Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection

Rapid growth in molecular structure data is renewing interest in featurizing structure. Featurizations that retain information on biological activity are particularly sought for protein molecules, where decades of research have shown that indeed structure encodes function. Research on featurization of protein structure is active, but here we assess the promise of autoencoders. Motivated by rapid progress in neural network research, we investigate and evaluate autoencoders on yielding linear and nonlinear featurizations of protein tertiary structures. An additional reason we focus on autoencoders as the engine to obtain featurizations is the versatility of their architectures and the ease with which changes to architecture yield linear versus nonlinear features. While open-source neural network libraries, such as Keras, which we employ here, greatly facilitate constructing, training, and evaluating autoencoder architectures and conducting model search, autoencoders have not yet gained popularity in the structure biology community. Here we demonstrate their utility in a practical context. Employing autoencoder-based featurizations, we address the classic problem of decoy selection in protein structure prediction. Utilizing off-the-shelf supervised learning methods, we demonstrate that the featurizations are indeed meaningful and allow detecting active tertiary structures, thus opening the way for further avenues of research.
Contextual and cross-modality modulation of auditory cortical processing through pulvinar mediated suppression

Lateral posterior nucleus (LP) of thalamus, the rodent homologue of primate pulvinar, projects extensively to sensory cortices. However, its functional role in sensory cortical processing remains largely unclear. Here, bidirectional activity modulations of LP or its projection to the primary auditory cortex (A1) in awake mice reveal that LP improves auditory processing in A1 supragranular-layer neurons by sharpening their receptive fields and frequency tuning, as well as increasing the signal-to-noise ratio (SNR). This is achieved through a subtractive-suppression mechanism, mediated largely by LP-to-A1 axons preferentially innervating specific inhibitory neurons in layer 1 and superficial layers. LP is strongly activated by specific sensory signals relayed from the superior colliculus (SC), contributing to the maintenance and enhancement of A1 processing in the presence of auditory background noise and threatening visual looming stimuli respectively. Thus, a multisensory bottom-up SC-pulvinar-A1 pathway plays a role in contextual and cross-modality modulation of auditory cortical processing.
Parafoveal and Peripapillary Perfusion Predict Visual Field Recovery in Chiasmal Compression due to Pituitary Tumors

Background: To evaluate the potential of vessel density alterations for predicting postoperative visual field (VF) improvement in chiasmal compression using optical coherence tomography angiography (OCT-A). Methods: The study investigated 57 eyes of 57 patients diagnosed with pituitary tumors and 42 eyes of 42 age and refractive error matched controls. All eyes with chiasmal compression for which preoperative optical coherence tomography (OCT) and OCT-A, and pre- and postoperative VF data were available. Preoperative vessel densities of superficial retinal capillary plexus (SRCP), deep retinal capillary plexus (DRCP), and radial peripapillary capillary (RPC) segment were utilized by OCT-A. Results: Preoperative peripapillary retinal nerve fiber layer and ganglion cell layer complex thickness and vessel densities of SRCP and RPC segments in eyes with chiasmal compression were significantly reduced compared with healthy controls (p < 0.001, p < 0.001, p = 0.007, and p = 0.020, respectively). In multivariate regression analysis, preoperative perimetric mean deviation (MD) (p = 0.002) and vessel density of SRCP (p = 0.025) were correlated significantly with postoperative perimetric MD. Spearman’s correlation analysis revealed significant correlations between preoperative MD on perimetry (r = 0.443, p = 0.001), vessel densities of SRCP (r = 0.288, p = 0.035) and RPC segment (r = 0.347, p = 0.009), and postoperative perimetric MD. Conclusions: Structural degeneration referred to as microvascular alterations measured by OCT-A and preoperative VF defects were associated with worse postoperative VF prognosis. Parafoveal and peripapillary vessel densities may serve as a sensitive, structural prognostic factors in the preoperative judgement of chiasmal compression.
The Antioxidant and Antihyperglycemic Activities of Bottlebrush Plant (Callistemon lanceolatus) Stem Extracts

