Miracle-dz/UniFAR-FTUs huggingface dataset:
Small Molecule Immunosensing Using Surface Plasmon Resonance

Surface plasmon resonance (SPR) biosensors utilize refractive index changes to sensitively detect mass changes at noble metal sensor surface interfaces. As such, they have been extensively applied to immunoassays of large molecules, where their high mass and use of sandwich immunoassay formats can result in excellent sensitivity. Small molecule immunosensing using SPR is more challenging. It requires antibodies or high-mass or noble metal labels to provide the required signal for ultrasensitive assays. Also, it can suffer from steric hindrance between the small antigen and large antibodies. However, new studies are increasingly meeting these and other challenges to offer highly sensitive small molecule immunosensor technologies through careful consideration of sensor interface design and signal enhancement. This review examines the application of SPR transduction technologies to small molecule immunoassays directed to different classes of small molecule antigens, including the steroid hormones, toxins, drugs and explosives residues. Also considered are the matrix effects resulting from measurement in chemically complex samples, the construction of stable sensor surfaces and the development of multiplexed assays capable of detecting several compounds at once. Assay design approaches are discussed and related to the sensitivities obtained.
Molecular characteristics and pathogenic assessment of porcine epidemic diarrhoea virus isolates from the 2018 endemic outbreaks on Jeju Island, South Korea

Abstract Since the 2013–2014 incursion of the virulent G2b porcine epidemic diarrhoea virus (PEDV) pandemic strains in South Korea, frequent moderate‐scale regional outbreaks have recurred. In particular, areas of Jeju Island with extensive swine production have faced repeated epidemics since the re‐emergence in 2014. The current study reports the complete genome sequences and molecular characterization of the representative PEDV strains responsible for the 2018 endemic outbreaks on Jeju Island. All isolates were determined to belong genetically to the highly pathogenic pandemic G2b group. Full‐length genome sizes of four isolates differed from that of the G2b epidemic field strain due to insertion or deletion (DEL) mutations in the non‐structural protein (nsp)‐ or spike (S) protein‐coding regions. The 2018 Jeju isolates shared 96.7%–98.7% and 98.5%–99.4% identity at the S gene and whole‐genome levels, respectively, compared to global G2b PEDV strains. Genetic and phylogenetic analyses indicated that the 2018 isolates were closest to the 2014 G2b re‐emergent Jeju strains, but appeared to have undergone substantial rapid independent evolution. Among the isolates, a notable nsp3 DEL variant strain, KOR/KNU‐1807/2018, was isolated and propagated by continuous passages in Vero cells, and displayed typical PEDV‐induced syncytia formation. Genomic sequencing identified a unique 8‐nt DEL in the extreme C‐terminal region of the S gene at the 4th passage (KNU‐1807‐P4) compared to its original sample. This DEL resulted in the premature termination of S by nine amino acid residues (EVFEKVHVQ), which contained a KxHxx motif that is a potential endoplasmic reticulum retrieval signal. In vivo animal studies showed that variant strain KNU‐1807 had decreased virulence in suckling piglets. These results advance our knowledge regarding the genetic variation and pathogenicity of the G2b PEDV endemic strains prevalent in Jeju swine herds in South Korea.
Imaging Performance for Two Row–Column Arrays

