Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel Nonnegative Matrix Factorization with Manifold Regularization

Nonnegative matrix factorization (NMF) decomposes a high-dimensional nonnegative matrix into the product of two reduced dimensional nonnegative matrices. However, conventional NMF neither qualifies large-scale datasets as it maintains all data in memory nor preserves the geometrical structure of data which is needed in some practical tasks. In this paper, we propose a parallel NMF with manifold regularization method (PNMF-M) to overcome the aforementioned deficiencies by parallelizing the manifold regularized NMF on distributed computing system. In particular, PNMF-M distributes both data samples and factor matrices to multiple computing nodes instead of loading the whole dataset in a single node and updates both factor matrices locally on each node. In this way, PNMF-M succeeds to resolve the pressure of memory consumption for large-scale datasets and to speed up the computation by parallelization. For constructing the adjacency matrix in manifold regularization, we propose a two-step distributed graph construction method, which is proved to be equivalent to the batch construction method. Experimental results on popular text corpora and image datasets demonstrate that PNMF-M significantly improves both scalability and time efficiency of conventional NMF thanks to the parallelization on distributed computing system; meanwhile it significantly enhances the representation ability of conventional NMF thanks to the incorporated manifold regularization.
Thallium isotopes reveal protracted anoxia during the Toarcian (Early Jurassic) associated with volcanism, carbon burial, and mass extinction

Significance Declining oxygen contents in today’s oceans highlight the need to better understand ancient, natural marine deoxygenation and associated extinctions. In the Early Jurassic, the Toarcian Oceanic Anoxic Event (T-OAE; ∼183 Ma) is associated with significant perturbations to the Earth system, historically defined by carbon isotopes. We reconstructed global oceanic (de)oxygenation using thallium isotopes from two ocean basins that suggest a stepwise decline of oxygen that initiated before and extended well after the classically defined T-OAE interval. This initial deoxygenation occurs with the start of massive volcanism and marine extinctions, while a later shift corresponds to the traditional T-OAE. This emphasizes the need for more nuanced records of ancient environmental and biogeochemical feedbacks that lead to and maintain widespread marine anoxia. For this study, we generated thallium (Tl) isotope records from two anoxic basins to track the earliest changes in global bottom water oxygen contents over the Toarcian Oceanic Anoxic Event (T-OAE; ∼183 Ma) of the Early Jurassic. The T-OAE, like other Mesozoic OAEs, has been interpreted as an expansion of marine oxygen depletion based on indirect methods such as organic-rich facies, carbon isotope excursions, and biological turnover. Our Tl isotope data, however, reveal explicit evidence for earlier global marine deoxygenation of ocean water, some 600 ka before the classically defined T-OAE. This antecedent deoxygenation occurs at the Pliensbachian/Toarcian boundary and is coeval with the onset of initial large igneous province (LIP) volcanism and the initiation of a marine mass extinction. Thallium isotopes are also perturbed during the T-OAE interval, as defined by carbon isotopes, reflecting a second deoxygenation event that coincides with the acme of elevated marine mass extinctions and the main phase of LIP volcanism. This suggests that the duration of widespread anoxic bottom waters was at least 1 million years in duration and spanned early to middle Toarcian time. Thus, the Tl data reveal a more nuanced record of marine oxygen depletion and its links to biological change during a period of climatic warming in Earth’s past and highlight the role of oxygen depletion on past biological evolution.
Face Interpretation Problems on Low Quality Images

Automatic age and gender prediction is applicable in many real-world problems (e.g. surveillance, commercial profiling, etc.). Often, only low-resolution(LR) images are available. The goal of the thesis is to compare a baseline CNN age and gender predictor trained on high-quality images with two proposed strategies for improving prediction accuracy on low-resolution images: (1) Data-augmentation strategy trains a CNN classifier on synthetically generated LR images. (2) Super-resolution strategy enhances image resolution using conditional generative adversarial network (cGAN) and the age and gender prediction is subsequently made using the baseline CNN. The intermediate step provides human-readable interpretation, unlike in the case of data-augmentation. The experiments show that both methods outperformed the baseline method and indeed improve prediction accuracy on LR images. The super-resolution noticeably exceeding the data-augmentation given comparable amount of training data.
Changes in conformation and quality of vegetable protein during texturization process by extrusion

Abstract Texturized Vegetable Protein (TVP), as meat analogs, has garnered attention due to the nutritional advantages it offers over conventional animal proteins. During the extrusion process of TVP, under the comprehensive effects of temperature, shear force, and pressure, complex conformational changes and molecular interactions amongst protein, carbohydrate, lipid, and other components occur, all of which influence the quality of TVP. Control of the extrusion process is still one of the largest challenges in its evolution. Therefore, this review aims to summarize the development and current status of food extrusion technology for TVP production and give detailed descriptions about the conformational changes of the main components during the extrusion process, focusing on the effects of barrel temperature, moisture content, feed rate and screw speed on TVP quality. Lastly, we discuss approaches to characterize the extrusion process and propose a new system analysis model.
How do people check polymorphic types?

