Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypes and Karyotypes of Human Malignant Mesothelioma Cell Lines

Background Malignant mesothelioma is an aggressive tumour of serosal surfaces most commonly pleura. Characterised cell lines represent a valuable tool to study the biology of mesothelioma. The aim of this study was to develop and biologically characterise six malignant mesothelioma cell lines to evaluate their potential as models of human malignant mesothelioma. Methods Five lines were initiated from pleural biopsies, and one from pleural effusion of patients with histologically proven malignant mesothelioma. Mesothelial origin was assessed by standard morphology, Transmission Electron Microscopy (TEM) and immunocytochemistry. Growth characteristics were assayed using population doubling times. Spectral karyotyping was performed to assess chromosomal abnormalities. Authentication of donor specific derivation was undertaken by DNA fingerprinting using a panel of SNPs. Results Most of cell lines exhibited spindle cell shape, with some retaining stellate shapes. At passage 2 to 6 all lines stained positively for calretinin and cytokeratin 19, and demonstrated capacity for anchorage-independent growth. At passage 4 to 16, doubling times ranged from 30–72 hours, and on spectral karyotyping all lines exhibited numerical chromosomal abnormalities ranging from 41 to 113. Monosomy of chromosomes 8, 14, 22 or 17 was observed in three lines. One line displayed four different karyotypes at passage 8, but only one karyotype at passage 42, and another displayed polyploidy at passage 40 which was not present at early passages. At passages 5–17, TEM showed characteristic features of mesothelioma ultrastructure in all lines including microvilli and tight intercellular junctions. Conclusion These six cell lines exhibit varying cell morphology, a range of doubling times, and show diverse passage-dependent structural chromosomal changes observed in malignant tumours. However they retain characteristic immunocytochemical protein expression profiles of mesothelioma during maintenance in artificial culture systems. These characteristics support their potential as in vitro model systems for studying cellular, molecular and genetic aspects of mesothelioma.
Descriptor Sigfox and LoRaWAN Datasets for Fingerprint Localization in Large Urban and Rural Areas

Because of the increasing relevance of the Internet of Things and location based services, 1 researchers are evaluating wireless positioning techniques, such as fingerprinting, on LPWAN 2 communication. In order to evaluate fingerprinting in large outdoor environments, extensive, 3 time-consuming measurement campaigns need to be conducted to create useful datasets. This paper 4 presents three LPWAN datasets which are collected in large-scale urban and rural areas. The goal 5 is to provide the research community with a tool to evaluate fingerprinting algorithms in large 6 outdoor environments. During a period of three months, numerous mobile devices periodically 7 obtained location data via a GPS receiver which was transmitted via a Sigfox or LoRaWAN message. 8 Together with network information, this location data is stored in the appropriate LPWAN dataset. 9 The results of our fingerprinting implementation, which is also clarified in this paper, indicate a 10 mean location estimation error of 214.58 m for the rural Sigfox dataset, 688.97 m for the urban Sigfox 11 dataset and 398.40 m for the urban LoRaWAN dataset. In the future, we will enlarge our current 12 datasets and use them to evaluate our fingerprinting methods. Also, we intend to collect additional 13 datasets for Sigfox, LoRaWAN as well as NB-IoT. 14
IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA

Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed during the cell-intrinsic immune response to viral infection. IFIT1 inhibits translation by binding directly to the 5′ end of foreign RNAs, particularly those with non-self cap structures, precluding the recruitment of the cap-binding eukaryotic translation initiation factor 4F and subsequent 40S recruitment. Interaction of different IFIT family members is well described, but little is known of the molecular basis of IFIT association or its impact on function. Here, we reconstituted different complexes of IFIT1, IFIT2 and IFIT3 in vitro, which enabled us to reveal critical aspects of IFIT complex assembly. IFIT1 interacts rapidly and strongly with IFIT3 forming a stable heterotetramer. IFIT2 and IFIT3 homodimers dissociate to form a more stable heterodimer that associates with IFIT1, forming an IFIT1:IFIT2:IFIT3 trimer. Site-directed mutagenesis revealed a C-terminal ‘YxxxL’ motif in IFIT1 that mediates its association with IFIT3. Using various reporter mRNAs, we demonstrate for the first time that IFIT3 stabilises IFIT1 binding to cap0-mRNA and enhances its translation inhibition activity. Disrupting the binding interface between IFIT1 and IFIT3 abrogated this enhancement. This work reveals molecular aspects of IFIT assembly and provides an important ‘missing link’ between IFIT interaction and function.
Robust Visual Responses and Normal Retinotopy in Primate Lateral Geniculate Nucleus following Long-term Lesions of Striate Cortex