This study evaluates the volumetric imaging performance of two prototyped 62 + 62 row–column-addressed (RCA) 2-D array transducer probes using three synthetic aperture imaging (SAI) emission sequences and two different beamformers. The probes are fabricated using capacitive micromachined ultrasonic transducer (CMUT) and piezoelectric transducer (PZT) technology. Both have integrated apodization to reduce ghost echoes and are designed with similar acoustical features, i.e., 3-MHz center frequency, $\lambda $ /2 pitch, and $24.8\times 24.8\,\,\text {mm}^{2}$ active footprint. Raw RF data are obtained using an experimental research ultrasound scanner, SARUS. The SAI sequences are designed for imaging down to 14 cm at a volume rate of 88 Hz. Two beamforming methods, spatial matched filtering and row–column adapted delay-and-sum, are used for beamforming the RF data. The imaging quality is investigated through simulations and phantom measurements. Both probes on average have similar lateral full-width at half-maximum (FWHM) values, but the PZT probe has 20% smaller cystic resolution values and 70% larger contrast-to-noise ratio (CNR) compared to the capacitive micromachined ultrasonic transducer (CMUT) probe. The CMUT probe can penetrate down to 15 cm, and the PZT probe down to 30 cm. The CMUT probe has 17% smaller axial FWHM values. The matched filter focusing shows an improved B-mode image for measurements on a cyst phantom with an improved speckle pattern and better visualization of deeper lying cysts. The results of this study demonstrate the potentials of RCA 2-D arrays against fully addressed 2-D arrays, which are low channel count (e.g., 124 instead of 3844), low acoustic intensity mechanical index (MI ≤ 0.88 and spatial-peak-temporal-average intensity $I_{\text {spta}}\leq 5.5~\text {mW/cm}^{2}$ ), and high penetration depth (down to 30 cm), which makes 3-D imaging at high volume rates possible with equipment in the price range of conventional 2-D imaging.
Mechanistic modeling of vertebrate spatial contrast sensitivity and acuity at low luminance

Abstract The validity of the Barten theoretical model for describing the vertebrate spatial contrast sensitivity function (CSF) and acuity at scotopic light levels has been examined. Although this model (which has its basis in signal modulation transfer theory) can successfully describe vertebrate CSF, and its relation to underlying visual neurophysiology at photopic light levels, significant discrepancies between theory and experimental data have been found at scotopic levels. It is shown that in order to describe scotopic CSF, the theory must be modified to account for important mechanistic changes, which occur as cone vision switches to rod vision. These changes are divided into photon management factors [changes in optical performance (for a dilated pupil), quantum efficiency, receptor sampling] and neural factors (changes in spatial integration area, neural noise, and lateral inhibition in the retina). Predictions of both scotopic CSF and acuity obtained from the modified theory were found to be in good agreement with experimental values obtained from the human, macaque, cat, and owl monkey. The last two species have rod densities particularly suited for scotopic conditions.
Component based localization in sparse wireless ad hoc and sensor networks

Localization is crucial for wireless ad hoc and sensor networks. As the distance-measurement ranges are often less than that of the communication range for many ranging systems, most communication-dense wireless networks are often localization-sparse. Consequently, most existing algorithms fail to provide accurate localization supports. In order to address this issue, by introducing a concept of component, we propose to group nodes into components, so that nodes are able to better share their ranging and anchor knowledge. This design, CALL, relaxes two essential restrictions in localization: node ordering and anchor distribution. We evaluate the effectiveness of CALL through extensive simulations. The results show that CALL locates 80% nodes in a network with average degree 7.5 and 5% percent anchors, which outperforms the state of the art design Sweeps about 20%.
A Bayesian network approach combining pitch and spectral envelope features to reduce channel mismatch in speaker verification and forensic speaker recognition

The aim of this paper is to reduce the effect of mismatch in recording conditions due to the transmission channel and recording device, using conditional dependencies of prosodic and spectral envelope features. The developed system is based on a Bayesian network framework which combines statistical models of the pitch and spectral envelope features. This approach is applied to forensic automatic speaker recognition, where mismatched recording conditions pose a serious problem to the accurate estimation of the strength of voice evidence. The method is evaluated using a forensic speaker recognition database that contains three different recording conditions typical to forensic tasks. The performance of the system is evaluated using both speaker verification as well as forensic speaker recognition measures.
Markov Random Fields for Information Extraction

