for the primary site and in 6.2% (31/503) for the neck. For the primary site, recurrence rates were 1.0% in NI-RADS category 1, 7.4 % in category 2a, 5.6 % in category 2b, 66.7 % in category 3, and 100.0% in NI-RADS 4. For the neck, recurrence rates were 0.5% in category 1, 7.0% in category 2, 80.0% in category 3, and 100.0% in category 4. NI-RADS demonstrated AUC of 0.934 for the primary site and 0.959 for the neck. Inter-reader agreement was 0.67 for the primary site and 0.81 for the neck. Conclusion: NI-RADS offers excellent discriminatory power in detection of OSCC recurrence, both for the primary site and the neck. Clinical Impact: Radiologists and maxillofacial surgeons should implement NI-RADS in surveillance regimens for post-operative OSCC to help detect recurrences in an effective and standardized fashion by imaging.
Reply to Wolf et al.: Why Trap-Neuter-Return (TNR) Is Not an Ethical Solution for Stray Cat Management

Simple Summary We provide a rebuttal to Wolf et al. (2019), outlining biological, ethical, and economic flaws in their argument that Trap-Neuter-Return (TNR) is an ethical solution for stray cat management. We contend that suppression of supplementary feeding of stray cats accompanied by proactive adoption or prompt euthanasia is more effective, humane, and economical. Abstract We critique the recent article by Wolf et al. (2019) that claims scientific merit for reducing the number of stray cats in Australia through Trap-Neuter-Return (TNR) programs, and then we provide an inventory of biological, welfare, and economic reasons why TNR is less successful than adoption and euthanasia for managing unowned cats. Like Crawford et al. (2019) and multiple other comprehensive and unbiased Australian and international scientific reviews, we refute the idea that returning neutered unowned cats to stray populations has any valid role in responsible, ethical, affordable, and effective cat management, or in wildlife conservation. The main purported objective of TNR proponents along with animal welfare, human health, and wildlife advocacy stakeholders is to reduce the number of unhomed cats. We contend that cessation of provisioning unowned cats with food is the most effective approach to achieve this objective. We also present evidence from the Brisbane City Council that informed cat management policy, advocacy, and laws, backed up by responsible rehoming or prompt ethical euthanasia, are together effective at reducing the stray cat problem.
Topography-Mediated Myotube and Endothelial Alignment, Differentiation, and Extracellular Matrix Organization for Skeletal Muscle Engineering

Understanding the response of endothelial cells to aligned myotubes is important to create an appropriate environment for tissue-engineered vascularized skeletal muscle. Part of the native tissue environment is the extracellular matrix (ECM). The ECM is a supportive scaffold for cells and allows cellular processes such as proliferation, differentiation, and migration. Interstitial matrix and basal membrane both comprise proteinaceous and polysaccharide components for strength, architecture, and volume retention. Virtually all cells are anchored to their basal lamina. One of the physical factors that affects cell behavior is topography, which plays an important role on cell alignment. We tested the hypothesis that topography-driven aligned human myotubes promote and support vascular network formation as a prelude to in vitro engineered vascularized skeletal muscle. Therefore, we used a PDMS-based topography substrate to investigate the influence of pre-aligned myotubes on the network formation of microvascular endothelial cells. The aligned myotubes produced a network of collagen fibers and laminin. This network supported early stages of endothelial network formation.
Dark noise and retinal degeneration from D190N-rhodopsin

Significance Rhodopsin mutations account for ∼30% of autosomal-dominant retinitis pigmentosa cases. While dozens of distinct mutations have been identified, the reported detriments that they cause in cell culture are not necessarily all consistent across studies and have often not been evaluated in animal models. Even when an animal model is available, it is typically not straightforward to isolate mutant-rhodopsin signals from related endogenous-rhodopsin signals. Here, we introduce an approach employing a largely “functionally silenced” endogenous rhodopsin in rods as background for isolating activity due to D190N-rhodopsin (D190N-Rho). We conclude that, despite D190N-Rho’s elevated molecular rate constant of spontaneous activation, it does not increase the overall cellular dark noise of the rod, thus excluding its increased noise as the reason for disease. Numerous rhodopsin mutations have been implicated in night blindness and retinal degeneration, often with unclear etiology. D190N-rhodopsin (D190N-Rho) is a well-known inherited human mutation causing retinitis pigmentosa. Both higher-than-normal spontaneous-isomerization activity and misfolding/mistargeting of the mutant protein have been proposed as causes of the disease, but neither explanation has been thoroughly examined. We replaced wild-type rhodopsin (WT-Rho) in RhoD190N/WT mouse rods with a largely “functionally silenced” rhodopsin mutant to isolate electrical responses triggered by D190N-Rho activity, and found that D190N-Rho at the single-molecule level indeed isomerizes more frequently than WT-Rho by over an order of magnitude. Importantly, however, this higher molecular dark activity does not translate into an overall higher cellular dark noise, owing to diminished D190N-Rho content in the rod outer segment. Separately, we found that much of the degeneration and shortened outer-segment length of RhoD190N/WT mouse rods was not averted by ablating rod transducin in phototransduction—also consistent with D190N-Rho’s higher isomerization activity not being the primary cause of disease. Instead, the low pigment content, shortened outer-segment length, and a moderate unfolded protein response implicate protein misfolding as the major pathogenic problem. Finally, D190N-Rho also provided some insight into the mechanism of spontaneous pigment excitation.
An Adapted Chronic Constriction Injury of the Sciatic Nerve Produces Sensory, Affective, and Cognitive Impairments: A Peripheral Mononeuropathy Model for the Study of Comorbid Neuropsychiatric Disorders Associated with Neuropathic Pain in Rats.

