Miracle-dz/UniFAR-FTUs huggingface dataset:
Transplantation of Embryonic Neural Stem Cells and Differentiated Cells in a Controlled Cortical Impact (CCI) Model of Adult Mouse Somatosensory Cortex

Traumatic brain injury (TBI) is a major cause of death worldwide. Depending on the severity of the injury, TBI can reflect a broad range of consequences such as speech impairment, memory disturbances, and premature death. In this study, embryonic neural stem cells (ENSC) were isolated from E14 mouse embryos and cultured to produce neurospheres which were induced to generate differentiated cells (DC). As a cell replacement treatment option, we aimed to transplant ENSC or DC into the adult injured C57BL/6 mouse cortex controlled cortical impact (CCI) model, 7 days post-trauma, in comparison to saline injection (control). The effect of grafted cells on neuroinflammation and neurogenesis was investigated at 1 and 4 weeks post-transplantation. Results showed that microglia were activated following mild CCI, but not enhanced after engraftment of ENSC or DC. Indeed, ipsilateral lesioned somatosensory area expressed high levels of Iba-1+ microglia within the different groups after 1 and 4 weeks. On the other hand, treatment with ENSC or DC demonstrated a significant reduction in astrogliosis. The levels of GFAP expressing astrocytes started decreasing early (1 week) in the ENSC group and then were similarly low at 4 weeks in both ENSC and DC. Moreover, neurogenesis was significantly enhanced in ENSC and DC groups. Indeed, a significant increase in the number of DCX expressing progenitor cells was observed at 1 week in the ENSC group, and in DC and ENSC groups at 4 weeks. Furthermore, the number of mature neuronal cells (NeuN+) significantly increased in DC group at 4 weeks whereas they decreased in ENSC group at 1 week. Therefore, injection of ENSC or DC post-CCI caused decreased astrogliosis and suggested an increased neurogenesis via inducing neural progenitor proliferation and expression rather than neuronal maturation. Thus, ENSC may play a role in replacing lost cells and brain repair following TBI by improving neurogenesis and reducing neuroinflammation, reflecting an optimal environment for transplanted and newly born cells.
An Energy Model for the Commercial Building Sector in Hong Kong

The building sector accounts for 15~40% of the energy consumption in cities and thus plays a significant role in promoting sustainable development. Hong Kong government established an ambitious target to reduce the energy intensity by 40% from the 2005 level by 2025, in which the energy efficiency in the commercial building sector is a key. This paper examines the role of human behavior, as well as regulations and technological advancements, in the commercial building sector in Hong Kong. Models in existing literature are not suitable for city-scale study due to the complexity in the commercial building sector in terms of the building scale and function, the energy systems and the technical characteristics, and the distribution of human behaviors among occupants. By developing an energy model accounting for those complexities, I first present the per m2 energy consumption in the commercial buildings in Hong Kong, which is much higher than the counterparts in OECD countries. I also evaluate the energy performance of various building regulations and technologies with the established model. My finding has direct implication for the Hong Kong government to allocate more resources in mobilizing citizens through various incentives and public education programs. My study bridges the gap between engineering simulations and the diversified real conditions in buildings for scholar conducting macroscopic studies and policy makers in cities.
Experimenting with a Multi-Approach Testing Strategy for Adaptive Systems

Context: Testing adaptive systems (ASs) is particularly challenging due to certain characteristics such as the high number of possible configurations, runtime adaptations and the interactions between the system and its surrounding environment. Therefore, the combination of different testing approaches in order to compose a strategy is expected to improve the quality of the designed test suites. Objective: To devise and experiment with a testing strategy for ASs that relies on particular characteristics of these systems. Method: We ranked testing approaches for ASs and devised a strategy that is composed of the three top-ranked ones. The rankings address the challenges that can be mitigated by the approaches, activities from a typical testing process, and characteristics observed in some AS implementations. The strategy was applied to two adaptive systems for mobile devices. Results: The approach was applied to both systems. We observed partial gains in terms of fault detection and structural coverage when results are analysed separately for each system, even though no improvements were obtained with the application of the third approach. Conclusion: The strategy, despite being incipient, is promising and motivates a deeper analysis of results and new experiment rounds. Furthermore, it can evolve as long as the rankings are updated with new approaches.
An investigation of shedding and super‐shedding of Shiga toxigenic Escherichia coli O157 and E. coli O26 in cattle presented for slaughter in the Republic of Ireland