In the automatic processing of languages, the ideal is to provide computers with the means to understand the texts, aiming to, little by little, leave it to the more modest and pragmatic objectives, which are formulated as specific tasks. The information extraction is typically one of these tasks. It aims to identify the factual information elements within a document, where the elements correspond to the fields that are previously defined from a form. In a way, it aims to fill the void that exists between the manner in which the humans apprehend the information, where the comprehension of natural languages plays a large part, and the manner in which computers process them, in other words in the form of typed data ordered in the structured files or in databases. In a review article on the subject, McCallum discusses an information distillation format [MCC 05]. To achieve such a task, several methods have been used. Since this is more and more the case for the set of linguistic engineering, these are the statistical models which are currently the most efficient. This is true only when we correctly reformulate the task such as an annotation or labeling problem. The best statistical models capable of learning data annotation are or crf, Conditional Random Fields Markov random fields or conditional random fields (CRFs). This chapter is an occasion to present the information extraction task and the statistical labeling models. The first two sections concentrate on the task, by discussing Chapter written by Isabelle Tellier and Marc Tommasi.
lnc-PKD2-2-3, identified by long non-coding RNA expression profiling, is associated with pejorative tumor features and poor prognosis, enhances cancer stemness and may serve as cancer stem-cell marker in cholangiocarcinoma

The present study aimed to explore the long non-coding RNA (lncRNA) expression profiles and correlation of lnc-PKD2-2-3 with tumor features and prognosis, and to investigate its effect on regulating cancer-cell stemness and its potential as a cancer stem cell (CSC) marker in cholangiocarcinoma (CCA). lncRNA expression profiles were determined in 3 pairs of CCA tumors and adjacent tissues by microarray analysis, and lnc-PKD2-2-3 expression was then validated in 60 paired samples by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Expression of common CSC markers [(CD44, CD133 and octamer-binding transcription factor 4 (OCT4)], CD44+CD133+ cell proportions, sphere formation efficiency and drug resistance to 5-fluorouracil (5-FU) were measured following ectopic overexpression of lnc-PKD2-2-3 or silencing via small hairpin RNA lentivirus transfection into the TFK-1 and Huh-28 CCA cell lines. Finally, lnc-PKD2-2-3 expression was measured in CCA stem-like cells and normal CCA cells. The results from the microarray analysis identified a total of 4,223 upregulated and 4,596 downregulated lncRNAs between CCA tumor tissue and paired adjacent tissue, which were enriched in regulating cancer-associated pathways. RT-qPCR validation revealed that lnc-PKD2-2-3 was upregulated in CCA and associated with a higher Eastern Cooperative Oncology Group performance score, poor differentiation, advanced TNM stage, increased carcinoembryonic antigen and poor overall survival in CCA patients. In vitro, lnc-PKD2-2-3 increased CD44, CD133 and OCT4 expression as well as the CD44+CD133+ cell proportion, raised the sphere formation efficiency and enhanced drug resistance to 5-FU in TFK-1 and Huh-28 cells. In addition, lnc-PKD2-2-3 was positively correlated with CSC markers in CCA tumor tissues and was markedly upregulated in CCA stem-like cells compared with that in normal CCA cells. In conclusion, lnc-PKD2-2-3, selected by lncRNA expression profiling, was associated with pejorative tumor features and poor prognosis, enhanced cancer stemness and may serve as a CSC marker in CCA.
Unprecedented Parallel Photosynthetic Losses in a Heterotrophic Orchid Genus

Abstract Heterotrophic plants are evolutionary experiments in genomic, morphological, and physiological change. Yet, genomic sampling gaps exist among independently derived heterotrophic lineages, leaving unanswered questions about the process of genome modification. Here, we have sequenced complete plastid genomes for all species of the leafless orchid genus Hexalectris, including multiple individuals for most, and leafy relatives Basiphyllaea and Bletia. Our objectives are to determine the number of independent losses of photosynthesis and to test hypotheses on the process of genome degradation as a result of relaxed selection. We demonstrate four to five independent losses of photosynthesis in Hexalectris based on degradation of the photosynthetic apparatus, with all but two species displaying evidence of losses, and variation in gene loss extending below the species level. Degradation in the atp complex is advanced in Hexalectris warnockii, whereas only minimal degradation (i.e., physical loss) has occurred among some “housekeeping” genes. We find genomic rearrangements, shifts in Inverted Repeat boundaries including complete loss in one accession of H. arizonica, and correlations among substitutional and genomic attributes. Our unprecedented finding of multiple, independent transitions to a fully mycoheterotrophic lifestyle in a single genus reveals that the number of such transitions among land plants is likely underestimated. This study underscores the importance of dense taxon sampling, which is highly informative for advancing models of genome evolution in heterotrophs. Mycoheterotrophs such as Hexalectris provide forward-genetic opportunities to study the consequences of radical genome evolution beyond what is possible with mutational studies in model organisms alone.
An investigation into the effect of pitch transformation on children speech recognition