Background: Diabetes mellitus, a metabolic disease, is a major health concern today throughout the world. Callistemon lanceolatus (Myrtaceae), commonly known as bottlebrush, has been used by Indian tribal communities for the treatment of many diseases. The purpose of this study was to explore antioxidant and antihyperglycemic potential of methanolic and aqueous extracts of the stem of C. lanceolatus in vitro and in vivo. Methods: Phytoconstituents of C. lanceolatus stem were extracted in methanol and water sequentially followed by phytochemical analysis. The in vitro antioxidant potential of aqueous and methanolic extracts was assessed by metal ion chelating, free radical scavenging, and reducing power assays. The in vivo antihyperglycemic activity of the oral methanolic extract was studied in alloxan-induced diabetic rats. Bodyweight and blood glucose were monitored regularly. After the treatment period, serum was examined for total cholesterol, triglycerides, high-density lipoprotein (HDL), bilirubin, creatinine, urea, glutamate pyruvate transaminase (SGPT), glutamate oxaloacetate transaminase (SGOT), and alkaline phosphatase (ALP). Results: Methanolic extract exhibited superior antioxidant activity to aqueous extract. A marked increase in levels of serum markers, viz., glucose, triglycerides, total cholesterol, bilirubin, urea, creatinine, SGOT, SGPT, and ALP along with a reduction in HDL was observed in diabetic rats. Methanol extract treatment for 28 days accounted for a decrease in blood glucose and other metabolic markers accompanied by an improvement in body weight and HDL level in hyperglycemic rats. Conclusions: The present study suggests that C. lanceolatus methanolic stem extract possesses antioxidant and antihyperglycemic activities and has potential as a therapeutic agent in diabetes.
Reduced Physical Activity Patterns in Patients With Thalassemia Compared To Healthy Controls

Background: Patients with Thal (Thalassemia) are presumed to be inactive for many of the same reasons as healthy adults, though there are limited published data to support this claim. The primary aim of this study was to compare physical activity patterns in subjects with Thal to healthy controls as well as to explore the effects of transfusion therapy on physical activity in transfusion dependent patients with Thal. Methods: 37 Thal (23 Thal major, 14 Thal intermedia, 21 Female, 27.3±10.1 years) and 30 healthy controls (17 Female, 28.0 ± 13.7 years) wore an ActiGraph accelerometer for one to two weeks. Results: Thal subjects recorded a significantly fewer total number of steps per day and lower total energy expenditure compared to healthy controls (p=0.001). None of the adult Thal subjects met the recommended 10,000 steps/day as opposed to 27% of healthy adult controls (p=0.004). Thal spent significantly less time in moderate (p=0.03) to vigorous (p=0.005) activities and more time in sedentary activity (p=0.006). Conclusion: It is now clear that Thal spend significantly less time in physically demanding activities than age-matched healthy controls, a result that has long been assumed though not previously documented. Further research is needed to define an appropriate physical activity regimen best suited for patients with Thal while examining its effect on mental and physical health. J O U R N A L O F H E M A T O L O G Y A N D O N C O L O G Y R E S E A R C H ISSN NO: 2372-6601 Research DOI : 10.14302/issn.2372-6601.jhor-15-776 Corresponding author Ellen B. Fung, PhD RD CCD, Department of Hematology, UCSF Benioff Children's Hospital, Oakland, 747 52 Street, Oakland, CA 94609, Phone: 510-428-3885 x 4939, Fax: 510-450-5877 , efung@mail.cho. org
Universidade de São Paulo

N. and Carbon nanotubes (CNT) have been the subject of several theoretical and experimental studies, especially in the field of composites, due to their superlative intrinsic physicochemical properties. Hybrid materials have properties that are different from those of their individual components, which results from the nature of their constituents, their quantities and interactions. This work aimed at investigating the hybrid properties that can arise when carbon nanostructures are vertically grown on different types of micrometric substrates. Particularly, the behavior of the micronanostructured composites in the chemical reduction of metal ions and in the mechanical reinforcement of a thermoplastic polymer (PVC) was investigated. In order to conduct this study, two types of CNT were grown on the surfaces of charcoal, graphite and titanium dioxide through the chemical vapor deposition (CVD) method. These substrates are traditionally used as reducing agents, adsorbents and reinforcing fillers. The main characterization techniques were: scanning electron microscopy (SEM), energy dispersive X-ray spectrometry (EDX), X-ray diffraction (XRD) and, in the case of the PVC composites, tensile tests and also thermogravimetric analysis. The results demonstrate that there are combinations between specific types of CNT and microstructured supports that can lead to properties not observed in the isolated constituents of the composite. Therefore, the growth of nanostructures on substrates can generate hybrid properties, such as the reduction of Ag and Cu ions and their direct adsorption on CNT without the need of a reducing agent or application of an external potential. Additionally, some of these composites can form mechanical fillers for PVC, which can lead to substantial increases in the elasticity modulus and tensile strength, (5.033,3% and 3.564%, respectively), when compared to the isolated PVC.
Is the writing on the walls for tabletops?