Lesions of striate cortex (V1) trigger massive retrograde degeneration of neurons in the LGN. In primates, these lesions also lead to scotomas, within which conscious vision is abolished. Mediation of residual visual capacity within these regions (blindsight) has been traditionally attributed to an indirect visual pathway to the extrastriate cortex, which involves the superior colliculus and pulvinar complex. However, recent studies have suggested that preservation of the LGN is critical for behavioral evidence of blindsight, raising the question of what type of visual information is channeled by remaining neurons in this structure. A possible contribution of LGN neurons to blindsight is predicated on two conditions: that the neurons that survive degeneration remain visually responsive, and that their receptive fields continue to represent the region of the visual field inside the scotoma. We tested these conditions in male and female marmoset monkeys (Callithrix jacchus) with partial V1 lesions at three developmental stages (early postnatal life, young adulthood, old age), followed by long recovery periods. In all cases, recordings from the degenerated LGN revealed neurons with well-formed receptive fields throughout the scotoma. The responses were consistent and robust, and followed the expected eye dominance and retinotopy observed in the normal LGN. The responses had short latencies and preceded those of neurons recorded in the extrastriate middle temporal area. These findings suggest that the pathway that links LGN neurons to the extrastriate cortex is physiologically viable and can support residual vision in animals with V1 lesions incurred at various ages. SIGNIFICANCE STATEMENT Patients with a lesion of the primary visual cortex (V1) can retain certain visually mediated behaviors, particularly if the lesion occurs early in life. This phenomenon (“blindsight”) not only sheds light on the nature of consciousness, but also has implications for studies of brain circuitry, development, and plasticity. However, the pathways that mediate blindsight have been the subject of debate. Recent studies suggest that projections from the LGN might be critical, but this finding is puzzling given that the lesions causes severe cell death in the LGN. Here we demonstrate in monkeys that the surviving LGN neurons retain a remarkable level of visual function and could therefore be the source of the visual information that supports blindsight.
Internal Geography, International Trade, and Regional Specialization

We introduce an internal geography to the canonical model of international trade driven by comparative advantages to study the regional effects of external economic integration. The model features a dual-economy structure, in which locations near international gates specialize in export-oriented sectors while more distant locations do not trade with the rest of the world. The theory rationalizes patterns of specialization, employment, and relative incomes observed in developing countries that opened up to trade. We find regional specialization patterns consistent with the model in industry-level data from Chinese prefectures. (JEL F11, O18, P23, P25, P33, R12, R32)
Contactless testing of on-chip oscillator operation

The on-chip oscillator operation can be verified in a contactless way if the oscillator tank inductance is also used as a transmitting antenna. When the probing (receiver) antenna located on the test head is close to the oscillator, both antennas together may be considered as a transformer. The receiving antenna moving to and from the oscillator disturbs the oscillation frequency and amplitude, and these disturbances are registered by the measuring device connected to the receiving antenna. These disturbances, which are not occurring in ordinary oscillators with constant components, are evaluated using the equivalent circuit of thus formed transformer. The variation of frequency and the primary and secondary amplitudes as functions of distance between antennas are calculated. The results are experimentally verified with the oscillator realized in 0.13 μm CMOS technology.
Human fatigue and the crash of the airship Italia