The degradation in the automatic speech recognition performance of the adult speech trained models for children speech data is a well known problem. In this work, motivated by the voice conversion approaches for addressing the acoustic mis-match between the adult and children speech, we investigated the effect of pitch transformation on children speech on telephone-based connected digit recognition task. Our preliminary results indicate that the effect of pitch transformation on the recognition performance of the children speech varies with their average pitch values. With the reduction of pitch, an improvement of 10% was observed in the speech recognition performance for children having pitch values more than 300 Hz. We have also proposed an explanation for this performance improvement based on the study of filter-bank smoothing in front-end signal processing.
[Poster] The posture angle threshold between airplane and window frame metaphors

Integrating different mental models and the corresponding interaction techniques for navigation and object manipulation tasks is a topic of concern for providing user interfaces for the wide variety of potential users. With a user controlled, egocentric hand-held device we aim at integrating the so far identified three major interaction techniques based on the metaphors of a steering wheel, a toy airplane and a window frame. Here, specifically the toy airplane and the window frame contradict each other, leaving the issue at which postural angle of the hand-held device the mental model of the users changes.
Satellite: Joint Analysis of CDNs and Network-Level Interference

Satellite is a methodology, tool chain, and data-set for understanding global trends in website deployment and accessibility using only a single or small number of standard measurement nodes. Satellite collects information on DNS resolution and resource availability around the Internet by probing the IPv4 address space. These measurements are valuable in their breadth and sustainability - they do not require the use of a distributed measurement infrastructure, and therefore can be run at low cost and by multiple organizations. We demonstrate a clustering procedure which accurately captures the IP footprints of CDN deployments, and then show how this technique allows for more accurate determination of correct and incorrect IP resolutions. Satellite has multiple applications. It reveals the prevalence of CDNs by showing that 20% of the top 10,000 Alexa domains are hosted on shared infrastructure, and that CloudFlare alone accounts for nearly 10% of these sites. The same data-set detects 4,819 instances of ISP level DNS hijacking in 117 countries.
Early Olfactory Environment Influences Antennal Sensitivity and Choice of the Host-Plant Complex in a Parasitoid Wasp

Early experience of olfactory stimuli associated with their host–plant complex (HPC) is an important driver of parasitoid foraging choices, notably leading to host fidelity. Mechanisms involved, such as peripheral or central modulation, and the impact of a complex olfactory environment are unknown. Using olfactometer assays, we compared HPC preference of Aphidius ervi Haliday (Hymenoptera:Braconidae) females originating from two different HPCs, either with the other HPC in close vicinity (complex environment) or without (simple environment). We also investigated antennal responses to volatiles differentially emitted by the two respective HPCs. In a simple environment, HPC of origin had an influence on olfactory choice, but the preferences observed were asymmetric according to parasitoid origin. Electroantennographic recordings revealed significant sensitivity differences for some of the tested individual volatiles, which are emitted differentially by the two HPCs. Besides, presence of an alternative HPC during early stages modified subsequent parasitoid preferences. We discuss how increased olfactory complexity could influence parasitoid host foraging and biological control in diversified cropping systems.
Can curriculum design influence medical students’ attitudes to psychiatry? A comparison of two different approaches

