Miracle-dz/UniFAR-FTUs huggingface dataset:
A survey of pulmonary nodule detection, segmentation and classification in computed tomography with deep learning techniques

Lung cancer is the top cause for deaths by cancers whose 5-year survival rate is less than 20%. To improve the survival rate of patients with lung cancers, the early detection and early diagnosis is significant. Furthermore, early detection of pulmonary nodules is essential for the detection and diagnosis of lung cancer in early stage. The National Lung Screening Trial (NLST) showed annual screening by low-dose computed tomography (LDCT) could help to reduce the deaths caused by lung cancer of high-risk subjects by 20% comparing with screening by chest radiography. In past decade, there has been lots of works on computer-aided detection (CADe) and computer-aided diagnosis (CADx) for pulmonary nodules in computed tomography (CT) scans, whose target is to detect, segment the nodules and further classify them into benign and malignant efficiently and precisely. This survey reviews some recent works on detection, segmentation and classification for pulmonary nodule in CT scans with deep learning techniques.
Mechanisms by which Bak and Bax permeabilise mitochondria during apoptosis

Mitochondrial outer membrane permeabilisation (MOMP) is the point of no return in many forms of apoptotic cell death. The killing effect of MOMP is twofold; it both initiates a proteolytic cascade of pro-apoptotic enzymes and damages mitochondrial function. Accordingly, prevention of MOMP can rescue cells from death. It is clear that either Bak or Bax, which are Bcl-2 family members, are required for MOMP to occur; however, the pore complexes that are formed by Bak and Bax remain poorly defined in terms of their composition, size, number and structure, as well as the mechanism by which they are regulated by other Bcl-2 family members. We recently reported that a key step leading to Bak homo-oligomerisation following an apoptotic stimulus involves transient exposure of the Bak BH3 domain before it binds to the hydrophobic groove of another activated Bak molecule to form a novel symmetric dimer. To form the higher-order oligomers that probably constitute the apoptotic pore complex, Bak dimers then interact via regions away from the BH3 domain and groove. The BH3:groove interaction within Bak homodimers supports a general model to explain the associations between Bcl-2 family members. In this Commentary, we discuss the implications of these findings for the regulation of apoptosis by Bcl-2 family proteins.
Incorporating tone-related MLP posteriors in the feature representation for Mandarin ASR

Overview Motivation • Tone has a crucial role in Mandarin speech • Tone depends on the F0 contour of a time span much longer than a frame; frame-level F0 and its derivatives only capture part of the tonal patterns Our approach • Use MLP with longer input window to extract tone-related posteriors as a better model of tone • Incorporate tone-related posteriors in feature vector Xin Lei, Mei-Yuh Hwang and Mari Ostendorf SSLI-LAB, Department of Electrical Engineering, University of Washington, Seattle, WA 98195
Neighbourhoods for Active Kids: study protocol for a cross-sectional examination of neighbourhood features and children's physical activity, active travel, independent mobility and body size

Introduction New Zealand children's physical activity, including independent mobility and active travel, has declined markedly over recent decades. The Neighbourhoods for Active Kids (NfAK) study examines how neighbourhood built environments are associated with the independent mobility, active travel, physical activity and neighbourhood experiences of children aged 9–12 years in primary and intermediate schools across Auckland, New Zealand's largest city. Methods and analysis Child-specific indices of walkability, destination accessibility and traffic exposure will be constructed to measure the built environment in 8 neighbourhoods in Auckland. Interactive online-mapping software will be used to measure children's independent mobility and transport mode to destinations and to derive measures of neighbourhood use and perceptions. Physical activity will be measured using 7-day accelerometry. Height, weight and waist circumference will be objectively measured. Parent telephone interviews will collect sociodemographic information and parent neighbourhood perceptions. Interviews with school representative will capture supports and barriers for healthy activity and nutrition behaviours at the school level. Multilevel modelling approaches will be used to understand how differing built environment variables are associated with activity, neighbourhood experiences and health outcomes. Discussion We anticipate that children who reside in neighbourhoods considered highly walkable will be more physically active, accumulate more independent mobility and active travel, and be more likely to have a healthy body size. This research is timely as cities throughout New Zealand develop and implement plans to improve the liveability of intensifying urban neighbourhoods. Results will be disseminated to participants, local government agencies and through conventional academic avenues.
Structurally Altered Peptides Reveal an Important Role for N-terminal Heptad Repeat Binding and Stability in the Inhibitory Action of HIV-1 Peptide DP178*