The airship Italia, commanded by General Umberto Nobile, crashed during its return flight from the North Pole in 1928. The cause of the accident was never satisfactorily explained. We present evidence that the crash may have been fatigue-related. Nobile's memoirs indicate that at the time of the crash he had been awake for at least 72 h. Sleep deprivation impairs multiple aspects of cognitive functioning necessary for exploration missions. Just prior to the crash, Nobile made three command errors, all of which are of types associated with inadequate sleep. First, he ordered a release of lift gas when he should have restarted engines (an example of incorrect data synthesis, with deterioration of divergent thinking); second, he inappropriately ordered the ship above the cloud layer (a deficiency in the assessment of relative risks); and third, he remained above the cloud layer for a prolonged period of time (examples of attention to secondary problems, and calculation problems). We argue that as a result of these three errors, which would not be expected from such an experienced commander, there was no longer enough static lift to maintain level flight when the ship went below the cloud layer. Applying Circadian Performance Simulation Software to the sleep–wake patterns described by Nobile in his memoirs, we found that the predicted performance for someone awake as long as he had been is extremely low. This supports the historical evidence that human fatigue contributed to the crash of the Italia.
Antioxidative effects of Kimchi under different fermentation stage on radical-induced oxidative stress

BACKGROUND/OBJECTIVES Kimchi is a traditional Korean fermented vegetable containing several ingredients. We investigated the protective activity of methanol extract of kimchi under different fermentation stages against oxidative damage. MATERIALS/METHODS Fresh kimchi (Fresh), optimally ripened kimchi (OptR), and over ripened kimchi (OvR) were fermented until the pH reached pH 5.6, pH 4.3, and pH 3.8, respectively. The radical scavenging activity and protective activity from oxidative stress of kimchi during fermentation were investigated under in vitro and cellular systems using LLC-PK1 cells. RESULTS Kimchi exhibited strong radical scavenging activities against 1,1-diphenyl-2-picrylhydrazyl, nitric oxide, superoxide anion, and hydroxyl radical. In addition, the free radical generators led to loss of cell viability and elevated lipid peroxidation, while treatment with kimchi resulted in significantly increased cell viability and decreased lipid peroxidation. Furthermore, the protective effect against oxidative stress was related to regulation of cyclooxygenase-2, inducible nitric oxide synthase, nuclear factor-κB p65, and IκB expression. In particular, OvR showed the strongest protective effect from cellular oxidative stress among other kimchi. CONCLUSION The current study indicated that kimchi, particularly OptR and OvR, played a protective role against free radical-induced oxidative stress. These findings suggest that kimchi is a promising functional food with an antioxidative effect and fermentation of kimchi led to elevation of antioxidative activity.
RF-powered cognitive radio networks: technical challenges and limitations

The increasing demand for spectral- and energy-efficient communication networks has spurred great interest in energy harvesting cognitive radio networks. Such a revolutionary technology represents a paradigm shift in the development of wireless networks, as it can simultaneously enable the efficient use of the available spectrum and the exploitation of RF energy in order to reduce reliance on traditional energy sources. This is mainly triggered by the recent advancements in microelectronics that puts forward RF energy harvesting as a plausible technique in the near future. On the other hand, it has been suggested that the operation of a network relying on harvested energy needs to be redesigned to allow the network to reliably function in the long term. To this end, the aim of this survey article is to provide a comprehensive overview of recent development and the challenges regarding the operation of CRNs powered by RF energy. In addition, the potential open issues that might be considered for future research are also discussed in this article.
Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis

