Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of SDF1 in prostate epithelial morphogenesis

Androgens induce rat prostate induction from the urogenital sinus epithelium at embryonic day 17.5. Subsequent morphogenesis, including epithelial cord growth, branching, and canalization, results from concerted paracrine interactions with the stroma. A significant number of paracrine factors bind heparan sulfate (HS). We hypothesized that interfering with overall sulfation could disrupt the signaling mediated by HS‐binding factors and that the undersulfated environment would allow investigation of individual exogenous morphogens. First, we investigated whether acinar morphogenesis involved HS‐proteoglycan expression and found that syndecans 1 and 3 were upregulated in RWPE1 cells in the transition from two‐ to three‐dimensional (3D) Matrigel, capable of promoting spheroid formation. We then investigated whether sodium chlorate, a general sulfation inhibitor, interfered with spheroid formation by RWPE1 cells and acinar morphogenesis in ex vivo ventral prostate (VP) organ culture. As expected, treatment with sodium chlorate inhibited spheroid formation by RWPE1 cells in 3D culture. Chlorate also inhibited ex vivo VP epithelial branching and canalization, resulting in long branchless epithelial structures. We then investigated whether the HS‐binding factors, FGF10, TGFβ1, and SDF1, could reverse the effect of sodium chlorate. Although no effect was seen in the FGF10‐ and TGFβ1‐treated samples, SDF1 promoted epithelial canalization in the low sulfated environment, highlighting its specific role in lumen formation. Altogether, the results show that sodium chlorate perturbed prostate morphogenesis and allowed investigation of factors involved in branching and/or canalization, implicating SDF1 signaling in epithelial canalization.
Recessive mutations in the neuronal isoforms of DST, encoding dystonin, lead to abnormal actin cytoskeleton organization and HSAN type VI

Hereditary sensory and autonomic neuropathies (HSAN) are clinically and genetically heterogeneous disorders, characterized by a progressive sensory neuropathy often complicated by ulcers and amputations, with variable motor and autonomic involvement. Several pathways have been implicated in the pathogenesis of neuronal degeneration in HSAN, while recent observations point to an emerging role of cytoskeleton organization and function. Here, we report novel biallelic mutations in the DST gene encoding dystonin, a large cytolinker protein of the plakin family, in an adult form of HSAN type VI. Affected individuals harbored the premature termination codon variant p.(Lys4330*) in trans with the p.(Ala203Glu) change affecting a highly conserved residue in an isoform‐specific N‐terminal region of dystonin. Functional studies showed defects in actin cytoskeleton organization and consequent delayed cell adhesion, spreading and migration, while recombinant p.Ala203Glu dystonin loses the ability to bind actin. Our data aid in the clinical and molecular delineation of HSAN‐VI and suggest a central role for cell‐motility and cytoskeletal defects in its pathogenesis possibly interfering with the neuronal outgrowth and guidance processes.
Management of individuals with chronic hepatitis B virus infection and persistent normal or mildly elevated aminotransferase levels

No consensus exists with respect to positive hepatitis B virus (HBV) DNA results and persistent normal or mildly elevated alanine aminotransferase (ALT). The aim of this study is to investigate the appropriate management and prognosis of these populations with chronic hepatitis B (CHB). A total of 235 subjects with positive HBV DNA results and persistent normal or mildly elevated ALT were enrolled in this study. Liver biopsy and liver stiffness measurements (LSM) were performed in all participants at baseline. Antiviral therapy was initiated in patients with significant hepatic inflammation (G ≥ 2) and/or fibrosis (S ≥ 2). The patients were divided into entecavir and adefovir groups based on HBV DNA load (>2000 IU/mL vs <2000 IU/mL). The liver biopsies were repeated at 72 weeks for the patients received antiviral therapy. We found that 112 subjects were hepatitis B e antigen (HBeAg) positive, and 123 subjects were negative. The corresponding median ALTs were 46 (39.5‐52.5) and 48 (41.5‐57.0) U/mL, respectively. G ≥ 2 and/or S ≥ 2 diseases were present in 48.8% (82/168) of the HBeAg‐positive and 51.2% (86/168) of HBeAg‐negative patients, respectively. In addition, 96 HBeAg‐positive and 72 HBeAg‐negative patients were divided into entecavir and adefovir groups. Meanwhile, liver biopsies had greater diagnostic accuracy for determining cirrhosis than LSM (0.711 vs 1.0, P < 0.0001). At the end of the study period, undetectable HBV DNA levels and normal ALT levels were observed in CHB‐infected patients. Furthermore, the patients showed histologic improvement at 72 weeks compared with baseline measurements (G, 1.72 ± 1.00 vs 0.73 ± 0.88, P = 0.0002; S, 1.484 ± 0.90 vs 0.99 ± 1.13, P < 0.0001). Collectively, liver biopsy enhanced diagnostic accuracy for CHB‐infected individuals with persistent normal or mildly elevated aminotransferase levels. Moreover, antiviral therapy can improve or regress the hepatic fibrosis and cirrhosis.
Effects of acute fructose loading on levels of serum uric acid—a pilot study