Shiga toxigenic Escherichia coli (STEC) are an important group of pathogens and can be transmitted to humans from direct or indirect contact with cattle faeces. This study investigated the shedding of E. coli O157 and O26 in cattle at the time of slaughter and factors associated with super‐shedding (SS) animals. Rectoanal mucosal swab (RAMS) samples were collected from cattle (n = 1,317) at three large Irish commercial beef abattoirs over an 18 month period, and metadata were collected at the time of sampling regarding farm of origin, animal age, breed and gender. RAMS swabs were examined for the presence and numbers of E. coli O157 and O26 using a previously developed quantitative real‐time PCR protocol. Samples positive by PCR were culturally examined and isolates analysed for the presence of stx subtypes, eae and phylogroup. Any samples with counts >104 CFU/swab of STEC O157 or O26 were deemed to be super‐shedders. Overall, 4.18% (55/1,317) of RAMS samples were positive for STEC O157, and 2.13% (28/1,317) were classified as STEC O157 SS. For STEC O26, 0.76% (10/1,317) of cattle were positive for STEC O26, and 0.23% (3/1,317) were classified as super‐shedders. Fewer STEC shedders and SS were noted among older animals (>37 months). There was a seasonal trend observed for STEC O157, with the highest prevalence of shedding and SS events in the autumn (August to October). The majority of E. coli O157 (50/55) isolates had stx2 and were eae positive, with no significant difference between SS and low shedders (LS). Interestingly, all STEC O26 (n = 10) were eae negative and had varied stx profiles. This study demonstrates that, while the overall shedding rates are relatively low in cattle at slaughter, among positive animals there is a high level of SS, which may pose a higher risk of cross‐contamination during slaughter.
Self-Erasing Network for Integral Object Attention

Recently, adversarial erasing for weakly-supervised object attention has been deeply studied due to its capability in localizing integral object regions. However, such a strategy raises one key problem that attention regions will gradually expand to non-object regions as training iterations continue, which significantly decreases the quality of the produced attention maps. To tackle such an issue as well as promote the quality of object attention, we introduce a simple yet effective Self-Erasing Network (SeeNet) to prohibit attentions from spreading to unexpected background regions. In particular, SeeNet leverages two self-erasing strategies to encourage networks to use reliable object and background cues for learning to attention. In this way, integral object regions can be effectively highlighted without including much more background regions. To test the quality of the generated attention maps, we employ the mined object regions as heuristic cues for learning semantic segmentation models. Experiments on Pascal VOC well demonstrate the superiority of our SeeNet over other state-of-the-art methods.
Fruit and Vegetable Consumption among Immigrants in Portugal: A Nationwide Cross-Sectional Study

This study aims to compare adequate fruit and vegetable (F&V) intake between immigrants and natives in Portugal, and to analyse factors associated with consumption of F&V among immigrants. Data from a population based cross-sectional study (2014) was used. The final sample comprised 17,410 participants (≥20 years old), of whom 7.4% were immigrants. Chi-squared tests and logistic regression models were conducted to investigate the association between adequate F&V intake, sociodemographic, anthropometric, and lifestyle characteristics. Adequate F&V intake was more prevalent among immigrants (21.1% (95% CI: 19.0–23.4)) than natives (18.5% (95% CI: 17.9–19.1)), (p = 0.000). Association between migrant status and adequate F&V intake was only evident for men: immigrants were less likely to achieve an adequate F&V intake (OR = 0.67, 95% CI = 0.66–0.68) when compared to Portuguese. Among immigrants, being female, older, with a higher education, and living in a low urbanisation area increased the odds of having F&V consumption closer to the recommendations. Adjusting for other factors, length of residence appears as a risk factor (15 or more years vs. 0–9 years: OR = 0.52, 95% CI = 0.50–0.53), (p = 0.000) for adequate F&V intake. Policies aiming to promote adequate F&V consumption should consider both populations groups, and gender-based strategies should address proper sociodemographic, anthropometric, and lifestyle determinants.
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree–Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard–Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute–solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
Diversity of Yersinia enterocolitica isolated from pigs in a French slaughterhouse over 2 years