We describe an ethnographic study that examines how low-tech and high-tech surfaces support creativity and collaboration during a workshop breakout session. The low-tech surfaces included post-it notes, flipcharts, and walls. The high tech surface comprised a multi-touch tabletop. Input was either by pen or fingertips. The breakout session comprised four groups using the different surfaces and inputs during three phases: i) brief presentation of position papers and discussion of themes, ii) creating a group presentation and iii) a report back session. During these phases, collaboration and creativity were found to be either restricted or facilitated depending on the physical, technological and social factors at play when using the different surfaces and inputs. We discuss why this is the case, noting how tabletops might not be such a good surface as low tech materials for supporting this form of collaborative experience.
EFFECT OF DEMOCRACY ON SUB-SAHARAN COUNTRIES ECONOMIC DEVELOPMENT

The objective of this work is to analyze the effect of democracy on the economic development of 43 sub-Saharan African countries over the 1996-2015 period using the generalized dynamic panel method of moments. The results of the growth model estimates of the total sample show that democracy has a significant effect on the growth of SSA countries, regardless of the democracy index used. However, this effect is negative at the level of the Freedom House index and positive with the Polity2 index. Country group results show that democracy has a positive and significant effect on the economic growth of SSA's democratic countries and has no significant effect on the growth of non-democratic countries. Ultimately, democracy has a beneficial effect on the economic development of SSA countries that embody democratic principles.
Neuropathy Detection, Quality of Life Tools & Treatment for Type 2 Diabetes

NEUROPATHY DETECTION, QUALITY OF LIFE TOOLS & TREATMENT FOR TYPE 2 DIABETES Jennifer J. Brown Old Dominion University, 2016 Director: Dr. Sheri Colberg-Ochs Type 2 diabetes (T2D) mellitus has become the epidemic of the new millennium, with an estimated 382 million people affected worldwide as of 2013, and statistics projected towards 592 million by the year 2035. With the development of diabetes, complications have risen, with diabetic neuropathy becoming one of the most prevalent, affecting between 10–90% of those with the disease. Diabetic peripheral neuropathy (DPN) is difficult to detect in early stages of pathology, yet devastating once significant damage has taken place. Cardiac autonomic neuropathy (CAN), which is often silent, is associated with autonomic nervous system (ANS) dysfunction and increased risk for sudden death. Therefore, the purposes of this dissertation were early detection, assessment of quality of life (QOL) and disease intervention. Study I explored the effectiveness of the 128-Hz tuning fork, the 1-g and 10-g monofilaments, and the QOL-DN as tools for the early detection of DPN in overweight, obese and inactive (OOI), prediabetes (PD), and type 2 diabetes (T2D) individuals. Study II compared three QOL assessments: the QOL-DN, the PN-QOL-97 and the NeuroQOL-28, in OOI, PD and T2D individuals. Study III involved the execution of a double blinded, placebo controlled exploration of melatonin as a potential intervention for the improvement of ANS and sleep dysfunction in T2D. The results of Study I suggest that the 1-g monofilament and QOL-DN measures correlate to NC-Stat DPN Check portable nerve conduction study (NCS) findings, that these
Frequency selective Rician fading MIMO channel and channel Rice factor estimation