Members of the NF-YB transcription factor gene family play important roles in diverse processes related to plant growth and development, such as seed development, drought tolerance, and flowering time. However, the function of NF-YB genes in cotton remains unclear. A total of 23, 24, and 50 NF-YB genes were identified in Gossypium arboreum (G. arboreum), Gossypium raimondii (G. raimondii), and G. hirsutum, respectively. A systematic phylogenetic analysis was carried out in G. arboretum, G. raimondii, G. hirsutum, Arabidopsis thaliana, cacao, rice and, sorghum, where the 150 NF-YB genes were divided into five groups (α–ε). Of these groups, α is the largest clade, and γ contains the LEC1 type NF-YB proteins. Syntenic analyses revealed that paralogues of NF-YB genes in G. hirsutum exhibited good collinearity. Owing to segmental duplication within the A sub-genome (At) and D sub-genome (Dt), there was an expanded set of NF-YB genes in G. hirsutum. Furthermore, we investigated the structures of exons, introns, and conserved motifs of NF-YB genes in upland cotton. Most of the NF-YB genes had only one exon, and the genes from the same clade exhibited a similar motif pattern. Expression data show that most NF-YB genes were expressed ubiquitously, and only a few genes were highly expressed in specific tissues, as confirmed by quantitative real-time PCR (qRT-PCR) analysis. The overexpression of GhDNF-YB22 gene, predominantly expressed in embryonic tissues, indicates that GhDNF-YB22 may affect embryogenesis in cotton. This study is the first comprehensive characterization of the GhNF-YB gene family in cotton, and showed that NF-YB genes could be divided into five clades. The duplication events that occurred over the course of evolution were the major impetus for NF-YB gene expansion in upland cotton. Collectively, this work provides insight into the evolution of NF-YB in cotton and further our knowledge of this commercially important species.
Growth and Characterization of GaN and AlGaN Thin Films and Heterostructures and the Associated Development and Evaluation of Ultraviolet Light Emitting Diodes

PARK, JI-SOO. Growth and Characterization of GaN and AlGaN Thin Films and Heterostructures and the Associated Development and Evaluation of Ultraviolet Light Emitting Diodes. (Under the direction of Professor Robert F. Davis) AlGaN-based thin film heterostructures have been grown and fabricated into ultraviolet light emitting diodes with and without p-type and/or n-type AlGaN carrierblocking layers at the top and the bottom of the quantum wells, respectively, and having the principal emission at 353 nm. The highest values of this peak intensity and light output power were measured in the devices containing p-type carrier-blocking layers. Growth of an n-type carrier-blocking layer had an adverse effect on these device characteristics. A broad peak centered at ~540nm exhibited yellow luminescence and was present in the spectra acquired from all the devices. This peak is attributed to absorption of the ultraviolet emission by and re-emission from the p-GaN and/or to the luminescence from the AlGaN within quantum wells by current injection. Individual AlxGa1-xN films (x<0≤1) have been grown on Siand C-terminated 6H-SiC{0001} substrates and characterized for electron emission applications. The large range in the values of x was achieved by changing the fraction of Al in the gas phase from 0 to 0.45. The ionized donor concentration in the n-type, Si-doped AlxGa1-xN films decreased as the mole fraction of Al was increased due to the reduction in the donor energy level and compensation. The use of the SiH4 flow rate, which yields a Si concentration of ~1 x 10 cm in GaN, established the upper limit of the mole fraction of Al wherein n-type doping could be achieved at ~0.61. The electron affinity of the Sidoped Al0.61Ga0. 39N films was as low as 0.1 eV. Increasing the Si doping concentration in AlN films to as high as 1 x 10cm caused slight degradation in crystal perfection. No difference was found in the Al core level binding energies between undoped and Sidoped AlN films. The results of XPS and UPS experiments showed that the work function of N-polar AlN films was 0.6 eV lower than that of Al-polar films. GROWTH AND CHARACTERIZATION OF GaN AND AlGaN THIN FILMS AND HETEROSTRUCTURES AND THE ASSOCIATED DEVELOPMENT AND EVALUATION OF ULTRAVIOLET LIGHT EMITTING DIODES
Observation of Pair Structures of Threading Dislocation and Surface Defect in 4H-SiC Wafer by Mirror Projection Electron Microscopy