The pig is one of the main reservoirs of Yersinia enterocolitica strains pathogenic to humans. A description of the Y. enterocolitica population in this reservoir, and accurate discriminatory techniques for typing isolates are needed for prevention, outbreak investigation, and surveillance. This study investigates the genetic diversity of pathogenic Y. enterocolitica isolates obtained from pig tonsils in a French pig slaughterhouse in 2009 (S1) and 2010 (S2). The use of Pulsed‐Field Gel Electrophoresis (PFGE) and MLVA as typing techniques was also compared and evaluated. First, a total of 167 isolates (12 of biotype 3 recovered during S1, and 155 of biotype 4 recovered during S1 and S2) were typed by PFGE using the XbaI enzyme. MLVA was then tested on all the biotype 3 isolates in addition to 70 selected biotype 4 isolates recovered over the 2 years. PFGE generated two specific XbaI‐PFGE profiles for biotype 3 isolates. Nine XbaI profiles were obtained for biotype 4, with a higher diversity (ID = 0.599) than biotype 3 (ID = 0.167). Two out of the nine XbaI profiles were reported during both surveys and at different months. MLVA improved the differentiation between isolates; the index of diversity reached 0.621 and 0.958, respectively, for biotype 3 (three MLVA types) and biotype 4 (32 MLVA types). The MLVA types for biotype 4 differed over the two surveys, but some isolates with different MLVA types were genetically closely related. This study provides an initial evaluation of the genetic diversity of Y. enterocolitica strains isolated from pigs in France. We show that some PFGE profiles are maintained in the pig production sector, and, through MLVA, that part of the Y. enterocolitica population remained genetically close over the two years. MLVA proved its effectiveness as a tool for investigating pathogenic Y. enterocolitica strains isolated from pigs.
Gas Chromatography–Mass Spectrometry (GC–MS) and Gas Chromatography–Infrared (GC–IR) Analyses of the Chloro-1-n-pentyl-3-(1-naphthoyl)-Indoles: Regioisomeric Cannabinoids

The analytical differentiation of the indole ring regioisomeric chloro-1-n-pentyl-3-(1-naphthoyl)-indoles is described in this report. The regioisomeric chloroindole precursor compounds, N-n-pentyl chloroindole synthetic intermediates, and the target chloro-substituted naphthoylindoles showed the equivalent gas chromatographic elution order based on the position of chlorine substitution on the indole ring. The regioisomeric chloro-1-n-pentyl-3-(1-naphthoyl)-indoles yield electron ionization mass spectra having equivalent major fragments resulting from cleavage of the groups attached to the central indole nucleus. Fragment ions occur at m/z 127 and 155 for the naphthyl and naphthoyl cations common to all indoles having the naphthoyl group substituted at the indole-3 position. Fragments resulting from the loss of the naphthoyl and/or n-pentyl groups from the molecular radical cation yield the cations at m/z 318, 304, 248, and 178. The characteristic (M–17)+ fragment ion at m/z 358 resulting from the loss of OH radical is significant in the mass spectra of all these compounds with 1-naphthoyl groups substituted at the indole-3 position. The vapor phase infrared spectra provide a number of characteristic absorption bands to identify the individual isomers.
A Local Fingertips Movement and Fingertips Clustering Based Virtual Keyboard Adopting a Camera

With the development of virtual reality technology, human-computer interaction (HCI) changed from the traditional keyboard, mouse into many virtual methods. Different from the traditional virtual keyboard system recording and processing the all fingertips, our system pays attention to the keys been stroked, which means we only process the fingertip coordinates located in the key region. In addition, we also propose a fingertip extraction algorithm based on contour feature restriction and coordinate clustering. Compared to other virtual keyboard system, our system is simple but still effective. The extensive experiments demonstrate that our virtual keyboard system is flexible (only requires the camera in front of and above the keyboard to make sure the whole panel is detected by the camera), efficient (15 FPS on average, robust to cluttered backgrounds and placement between the camera and the paper keyboard, accurate (a 95.20% mean accuracy on 59 common used keys).
What can AI do for me?: evaluating machine learning interpretations in cooperative play

Machine learning is an important tool for decision making, but its ethical and responsible application requires rigorous vetting of its interpretability and utility: an understudied problem, particularly for natural language processing models. We propose an evaluation of interpretation on a real task with real human users, where the effectiveness of interpretation is measured by how much it improves human performance. We design a grounded, realistic human-computer cooperative setting using a question answering task, Quizbowl. We recruit both trivia experts and novices to play this game with computer as their teammate, who communicates its prediction via three different interpretations. We also provide design guidance for natural language processing human-in-the-loop settings.
Energetic constraints on the reproduction of female mantled howlers

The reproductive process of female primates is energetically constrained. However, while there is extensive evidence about factors that influence the maintenance of gestation and lactation, less is known about energetic correlates of cycling and the occurrence of conception in wild primates. We examined how female physical condition affected the occurrence of conception and interbirth intervals (IBI) in female mantled howler monkeys, a species in which females experience long non‐conceptive periods. For 6 years we followed 7 females at La Flor de Catemaco (Los Tuxtlas, Mexico). In addition to noting the presence of dependent immatures, we collected fecal samples that were analyzed for thyroid hormone and glucocorticoid metabolite concentrations (N = 1,460). Conception was more likely following months when females were not lactating and had higher thyroid hormone and lower glucocorticoid levels. IBIs were shorter when females had higher thyroid hormone and lower glucocorticoid levels, and when the infant at the beginning of the interval died. Due to their obvious impact on female fecundity and fertility, gestation and lactation are the stages of the reproductive process that have traditionally received more attention in studies of female reproductive performance. Still, the cycling stage accounts for a large proportion of IBIs in many primate species. Here we demonstrate that the reproductive rates of female mantled howler monkeys are energetically constrained: both the occurrence of conception and IBI are positively affected by female energetic condition.
Small mammal diversity of Mt. Kenya based on carnivore fecal and surface bone remains