Fructose intake may lead to hyperuricaemia, which is associated with increased risk and progression of kidney disease. We aimed to explore the acute effects of fructose loading from different sources, with and without a pizza, on levels of serum uric acid in patients with chronic kidney disease (CKD), type 2 diabetes (T2D) without CKD, and in healthy subjects (HS).
Clinical applications of in vivo magnetic resonance spectroscopy in oncology

Magnetic resonance spectroscopy (MRS) can be performed in vivo using commercial MRI systems to obtain biochemical information about tissues and cancers. Applications in brain, prostate and breast aid lesion detection and characterisation (differential diagnosis), treatment planning and response assessment. Multi-centre clinical trials have been performed in all these tissues. Single centre studies have been performed in many other tissues including cervix, uterus, musculoskeletal and liver. While generally MRS is used to study endogenous metabolites it has also been used in drug studies, for example those that include 19F as part of their structure. Recently the hyperpolarisation of compounds enriched with 13C such as [1-13C] pyruvate has been demonstrated in animal models and now in preliminary clinical studies, permitting the monitoring of biochemical processes with unprecedented sensitivity. This review briefly introduces the underlying methods and then discusses the current status of these applications.
Real‐time detection of breast cancer at the cellular level

Novel optoelectronic instrumentation has been developed for the multispectral imaging of autofluorescence emitted by metabolic fluorophores. The images resolve individual cells while spectra are collected for each pixel in the images. These datacubes are generated at a rate of 10 per second—fast enough for surgical guidance. The data is processed in real time to provide a single color‐coded image to the surgeon. To date, the system has been applied to fresh, ex vivo, human surgical specimens and has distinguished breast cancer from benign tissue. The approach is applicable to in vivo measurements of surgical margins and needle‐based optical biopsies. Ongoing work demonstrates that the system has great potential for translation to a hand‐held probe with high sensitivity and specificity.
Service-Oriented Architecture and Process Modeling

Today enterprises are enforced to use new models for the interpretability and combination of the procedures and services because of business world uncertainties. Thus, enterprises have, over time, shifted towards IT-based business procedures on basis of Serviceoriented Architecture (SOA) to enhance the agility, combination, and flexibility of IT-based uses in enterprise networks. Therefore, enterprises have started to implement integrated information systems for supporting their business procedures. In order to this effect, SOA, as an extremely capable paradigm in IT, has been progressively applied in Business Process Management (BPM) and enterprise information systems by the Web service technologies. This has aided the achievement of needed agility and flexibility for inter-organizational networks. The purpose of current study is to review the basic concepts of SOA and to recognize the mechanism of SOA business process.
Contemporary Management of Acute Mesenteric Ischemia in the Endovascular Era