BACKGROUND Chronic constriction injury (CCI) is a model of neuropathic pain induced by four loose ligatures around the sciatic nerve. This work aimed to investigate the sensory, affective, cognitive, and motor changes induced by an adaptation of the CCI model by applying a single ligature around the sciatic nerve. METHODS Mechanical allodynia was measured from day 1 to day 28 postsurgery by the von Frey test. The beam walking test (BWT) was conducted weekly until 28 days after surgery. Anxiety- and depression-like behaviors, and cognitive performance were assessed through the open field (OF), forced swimming (FS), and novel object recognition (NOR) tests, respectively, 21 days after surgery. RESULTS The two CCI models, both Bennett and Xie's model (four ligatures of the sciatic nerve) and a modification of it (one ligature), induced mechanical allodynia, increased immobility in the FS, and reduced recognition index in the NOR. The exploratory behavior and time spent in the central part of the arena decreased, while the defensive behavior increased in the OF. The animals subjected to the two CCI models showed motor alterations in the BWT; however, autotomy was observed only in the group with four ligatures and not in the group with a single ligature. CONCLUSIONS Overall these results demonstrate that our adapted CCI model, using a single ligature around the sciatic nerve, induces sensory, affective, cognitive, and motor alterations comparable to the CCI model with four ligatures without generating autotomy. This adaptation to the CCI model may therefore represent an appropriate and more easily performed model for inducing neuropathic pain and study underlying mechanisms and effective treatments.
Laboratory Insights into the Diel Cycle of Optical and Chemical Transformations of Biomass Burning Brown Carbon Aerosols

Transformations of biomass burning brown carbon aerosols (BB-BrC) over their diurnal lifecycle are currently not well studied. In this study, the aging of BB tar proxy aerosols processed by NO3• under dark conditions followed by the photochemical OH• reaction and photolysis were investigated in tandem flow reactors. The results show that O3 oxidation in the dark diminishes light absorption of wood tar aerosols, resulting in higher particle single-scattering albedo (SSA). NO3• reactions augment the mass absorption coefficient (MAC) of the aerosols by a factor of 2–3 by forming secondary chromophores, such as nitroaromatic compounds (NACs) and organonitrates. Subsequent OH• oxidation and direct photolysis both decompose the organic nitrates (ONs, representing bulk functionalities of NACs and organonitrates) in the NO3•-aged wood tar aerosols, thus decreasing particle absorption. Moreover, NACs degrade faster than organonitrates by photochemical aging. The NO3•-aged wood tar aerosols are more susceptible to photolysis than to OH• reactions. The photolysis lifetimes for the ONs and for the absorbance of the NO3•-aged aerosols are on the order of hours under typical solar irradiation, while the absorption and ON lifetimes toward OH• oxidation are substantially longer. Overall, nighttime aging via NO3• reactions increases the light absorption of wood tar aerosols and shortens their absorption lifetime under daytime conditions.
Epstein-Barr Virus Mediated Signaling in Nasopharyngeal Carcinoma Carcinogenesis

Simple Summary Epstein-Barr virus (EBV) infection is known to contribute in nasopharyngeal carcinoma (NPC) carcinogenesis. The oncogenic roles of the EBV proteins and non-coding RNAs in NPC are becoming evident with the aid of current advances in genome-wide and in-depth molecular analyses. This current work provides a comprehensive overview, which covers recent understandings of the pathogenic role of EBV infection in NPC. Perspectives on molecular mechanisms, which are involved in the pathogenesis of NPC, focusing on the connection between EBV and NPC cells and the corresponding signaling pathways are highlighted. Cancer hallmarks associated with EBV in NPC development are also discussed herein. Abstract Nasopharyngeal carcinoma (NPC) is one of the most common tumors occurring in China and Southeast Asia. Etiology of NPC seems to be complex and involves many determinants, one of which is Epstein-Barr virus (EBV) infection. Although evidence demonstrates that EBV infection plays a key role in NPC carcinogenesis, the exact relationship between EBV and dysregulation of signaling pathways in NPC needs to be clarified. This review focuses on the interplay between EBV and NPC cells and the corresponding signaling pathways, which are modulated by EBV oncoproteins and non-coding RNAs. These altered signaling pathways could be critical for the initiation and progression of NPC.