Ecological dynamics and faunal diversity documentation is normally conducted by direct observation and trapping of live animals. However, surveys of carnivore scat prey and surface bone remains, which are relatively inexpensive, can provide complementary data that expand carnivore diet breadth and may improve accuracy regarding inferences of the ecological dynamics of a given ecosystem. We used this inexpensive method to document species diversity variation with elevation on the leeward (Sirimon) and windward (Chogoria) areas of Mt. Kenya. Bone and fecal specimens were opportunistically collected by walking 2 km in opposite directions from transect points selected at 200-m intervals along the elevational gradient of the study areas. We collected a total of 220 carnivore fecal and owl pellet specimens from both study sites, which were mainly deposited by the spotted hyena (Crocuta crocuta), leopard (Panthera pardus), serval (Leptailurus serval), genet (Genetta sp.), and Mackinder’s Cape owl (Bubo capensis mackinderi). Serval scats were the most common, followed by those of the spotted hyena. Scats and bones were found at the lowest density at the lowest elevations, peaked at mid-higher elevations, and then declined at the highest elevations. Based on skeletal analysis only, there were more species in Sirimon (19) than in Chogoria (12). Small fauna (rodents to duiker size bovids) formed the bulk of the identified remains, representing 87.9% of the Sirimon fauna and 90.9% of the Chogoria fauna. The genus Otomys was the dominant prey of the owl and serval in both sites. Three giraffe teeth were found at 3 500 m a.s. l. in Chogoria on the edge of Lake Ellis, suggesting that it is an occasional visitor to such high elevations. This study underscores the value of fecal and bone surveys in understanding the diet and diversity of mammals in ecological ecosystems, but such surveys should be complemented with analysis of hairs found in scats to obtain a more complete list of carnivore prey at Mt. Kenya.
Antiviral 4-Hydroxypleurogrisein and Antimicrobial Pleurotin Derivatives from Cultures of the Nematophagous Basidiomycete Hohenbuehelia grisea

4-Hydroxypleurogrisein, a congener of the anticancer-lead compound pleurotin, as well as six further derivatives were isolated from the basidiomycete Hohenbuehelia grisea, strain MFLUCC 12-0451. The structures were elucidated utilizing high resolution electron spray ionization mass spectrometry (HRESIMS) and 1D and 2D nuclear magnetic resonance (NMR) spectral data and evaluated for their biological activities; for leucopleurotin, we provide Xray data. While most congeners showed moderate antimicrobial and cytotoxic activity, 4-hydroxypleurogrisein emerged as an inhibitor of hepatitis C virus infectivity in mammalian liver cells.
Colorectal cancer susceptibility loci and influence on survival

Genome‐wide association studies (GWAS) have identified multiple single‐nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. To evaluate the potential influence of colorectal cancer susceptibility SNPs on disease prognosis, we investigated whether GWAS‐identified colorectal cancer risk SNPs and polygenic risk scores (PRSs) might be associated with survival among colorectal cancer patients. A total of 1374 colorectal cancer patients were recruited from the Korean National Cancer Center. For genotyping, 30 colorectal cancer‐susceptibility SNPs previously identified by GWAS were selected. The Cox proportional hazard model was used to evaluate associations of these risk SNPs and PRSs with disease‐free survival (DFS) and overall survival (OS). The prognostic values were compared between genetic and nongenetic models using Harrell's c index. During the follow‐up period (median: 88, 91 months for DFS and OS), 570 DFS (41.5%) and 487 OS (35.4%) events were observed. We found that 5 SNPs were significantly associated with DFS or OS among colorectal cancer patients at P < . 05: rs10936599 at 3q26.2 (MYNN), rs704017 at 10q22.3 (ZMIZ1‐AS1), rs11196172 at 10q25.2 (TCF7L2), rs3802842 at 11q23.1 (COLCA1‐2), and rs9929218 at 16q22.1 (CDH1). The PRSs constructed using these 5 SNPs were associated with worse survival (DFS: Ptrend = .02 unweighted PRS, Ptrend = .01 weighted PRS, OS: Ptrend = 3.7 × 10−3 unweighted, Ptrend = .02 weighted PRS). Our results suggest that several colorectal cancer susceptibility SNPs might also be related to survival by influencing disease progression.