Abstract Medical students with poor attitudes toward psychiatry are unlikely to choose it as a career, and current psychiatry recruitment is inadequate for future NHS needs. Amending medical school curricula has been suggested as one solution. We performed a unique naturalistic mixed-methods cross-sectional survey of two sequential cohorts in a UK medical school, before and after the restructuring of the entire MBChB curriculum. As well as increasing integration with other specialties, the emphasis placed on psychiatry increased throughout the course, but the final psychiatry block reduced from 8 to 6 weeks. Students experiencing the refreshed curriculum had better attitudes to psychiatry and psychiatric patients and were more positive about psychiatry as a career for themselves and others, compared to students on the old curriculum. This was demonstrated both quantitatively using validated rating scales (12/30 questions ATP-30 and 1/6 questions PEAK-6) and qualitatively using free-text responses. Restructuring undergraduate medical curricula to enhance integration may yield added value, including the potential to improve attitudes to specialties previously learned in silos, such as psychiatry. This may improve recruitment and the understanding of mental health for all future doctors.
NONMEM Tutorial Part I: Description of Commands and Options, With Simple Examples of Population Analysis

In this tutorial, the various components of NONMEM will be described, and the basic steps of setting up NONMEM control stream files and data files will be demonstrated. Some basic concepts of nonlinear mixed effects modeling will be discussed, along with simple examples demonstrating how to use NONMEM to perform population analysis of clinical data.
Lgr6 Marks Stem Cells in the Hair Follicle That Generate All Cell Lineages of the Skin

Hair Today, Skin Tomorrow The epidermis of mammals contains hair follicles, sebaceous glands, and interfollicular epidermis, but it has not been clear how the development and repair of these structures is regulated. Snippert et al. (p. 1385) show that a stem-cell cluster in the hair follicle, characterized by the expression of Lgr6, a close homolog of the Lgr5 marker for stem cells in the small intestine and colon, resides directly above the hair bulge and gives rise to all cell lineages of the skin. Skin wounds in adult mice are repaired by Lgr6 stem cells in the hair follicles that flank the damage. After hair morphogenesis, Lgr6 stem cells give rise to epidermal and sebaceous gland lineages to generate fully differentiated new skin. Skin wounds can be repaired by primitive stem cells into fully differentiated tissue, complete with hairs and sebaceous glands. Mammalian epidermis consists of three self-renewing compartments: the hair follicle, the sebaceous gland, and the interfollicular epidermis. We generated knock-in alleles of murine Lgr6, a close relative of the Lgr5 stem cell gene. Lgr6 was expressed in the earliest embryonic hair placodes. In adult hair follicles, Lgr6+ cells resided in a previously uncharacterized region directly above the follicle bulge. They expressed none of the known bulge stem cell markers. Prenatal Lgr6+ cells established the hair follicle, sebaceous gland, and interfollicular epidermis. Postnatally, Lgr6+ cells generated sebaceous gland and interfollicular epidermis, whereas contribution to hair lineages gradually diminished with age. Adult Lgr6+ cells executed long-term wound repair, including the formation of new hair follicles. We conclude that Lgr6 marks the most primitive epidermal stem cell.
High expression of DLC family proteins predicts better prognosis and inhibits tumor progression in NSCLC

The incidence of primary lung cancer (PLC) is increasing and is becoming a leading cause of cancer-associated mortality worldwide. Non-small cell lung cancer (NSCLC) accounts for ~80% of PLC cases and has the worst prognosis among malignant tumors. Deleted in liver cancer (DLC) proteins belong to the RhoGTPase-activating protein family and are considered to be tumor suppressor genes. However, the role of the proteins, particularly DLC2 and DLC3, in NSCLC, has not been fully elucidated. The present study investigated the expression levels and prognostic values of DLCs in NSCLC using The Cancer Genome Atlas, the Genotype-Tissue Expression project and Kaplan-Meier plotter datasets. The current study demonstrated that the three DLCs were downregulated in NSCLC. High expression levels of DLC1 and DLC2 were associated with an improved survival in NSCLC. Additionally, the effects of DLCs on the proliferation and apoptosis of the lung cancer cell line A-549 were investigated in vitro using a Cell Counting Kit-8 assay and flow cytometry analysis. DLC2 and DLC3 overexpression inhibited proliferation and induced apoptosis in A549 cells. To the best of our knowledge, the current study was the first to investigate the expression level and prognostic values of DLC2 and DLC3 in NSCLC. The results indicated that DLC1 DLC2 and DLC3 serve specific roles in the occurrence and development of NSCLC, and may be considered as potential prognostic indicators in NSCLC.