Human immunodeficiency virus 1 gp41 folds into a six-helix bundle whereby three C-terminal heptad repeat regions pack in an anti-parallel manner against the coiled-coil formed by three N-terminal heptad repeats (NHR). Peptides that inhibit bundle formation contributed significantly to the understanding of the entry mechanism of the virus. DP178, which partially overlaps C-terminal heptad repeats, prevents bundle formation through an undefined mechanism; additionally it has been suggested to bind other ENV regions and arrest fusion in an unknown manner. We used two structurally altered DP178 peptides; in each, two sequential amino acids were substituted into their d configuration, d-SQ in the hydrophilic N-terminal region and d-LW in the hydrophobic C-terminal. Importantly, we generated an elongated NHR peptide, N54, obtaining the full N-helix docking site for DP178. Interestingly, d-LW retained wild type fusion inhibitory activity, whereas d-SQ exhibited significantly reduced activity. In correlation with the inhibitory data, CD spectroscopy and fluorescence studies revealed that all the DP178 peptides interact with N54, albeit with different stabilities of the bundles. We conclude that strong binding of DP178 N-terminal region to the endogenous NHR, without significant contribution of the C-terminal sequence of DP178 to core formation, is vital for DP178 inhibition. The finding that d-amino acid incorporation in the C terminus did not affect activity or membrane binding as revealed by surface plasmon resonance correlates with an additional membrane binding site, or membrane anchoring role, for the C terminus, which works synergistically with the N terminus to inhibit fusion.
The E‐cadherin gene is silenced by CpG methylation in human oral squamous cell carcinomas

Reduction of E‐cadherin strongly relates to invasiveness and metastasis in vitro. To clarify CpG methylation around the promoter region of the E‐cadherin gene in oral squamous cell carcinoma (SCC), we examined the DNA samples of various human SCC cell lines and primary oral SCC tissues by methylation‐specific polymerase chain reaction (MSP). CpG methylation of the E‐cadherin gene markedly correlated to the reduction of E‐cadherin expression in human oral SCC cell lines. In primary oral SCC tissues, only 1 of 5 preserved E‐cadherin‐expressing tissues was methylated, whereas methylation was found in 17 (94.4%) of 18 E‐cadherin‐reduced tissues. Our results suggest that reduction of E‐cadherin expression is associated with CpG methylation of the E‐cadherin gene promoter. We recently established two cell lines with high and low metastatic potential, UM1 and UM2, from SCC primary tongue tissue of a patient. E‐cadherin expression of high‐metastatic UM1 was clearly lower than that of low‐metastatic UM2, and MSP results showed CpG methylation in the UM1 but not the UM2 cell line. To investigate whether demethylation of CpG methylation of the E‐cadherin gene could restore expression and function of E‐cadherin, we treated UM1 with the demethylating agent 5‐azacytidine (5‐aza) and found that E‐cadherin expression was indeed restored by demethylation. Moreover, in the demethylated UM1, invasion of the collagen gel was clearly suppressed compared with the untreated UM1. These results suggested that inactivation of E‐cadherin expression resulted from CpG methylation of the gene promoter; a correlation between CpG methylation of the E‐cadherin gene promoter and invasive potential was also suggested. © 2001 Wiley‐Liss, Inc.
Real-time wireless OFDM communication in THz-band using optical dft processing