In this paper, to estimate Rician frequency selective fading Multiple-Input Multiple-Output (MIMO) channels, the Shifted Scaled Least Squares (SSLS) and General form of the Linear Minimum Mean Square Error (GLMMSE) channel estimators are proposed. It is shown that these estimators achieve much better minimum possible Bayesian Cramér-Rao Lower Bounds (CRLBs) in the frequency selective Rician fading MIMO channels compared with those of the Rayleigh one. Numerical examples show that the performance of these estimators is not more sensitive to accurate estimation of the channel Rice factor. Furthermore, to estimate the channel Rice factor at the receiver, we propose two new algorithms which perform based on the Least Squares (LS) estimates and training sequences. Simulation results confirm the efficiency of these algorithms.
NASA Langley's Research and Technology-Transfer Program in Formal Methods

This paper presents an overview of NASA Langley's research program in formal methods. The major goals of this work are to make formal methods practical for use on life critical systems, and to orchestrate the transfer of this technology to U.S. industry through use of carefully designed demonstration projects. Several direct technology transfer efforts have been initiated that apply formal methods to critical subsystems of real aerospace computer systems. The research team consists of ve NASA civil servants and contractors from Odyssey Research Associates, SRI International, and V GYAN Inc. 1 Rationale For Formal Methods Re-
CS678A COURSE PROJECT Domain Invariant Transfer Kernel Learning

Domain transfer learning generalizes a learning model across training data and testing data with diﬀerent distributions. A general principle to face this issue is by reducing the distribution diﬀerence between the training and the testing data such that the generalization error can be bounded. The technique proposed in our project is through Transfer Kernel Learning, to learn a domain invariant kernel. Speciﬁcally, we design a family of spectral kernels by extrapolating target eigensystem on source data points with Mercer’s Theorem and Nystr¨om approximation.The spectral kernel minimizing the approximation error to the original source kernel is selected to construct the domain invariant kernel. Several experiments have been performed over text, image and brain data to identify the eﬀectiveness of Transfer Kernel Learning over normal SVM algorithm.
Warmth and Competence in the Market: How Explicit and Implicit Country Stereotypes Predict Product Choice

Past research on the impact of products’ country-of-origin (COO) upon consumers’ evaluations shows the shortcoming of almost exclusively relying on explicit measurement whilst neglecting the implicit measurement of COO. Findings in the area of cognitive psychology indicate that people can have explicit and implicit attitudes at the same time (Wilson, Lindsey, & Schooler, 2000) but depending on the type of behavior involved, either the one or the other becomes relevant to behavioral outcome (Dovidio, Kawakami, Johnson, Johnson, & Howard, 1997). Therefore, the present study investigated the relationship between explicit measured (questionnaire) and implicit measured (IAT) country stereotypes and product choice made either spontaneously or deliberately. For the purpose of operationalizing country stereotypes the stereotype content model was used (SCM; Fiske, Cuddy, Glick, & Xu, 2002), which partitions stereotypes into the two dimensions warmth and competence. Participants had to evaluate Germany and the USA upon these dimensions and were to choose between a German and a US-made product, while processing resources were manipulated. Germany was perceived as more implicitly and explicitly competent and more implicitly warm than the USA. Further, regression analyses showed that perceived implicit warmth of a country became especially relevant when the product choice was made spontaneously, whereas perceived explicit competence of a country was predictive in deliberate product choice. Thus, higher implicit warmth perceptions in spontaneous and higher explicit competence perceptions in deliberate evaluation situations in favor of Germany, induced the selection of a German digital camera. Possible reasons for these results, suggestions for future research, and limitations of the present study are discussed.
Oncogenes ras from Cell Lines Expressing Different Activated Suppression of Tumorigenicity in Human Cell Hybrids Derived

Four different human tissue-derived cell lines, each previously shown to express either a Ha-, Ki-, or N-ras-activated oncogene, were fused in four different paired combinations. The three combinations that involved the tumor line HT1080 (activated N-ras oncogene) were found to be tumorigenic in nude mice, but to different degrees. However, the fusion of the tumor lines EJ and SW480 (activated I Ia-w.v and Ki-ra.v,respec tively) resulted in hybrid cells suppressed for tumorigenicity. The EJ x SW480 hybrids were found to harbor and express both of the activated ras oncogenes. The results suggest that tumorigenic suppression can occur in the presence of two transforming oncogenes of the rus family and that tumorigenicity associated with ras oncogene activation involves additional mechanisms that may differ among tumor cells.
Activity in Human Alveolar Macrophages Phosphatidylinositol 3-Kinase and Akt Lipopolysaccharide-Induced Ceramide Regulates