Two types of shallow surface defects associated with treading dislocation were found out by using mirror projection electron microscope. One was single groove with a dimension of about 4 nm in depth, 2 μm in width and 15 μm in length, named “as nanogroove”. The other was a shallow groove at 1.3nm in depth being between pair of hillocks at 2-3 nm in height and 1.5 μm in distance, named as “nanohillock pair”. Dislocations combined with the defects were found out by micro-KOH etching method with low-energy scanning electron microscopy. The dislocations were identified by g-b analysis using scanning transmission electron microscopy as threading edge dislocations converted from basal plane dislocation at bulk-epi layer interface or within epi layer.
Juvenile Coffee Leaves Acclimated to Low Light Are Unable to Cope with a Moderate Light Increase

The understorey origin of coffee trees and the strong plasticity of Coffea arabica leaves in relation to contrasting light environments have been largely shown. The adaptability of coffee leaves to changes in light was tested under controlled conditions by increasing the illumination rate on C. arabica var. Naryelis seedlings acclimated to low light conditions and observing leaf responses at three different developmental stages (juvenile, growing and mature). Only mature leaves proved capable of adapting to new light conditions. In these leaves, different major mechanisms were found to contribute to maintaining a good photosynthetic level. With increased illumination, a high photosynthetic response was conserved thanks to fast nitrogen remobilization, as indicated by SPAD values and the photorespiration rate. Efficient photoprotection was accompanied by a great ability to export sucrose, which prevented excessive inhibition of the Calvin cycle by hexose accumulation. In contrast, in younger leaves, increased illumination caused photodamage, observable even after 9 days of treatment. One major finding was that young coffee leaves rely on the accumulation of chlorogenic acids, powerful antioxidant phenolic compounds, to deal with the accumulation of reactive oxygen species rather than on antioxidant enzymes. Due to a lack of efficient photoprotection, a poor ability to export sucrose and inadequate antioxidant protection, younger leaves seemed to be unable to cope with increased illumination. In these leaves, an absence of induced antioxidant enzyme activity was accompanied, in growing leaves, by an absence of antioxidant synthesis or, in juvenile leaves, inefficient synthesis of flavonoids because located in some epidermis cells. These observations showed that coffee leaves, at the beginning of their development, are not equipped to withstand quick switches to higher light levels. Our results confirm that coffee trees, even selected for full sunlight conditions, remain shade plants possessing leaves able to adapt to higher light levels only when mature.
Object of interest discovery in video sequences

Video categorization is a process of extracting important information summarizing a given set of images and videos. Traditionally, the analysis was done using object detection involving numerous human labors for labeling the images, and has difficulty of handling a large number of object categories. In this report, we will present a method, unsupervised in nature, to discover the objects of interest (OOI) in multiple videos for categorization. Unsupervised meaning no labeling is adapted to pre-train or to initialize the system. The OOI system presented here works on variety of videos with different characteristics, such as videos contain compact scenes with distracting backgrounds, videos have their object of interest in motion, and videos have their object of interest moving across frames. For this project, we implemented an unsupervised OOI system that retrieves object of interests in a given video. The system consists of two top levels, one at the image level and the other at the videos level with the following system architecture. The system first samples a given video into multiple images for the analysis. From each sampled image, local features, each represented using a 128 dimensions descriptor, are extracted from the Maximally Stable Extremal Regions (MSER) [1] using Scale Invariant Feature Transform (SIFT) [2]. MSER are patches in an image that contain high local contrast pixels and the features extracted from these regions are referred to as the SIFT features. After feature extraction, SIFT descriptors are partitioned into J clusters (J = 50 in our case) using k-means clustering [3], the clusters then form the dictionary of visuals words that represent the given MSER patch. K-means essentially partition the 128 dimensional descriptors into clusters so each descriptor belongs to the cluster with the nearest mean. The method adapted for object of interest (OOI) discovery in this project rely mainly on a probabilistic frame work, a frame work consist of an appearance model and a motion model. The appearance model provides location and scale estimates of objects in each image frame. The information given by the appearance model will then be integrated with motion information using a motion model for object discovery. Details of both models will be discussed in the main report followed by the system simulation results.