Real-time THz-wave wireless OFDM communication, which is assisted by optical technology, is reported. A 4 × 10 Gbit/s THz-wave OFDM signal is transferred into an optical OFDM signal, and the optical OFDM signal is successfully demultiplexed into four sub-carrier channels with an integrated-optic DFT circuit.
MODS: Multiple One-class Data Streams Learning from Homogeneous Data

This paper presents a novel approach, called MODS, to build an accurate time evolving classifier from multiple one-class data streams learning time evolving classifier. Our proposed MODS approach works in two steps. In the first step, we first construct local one-class classifiers on the labeled positive examples from each sub-data stream respectively. We then collect the informative examples (support vectors) around each local one-class classifier, which can support the decision boundary of the classifier. This is called support vector preservation principle. In the second step, we construct a global one-class classifier on the collected informative examples. By using the support vector preservation principle, our proposed MODS explicitly addresses the problem of building accurate classifier from multiple one-class data streams. Extensive experiments on real life data streams have demonstrated that our MODS approach can achieve high performance and efficiency for the multiple one-class data streams learning in comparison with other approaches.
Improving Nutrition, Physicochemical and Antioxidant Properties of Rice Noodles with Fiber and Protein-rich Fractions Derived from Cassava Leaves

Introduction: Noodles are rich in fibre and important nutrients which help promote health. This study was an attempt to determine the impacts of using different levels of cassava leaves on antioxidant features, nutritional values, and the quality of rice noodles. Methods: Wheat flour and rice were used to prepare rice noodles which used cassava leaves which were on the basis of flour weight (0, 10, 20, 30 and 40%). The proximate analysis, antioxidant activities, texture, color, and total cyanide content of the noodles were then determined. Results: The present findings suggest that using cassava leaves at different levels helps modify the structure of the noodles, finally leading to a softer product in comparison with the control samples. Furthermore, the addition of cassava leaves increased the amount of protein and fiber content and improved the antioxidant activities of rice noodles. Conclusion: It could be implied that cassava leaves with a lot of advantageous components -could be a great ingredient to enhance antioxidant features and nutritional value (protein and fiber) of noodle.
WHY BREEDING TIME HAS NOT RESPONDED TO SELECTION FOR EARLIER BREEDING IN A SONGBIRD POPULATION

Abstract A crucial assumption underlying the breeders' equation is that selection acts directly on the trait of interest, and not on an unmeasured environmental factor which affects both fitness and the trait. Such an environmentally induced covariance between a trait and fitness has been repeatedly proposed as an explanation for the lack of response to selection on avian breeding time. We tested this hypothesis using a long-term dataset from a Dutch great tit (Parus major) population. Although there was strong selection for earlier breeding in this population, egg-laying dates have changed only marginally over the last decades. Using a so-called animal model, we quantified the additive genetic variance in breeding time and predicted breeding values for females. Subsequently, we compared selection at the phenotypic and genetic levels for two fitness components, fecundity and adult survival. We found no evidence for an environmentally caused covariance between breeding time and fitness or counteracting selection on the different fitness components. Consequently, breeding time should respond to selection but the expected response to selection was too small to be detected.
Confidence in risk assessments

Risk is assessed with varying degrees of confidence, and the degree of confidence is relevant to the risk manager. The paper proposes an operational framework for representing confidence, based on an expert's current beliefs about how her beliefs might be different in the future. Two modelling simplifications, ‘no unknown unknowns’ and a homogeneous Poisson process, make this framework trivial to apply. This is illustrated for assessing an exceedance probability for a large event, with volcanic risk as a specific example. The paper ends with a discussion about risk and confidence assessments for national scale risk assessment, including several further illustrations.
Blood eosinophilia in chronic obstructive pulmonary disease: is there a relation with airway eosinophilia?