The phosphatidylinositol (PI) 3-kinase pathway is an important regulator of cell survival. In human alveolar macrophages, we found that LPS activates PI 3-kinase and its downstream effector, Akt. LPS exposure of alveolar macrophages also results in the generation of ceramide. Because ceramide exposure induces apoptosis in other cell types and the PI 3-kinase pathway is known to inhibit apoptosis, we determined the relationship between LPS-induced ceramide and PI 3-kinase activation in alveolar macrophages. We found that ceramide exposure activated PI 3-kinase and Akt. When we blocked LPS-induced ceramide with the inhibitor D609, we blocked LPS-induced PI 3-kinase and Akt activation. Evaluating cell survival after ceramide or LPS exposure, we found that blocking PI 3-kinase induced a signiﬁcant increase in cell death. Because these effects of PI 3-kinase inhibition were more pronounced in ceramide- vs LPS-treated alveolar macrophages, we also evaluated NF- (cid:1) B, which has also been linked to cell survival. We found that LPS, to a greater degree than ceramide, induced NF- (cid:1) B translocation to the nucleus. As a composite, these studies suggest that the effects of ceramide exposure in alveolar macrophages may be very different from the effects described for other cell types. We believe that LPS induction of ceramide results in PI 3-kinase activation and represents a novel effector mechanism that promotes survival of human alveolar macrophages in the setting of pulmonary sepsis. The Journal of Immunology, 2001, 167: 5977–5985. macrophages. Our results demonstrate that ceramide (and LPS-induced ceramide) can activate PI 3-kinase and Akt in alveolar macrophages and that this is linked to maintenance of cell viability. We found that the proapoptotic effect of ceramide is observed in these cells only if the PI 3-kinase pathway is inhibited.
Fault diagnosis for BLDCM system used FFT algorithm and support vector machines

To effectively solve the fault diagnosis problem of BLDCM unbalanced three-phase winding under the unsteady case, this article puts forward a fault diagnosis method based on Support Vector Machine (SVM) and FFT. Using FFT to analyze the time-frequency of local signal can extract fault features, which are utilized for SVM training. Once satisfied effects are achieved, SVM structure and internal parameters should be freezed. To compare the output and fault codes with given input can realize the goal of winding unbalanced fault diagnosis. At the same time, to simulate the unbalanced three-phase winding by building BLDCM position servo model with MATLAB/SIMULINK verifies the validity of the proposed fault diagnosis method. The example simulation results show that the method can not only diagnose fault existence, but also judge the level of fault effectively. As a reliable fault diagnosis approach, the method is simple and effective with the capability of making up existing flaws.
Design and Simulation of Power efficient All Digital Phase Locked Loops (ADPLL)

- We presents a new^generalised power efficient ADPLL design & Simulation^using Verilog*. Xilinx ISE 10.1 Simulator is^used for simulating Verilog Code and is synthesized using Cadence RTL compiler using gpdk 45 nm technology. To validate its functionality, verification and simulation is done by using^the Cadence IES (Incisive Enterprise Simulator) tool. This paper gives the details of basic building^blocks of the absolute ADPLL*design. And the planned power optimized clock gating technique*that is implemented in the Digital loop filter without^altering the performance of overall system. The power^consumption of this ADPLL is 0.704 μW at a center frequency*(fc) of 625 KHz. The total chip area is 207 μm².
Comparision of different Image Resolution Enhancement techniques using wavelet transform

—We propose an Image resolution enhancement techniques based on interpolation of the high frequency subband images obtained from wavelet zero padding-cycle spinning, discrete, stationary and Dual tree Complex wavelet transform (DT-CWT). In this study, a comparison of three different image resolution enhancement techniques in wavelet domain is done. Each method is analyzed quantitatively and visually. Based on the analysis, the most efficient method is proposed. All the three algorithms uses low resolution image as the input image and then wavelet transform is applied to decompose the input image into different high and low frequency subbands. Then these subband images along with the input image are interpolated. Finally all these images are combined to generate a new resolution enhanced image by using inverse process.