Objective: Acute mesenteric ischemia is a rare disease entity associated with high morbidity and mortality. Disparate etiologies and nonspecific symptoms make the diagnosis challenging and often result in delayed diagnosis and intervention. Open laparotomy with mesenteric revascularization and resection of necrotic bowel has been considered the gold standard of care. With recent advances in percutaneous catheter-directed techniques, multiple retrospective studies have demonstrated the outcomes of endovascular therapy. Herein, we review the etiology, presentation, and diagnosis of acute mesenteric ischemia with contemporary outcomes associated with both open and endovascular treatments. Methods: The PubMed electronic database was queried in the English language using the search words mesenteric, acute ischemia, embolism, thromboembolism, thrombosis, revascularization, and endovascular in various combinations. Abstracts of the relevant titles were examined to confirm their relevance and the full articles then extracted. References from extracted articles were checked for any additional relevant articles. This systematic review encompassed literature for the past 5 years (between 2011 and 2016). Results: Early diagnosis and intervention improves acute mesenteric ischemia outcomes. Early restoration of mesenteric flow minimizes morbidity and mortality. In comparison to open laparotomy with mesenteric revascularization and resection of necrotic bowel, several retrospective studies using administrative data and single-center chart reviews demonstrate noninferior outcomes of an endovascular first approach in acute arterial mesenteric occlusion. Conclusions: For acute mesenteric arterial occlusive disease, both endovascular and open revascularization techniques are viable options. Although there is lack of level 1 evidence, single-center retrospective studies and administrative database studies demonstrated that an endovascular first approach may have improved outcomes in the immediate postoperative period. However, selection and other bias in these studies necessitate the need for definitive randomized prospective studies between endovascular and open mesenteric intervention. In contrast, mesenteric venous thrombosis may be treated with systemic anticoagulation without surgical revascularization. Catheter-directed thrombectomy and thrombolysis can be considered at the discretion of the clinician.
Gender-Related Differences in Collaborative Learning in a 3D Virtual Reality Environment by Elementary School Students

This study aimed to understand how children collaborated to create their own stories in a 3D virtual reality (VR) environment and to explore whether there were any gender-related differences in this learning setting. A total of 65 students (38 females and 27 males) of grades 4-5 participated in this study. A qualitative methodology was adopted in this research to answer three research questions about how the participants work collaboratively, whether a gender difference exists in the process of 3D construction and how they think about learning in a 3D virtual environment. Based on the behavior patterns of these participants in a 3D world, the research findings revealed two types of collaboration: a team either with or a team without a strong leader. In addition, gender-related differences in this learning environment were also depicted in this study.
CMOS Switched-Capacitor DSB-SSB Converter Using a Hilbert Transformer

The realization of an analog integrated circuit for conversion of double-sideband amplitude-modulated signals into single-sideband is presented. The converter is implemented by discrete-time switched-capacitor circuits, and it adopts structurally all-pass filters to realize a Hilbert transformer with low sensitivity to capacitor mismatch. The use of variable-gain amplifiers in place of frequency mixers greatly reduces circuit complexity and associated non-linearities. The chip is fabricated in a 180-nm CMOS technology with metal–metal capacitors. For 1.8-V power supply and 1-V differential input/output signals, experimental results show the converter achieves image rejection ratio (IRR) greater than 39.5 dB for lower-sideband modulation and 38.0 dB for upper-sideband modulation with input frequency ranging from 25% to 75% of the carrier frequency. Its silicon area is 1.09 mm $^{2}$ and the converter consumes only 17.7 mW for 1-MHz sampling frequency while its IRR presents standard deviation of only 0.5 dB among 20 chip samples without any circuit trimming.
Galectin-3 Targeting in Thyroid Orthotopic Tumors Opens New Ways to Characterize Thyroid Cancer