Background Blood eosinophilia was considered an indicator of sputum eosinophilia in asthmatic patients. Nevertheless, its role in chronic obstructive pulmonary disease (COPD) was not completely examined. Aim The aim was to investigate if peripheral blood eosinophilic cells represent an indicator (marker) of eosinophilia of the airway in stable cases. Patients and methods The trial was held at Al-Azhar University Hospital (Damietta), between October 2015 and March 2017. It included 264 persons with stable COPD. All cases were assessed for demographic features, smoking history, history of exacerbation in the last year, dyspnea, associated comorbidities, quality of life, lung functions, sputum, and peripheral blood eosinophilic cell counts. The included participants were allocated into two sets: group with eosinophilia (n=76) and patients without eosinophilia (n=188). Results There was proportional correlation between eosinophilia of the blood and sputum; and blood eosinophilia can differentiate between cases who had or had no sputum eosinophilia at a cutoff of 2.5%. In addition, eosinophil/lymphocyte ratio and eosinophil/neutrophil ratio were higher in eosinophilic COPD and are associated ELR with eosinophilia of the sputum ENR. Conclusion There is correlation between eosinophils of the peripheral blood and sputum in stable cases. Thus, the count of blood eosinophil may act as a dependable marker for eosinophilic COPD
Deconvoluting complex tissues for expression quantitative trait locus-based analyses

Breast cancer genome-wide association studies have pinpointed dozens of variants associated with breast cancer pathogenesis. The majority of risk variants, however, are located outside of known protein-coding regions. Therefore, identifying which genes the risk variants are acting through presents an important challenge. Variants that are associated with mRNA transcript levels are referred to as expression quantitative trait loci (eQTLs). Many studies have demonstrated that eQTL-based strategies provide a direct way to connect a trait-associated locus with its candidate target gene. Performing eQTL-based analyses in human samples is complicated because of the heterogeneous nature of human tissue. We addressed this issue by devising a method to computationally infer the fraction of cell types in normal human breast tissues. We then applied this method to 13 known breast cancer risk loci, which we hypothesized were eQTLs. For each risk locus, we took all known transcripts within a 2 Mb interval and performed an eQTL analysis in 100 reduction mammoplasty cases. A total of 18 significant associations were discovered (eight in the epithelial compartment and 10 in the stromal compartment). This study highlights the ability to perform large-scale eQTL studies in heterogeneous tissues.
Robust Sign Language Recognition System Using ToF Depth Cameras

Sign language recognition is a difficult task, yet required for many applications in real-time speed. Using RGB cameras for recognition of sign languages is not very successful in practical situations and accurate 3D imaging requires expensive and complex instruments. With introduction of Time-of-Flight (ToF) depth cameras in recent years, it has become easier to scan the environment for accurate, yet fast depth images of the objects without the need of any extra calibrating object. In this paper, a robust system for sign language recognition using ToF depth cameras is presented for converting the recorded signs to a standard and portable XML sign language named SiGML for easy transferring and converting to real-time 3D virtual characters animations. Feature extraction using moments and classification using nearest neighbor classifier are used to track hand gestures and significant result of 100% is achieved for the proposed approach.
Structure of HrcQB-C, a conserved component of the bacterial type III secretion systems

Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. In addition, type III secretion systems are also required for biogenesis of the bacterial flagellum. The HrcQB protein, a component of the secretion apparatus of Pseudomonas syringae with homologues in all type III systems, has a variable N-terminal and a conserved C-terminal domain (HrcQB-C). Here, we report the crystal structure of HrcQB-C and show that this domain retains the ability of the full-length protein to interact with other type III components. A 3D analysis of sequence conservation patterns reveals two clusters of residues potentially involved in protein–protein interactions. Based on the analogies between HrcQB and its flagellum homologues, we propose that HrcQB-C participates in the formation of a C-ring-like assembly.
Artificial neural network algorithm for online glucose prediction from continuous glucose monitoring.

BACKGROUND AND AIMS Continuous glucose monitoring (CGM) devices could be useful for real-time management of diabetes therapy. In particular, CGM information could be used in real time to predict future glucose levels in order to prevent hypo-/hyperglycemic events. This article proposes a new online method for predicting future glucose concentration levels from CGM data. METHODS The predictor is implemented with an artificial neural network model (NNM). The inputs of the NNM are the values provided by the CGM sensor during the preceding 20 min, while the output is the prediction of glucose concentration at the chosen prediction horizon (PH) time. The method performance is assessed using datasets from two different CGM systems (nine subjects using the Medtronic [Northridge, CA] Guardian and six subjects using the Abbott [Abbott Park, IL] Navigator. Three different PHs are used: 15, 30, and 45 min. The NNM accuracy has been estimated by using the root mean square error (RMSE) and prediction delay. RESULTS The RMSE is around 10, 18, and 27 mg/dL for 15, 30, and 45 min of PH, respectively. The prediction delay is around 4, 9, and 14 min for upward trends and 5, 15, and 26 min for downward trends, respectively. A comparison with a previously published technique, based on an autoregressive model (ARM), has been performed. The comparison shows that the proposed NNM is more accurate than the ARM, with no significant deterioration in the prediction delay. CONCLUSIONS The proposed NNM is a reliable solution for the online prediction of future glucose concentrations from CGM data.
Characterization of genetically inactivated pertussis toxin mutants: candidates for a new vaccine against whooping cough

the introduction of two amino acid substitutions within the enzymatically active subunit S1 of pertussis toxin (PT) abolishes its ADP-ribosyltransferase activity and toxicity on CHO cells (Pizza et al., Science 246:497-500, 1989). These genetically inactivated molecules are also devoid of other in vivo adverse reactions typical of PT, such as induction of leukocytosis, potentiation of anaphylaxis, stimulation of insulin secretion, and histamine sensitivity. However, the mutant PT molecules are indistinguishable from wild-type PT in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and maintain all the physical and chemical properties of PT, including affinity for toxin-neutralizing poly- and monoclonal antibodies. Either alone or stabilized with formaldehyde, PT mutants are able to induce high levels of neutralizing antibodies and to protect mice in a dose-dependent fashion against intracerebral challenge with virulent B. pertussis. These results clearly show that these genetically inactivated PT molecules are nontoxic but still immunogenic and justify their development as a component of a new, safer acellular vaccine against whooping cough.
"Will Check-in for Badges": Understanding Bias and Misbehavior on Location-Based Social Networks

Social computing researchers are using data from location-based social networks (LBSN), e.g., "Check-in" traces, as approximations of human movement. Recent work has questioned the validity of this approach, showing large discrepancies between check-in data and actual user mobility. To further validate and understand such discrepancies, we perform a crowdsourced study of Foursquare users that seeks to a) quantify bias and misrepresentation in check-in datasets and the impact of self-selection in prior studies, and b) understand the motivations behind misrepresentation of check-ins, and the potential impact of any system changes designed to curtail such misbehavior. Our results confirm the presence of significant misrepresentation of location check-ins on Foursquare. They also show that while "extraneous" check-ins are motivated by external rewards provided by the system, "missing" check-ins are motivated by personal concerns such as location privacy. Finally, we discuss the broader implications of our findings to the use of check-in datasets in future research on human mobility.
Communities , Schools , and Teachers

• Two definitions of community—as neighborhoods and as social networks— relate to students' education outcomes. • Three factors have changed the composition and structure of U.S. communities. • There are benefits and challenges with school-community collaboration. • Teachers can become agents for community responsiveness in schools. Children develop and learn within complex systems that include their families , schools, and communities (Bronfenbrenner, 1994). Epstein (2011) contends that when there is overlap between and among caring adults in students' families , schools, and communities, or "spheres of influence," students' learning and development are enhanced. This theory has been supported by over two decades of research showing the quantitative and qualitative impact of family and community engagement on students' learning and achievement In this chapter, we focus specifically on the relationship between communities and schools, which has been an enduring topic in the field of education. It was central in the work of Dewey (1976) and remains a critical component in constructivist approaches to learning and in reform initiatives such as integrated services in schools (Sanders & Hembrick-Roberts, 2013). We also describe how teachers can serve as agents for community responsiveness within schools through collaborative and inclusive professional practices.