Preoperative characterization of thyroid nodules is challenging since thyroid scintigraphy fails to distinguish between benign and malignant lesions. Galectin-3 (gal-3) is expressed in well-differentiated and in undifferentiated thyroid cancer types but not in normal thyrocytes and benign thyroid lesions. Herein, we aimed to validate gal-3 targeting as a specific method to detect non–radioiodine-avid thyroid cancer in thyroid orthotopic tumor models. Methods: Papillary (BcPAP) and anaplastic (CAL62 and FRO82-1) thyroid carcinoma cell lines were characterized via Western blot and polymerase chain reaction for gal-3 and sodium-iodide symporter (NIS) expression. An 89Zr-labeled F(ab′)2 antigal-3 was generated and characterized for binding versus 125I on 2- and 3-dimensional cell cultures. The thyroid carcinoma cells were inoculated into the left thyroid lobe of athymic nude mice, and the orthotopic tumor growth was monitored via ultrasound and fluorescence molecular tomography. Head-to-head PET/CT comparison of 124I versus 89Zr-deferoxamine (DFO)-F(ab′)2 antigal-3 was performed, followed by biodistribution studies and immunohistochemical analysis for gal-3 and NIS expression. Results: The thyroid carcinoma cells investigated were invariably gal-3–positive while presenting low or lost NIS expression. 89Zr-DFO-F(ab′)2 antigal-3 tracer showed high affinity to gal-3 (dissociation constant, ∼3.9 nM) and retained immunoreactivity (>75%) on 2-dimensional cell cultures and on tumor spheroids. 125I internalization in FRO82-1, BcPAP, and CAL62 was directly dependent on NIS expression, both in 2-dimensional and tumor spheroids. PET/CT imaging showed 89Zr-DFO-F(ab′)2 antigal-3 signal associated with the orthotopically implanted tumors only; no signal was detected in the tumor-free thyroid lobe. Conversely, PET imaging using 124I showed background accumulation in tumor-infiltrated lobe, a condition simulating the presence of non–radioiodine-avid thyroid cancer nodules, and high accumulation in normal thyroid lobe. Imaging data were confirmed by tracer biodistribution studies and immunohistochemistry. Conclusion: A specific and selective visualization of thyroid tumor by targeting gal-3 was demonstrated in the absence of radioiodine uptake. Translation of this method into the clinical setting promises to improve the management of patients by avoiding the use of unspecific imaging methodologies and reducing unnecessary thyroid surgery.
Feature Extraction for Incomplete Data Via Low-Rank Tensor Decomposition With Feature Regularization

Multidimensional data (i.e., tensors) with missing entries are common in practice. Extracting features from incomplete tensors is an important yet challenging problem in many fields such as machine learning, pattern recognition, and computer vision. Although the missing entries can be recovered by tensor completion techniques, these completion methods focus only on missing data estimation instead of effective feature extraction. To the best of our knowledge, the problem of feature extraction from incomplete tensors has yet to be well explored in the literature. In this paper, we therefore tackle this problem within the unsupervised learning environment. Specifically, we incorporate low-rank tensor decomposition with feature variance maximization (TDVM) in a unified framework. Based on orthogonal Tucker and CP decompositions, we design two TDVM methods, TDVM-Tucker and TDVM-CP, to learn low-dimensional features viewing the core tensors of the Tucker model as features and viewing the weight vectors of the CP model as features. TDVM explores the relationship among data samples via maximizing feature variance and simultaneously estimates the missing entries via low-rank Tucker/CP approximation, leading to informative features extracted directly from observed entries. Furthermore, we generalize the proposed methods by formulating a general model that incorporates feature regularization into low-rank tensor approximation. In addition, we develop a joint optimization scheme to solve the proposed methods by integrating the alternating direction method of multipliers with the block coordinate descent method. Finally, we evaluate our methods on six real-world image and video data sets under a newly designed multiblock missing setting. The extracted features are evaluated in face recognition, object/action classification, and face/gait clustering. Experimental results demonstrate the superior performance of the proposed methods compared with the state-of-the-art approaches.
Continuous Wave Terahertz Generation from Photodiode-Based Emitters with up to 200 μ W Terahertz Power

The output characteristics of an optoelectronic terahertz (THz) transmitter based on a high-speed, waveguide-integrated photodiode is demonstrated. THz power measurements are performed with a calibrated pyroelectric detector. 1.4 J.lW at 1 THz and up to 200 μW at 52 GHz are obtained. Up to 35 mW, the current system limit for optical illumination power, no saturation of the THz output is observed.
SMCT - An Innovative Tool for Mental Health Analysis of Twitter Data

Mental health conditions affect individuals, families and the wider community. It is estimated by the Australian Institute of Health and Welfare that 45% of Australians will experience some form of mental health issue in their lifetime. The World Health Organization (WHO; Switzerland) has assessed that mental health is a cornerstone of overall health.Large-scale collection of data related to mental health is traditionally difficult and carried out infrequently. It is a challenge for researchers to assess seasonal, weekly or diurnal mental health trends. Social media has been demonstrated to present opportunities to extend traditional data collection techniques, particularly the expression of an individual's state of mind.The “Social Media Collection Tool” (SMCT) is a research tool developed to collect Twitter data for mental health analysis. Data collected is filtered to identify “of interest” users, allowing for cross-sectional analysis. Additionally, SMCT provides the capability to “re-poll” of interest users to develop a contextual understanding for these users on Twitter, providing a longitudinal analysis. SMCT, for the first time, combined the two data analysis techniques into a single tool.In demonstrative analysis scenarios the SMCT has collected more than 500,000 tweets and identified almost 6,000 as being of interest. The tool has also been used to investigate trends in the responses made by other users to an of interest tweet.
Classifying the mental representation of word meaning in children with Multivariate Pattern Analysis of fNIRS

This study presents the implementation of a within-subject neural decoder, based on Support Vector Machines, and its application for the classification of distributed patterns of hemodynamic activation, measured with Functional Near Infrared Spectroscopy (fNIRS) on children, in response to meaningful and meaningless auditory stimuli. Classification accuracy nominally exceeds chance level for the majority of the participants, but fails to reach statistical significance. Future work should investigate whether individual differences in classification accuracy may relate to other characteristics of the children, such as their cognitive, speech or reading abilities.
Nonlinear Robust Safety Factor Profile Control in Tokamaks via Feedback Linearization and Nonlinear Damping Techniques

Tokamaks are toroidal devices in which a plasma is confined by means of helical magnetic fields with the purpose of obtaining energy from nuclear fusion reactions. The safety factor, $q$, measures the pitch of the helical magnetic field lines in a tokamak. Active control of the $q$ profile (i.e., spatial shape) is needed due to its relationship with plasma performance, steady-state operation, and magneto-hydrodynamic stability. However, the responses of some plasma magnitudes, such as the electron temperature, are difficult to model and introduce a high level of uncertainty in the model used for $q$-profile control design. Control algorithms that are robust against such model uncertainties must be developed in order to ensure successful q-profile regulation. In this work, a nonlinear, robust $q$-profile controller is designed using feedback linearization and nonlinear damping techniques. The controller makes use of plasma current modulation, neutral beam injection, electron-cyclotron heating & current drive, and electron density modulation as actuation methods. A simulation study is carried out for a DIII-D scenario to test the controller's performance under the presence of electron temperature uncertainties.
AntNLP at CoNLL 2018 Shared Task: A Graph-Based Parser for Universal Dependency Parsing

We describe the graph-based dependency parser in our system (AntNLP) submitted to the CoNLL 2018 UD Shared Task. We use bidirectional lstm to get the word representation, then a bi-affine pointer networks to compute scores of candidate dependency edges and the MST algorithm to get the final dependency tree. From the official testing results, our system gets 70.90 LAS F1 score (rank 9/26), 55.92 MLAS (10/26) and 60.91 BLEX (8/26).
Automating the Detection of REM Sleep Behaviour Disorder

This study aims to develop automated diagnostic tools to aid in the identification of rapid-eye-movement (REM) sleep behaviour disorder (RBD). Those diagnosed with RBD enact their dreams and therefore present an abnormal characteristic of movement during REM sleep. Several methods have been proposed for RBD detection that use electromyogram (EMG) recordings and manually annotated sleep stages to objectively quantify abnormal REM movement. In this work we further develop these proven techniques with additional features that incorporate the relationship of muscle movement between sleep stages and general sleep architecture. Performance is evaluated using polysomnography (PSG) recordings from 43 aged-matched healthy controls and subjects diagnosed with RBD obtained from multiple institutions and publicly available resources. Using a random forest classifier with established and additional features, the performance of RBD detection was shown to improve upon established metrics (achieving 88% accuracy, 91% sensitivity, and 86% specificity).