Polymorphic typechecking algorithms efficiently locate type errors in programs, but users find error reporting from such algorithms hard to comprehend. We are investigating the development of a new polymorphic type checker that reports type errors in a more understandable form. Here we present the results of experiments into human checking of both correct and incorrect polymorphic typed programs, and briefly discuss their implications for our proposed new checker.
The Corrosion Behavior of AZ91D Magnesium Alloy in Simulated Haze Aqueous Solution

The corrosion process of AZ91D magnesium alloy in simulated haze aqueous solution has been studied by electrochemical measurements, immersion tests and morphology characterization. Results show that AZ91D was corroded heavily in simulated haze aqueous solution due to the loose and breakable product film on the surface providing little corrosion barrier. The effect of different ions was investigated. It was found that both NO3− and NH4+ played an important role in the corrosion process. NO3− helped to form passive film to protect the matrix, yet NH4+ consumed OH−, resulting in the absence of Mg(OH)2 and serious corrosion. Meanwhile, SO42− and Cl− had influence on pitting corrosion. Magnesium aluminum oxide and MgAl2(SO4)4·22H2O instead of Mg(OH)2 were the dominate products, which is different from the former study. Corrosion rate changed with time, especially in the first 3 h. A two-stage corrosion mechanism is proposed after considering both the corrosion process and the influence of ions.
Chromatin remodeling by the NuRD complex regulates development of follicular helper and regulatory T cells

Significance Production of high-affinity antibody responses after infection or vaccination requires precise control of germinal center B cells by follicular helper T cells and follicular regulatory T cells. Although the Bcl6 transcription factor plays a central role in follicular T cell differentiation, the molecular basis of Bcl6 control has been clouded in uncertainty. Here we report that Bcl6-dependent control reflects the formation of a macromolecular complex between Bcl6 and the Mi-2β-nucleosome remodeling deacetylase complex (Mi-2β-NuRD). The repressive activity of this intranuclear complex potentiates the follicular T cell phenotype and inhibits alternative T cell fates. Identification of this intracellular complex may facilitate new targeted approaches to the treatment of autoimmune disorders. Lineage commitment and differentiation into CD4+ T cell subsets reflect an interplay between chromatin regulators and transcription factors (TF). Follicular T cell development is regulated by the Bcl6 TF, which helps determine the phenotype and follicular localization of both CD4+ follicular helper T cells (TFH) and follicular regulatory T cells (TFR). Here we show that Bcl6-dependent control of follicular T cells is mediated by a complex formed between Bcl6 and the Mi-2β-nucleosome-remodeling deacetylase complex (Mi-2β-NuRD). Formation of this complex reflects the contribution of the intracellular isoform of osteopontin (OPN-i), which acts as a scaffold to stabilize binding between Bcl6 and the NuRD complex that together regulate the genetic program of both TFH and TFR cells. Defective assembly of the Bcl6–NuRD complex distorts follicular T cell differentiation, resulting in impaired TFR development and skewing of the TFH lineage toward a TH1-like program that includes expression of Blimp1, Tbet, granzyme B, and IFNγ. These findings define a core Bcl6-directed transcriptional complex that enables CD4+ follicular T cells to regulate the germinal center response.
Clinical evaluation of the reproducibility of volume measurements of pulmonary nodules

High reproducibility of volumetric measurements is an important prerequisite for follow-up of small lung nodules in order to differentiate malignant from benign lesions in a lung cancer screening setting. This study was aimed to evaluate the measurement reproducibility of a new software tool for pulmonary nodule volumetry. In an ongoing study, 147 pulmonary nodules (size 1.6-17.5 mm) were examined with low-dose multidetector CT (Siemens Somatom Volume Zoom, 120 kVp, 20 mAs, detector collimation 4x1 mm, normalized pitch 1.75, slice thickness 1.25 mm, reconstruction increment 0.8 mm). Two consecutive low-dose scans covering the whole lung volume were performed within a few minutes. Between both scans, patients were asked to leave the CT scanner, and the second scan was planned independently from the first one. For all visually detected pulmonary nodules with a diameter <20 mm nodule volume was determined on both scans using a software prototype containing segmentation and volumetry algorithms. Results from both scans were compared. Nodule volume differences were determined as difference between the first and second measurement and ranged from 169 to 87%. The performance of the diagnostic test was measured using ROC analysis. For the detection of a volume doubling the area under curve (Az) was 0.98, for a growth of 50% the Az was 0.89. Further refinement of the segmentation algorithm should lead to more consistent measurements in ill-defined nodules. In conclusion, volumetric measurement of pulmonary nodules in multislice CT data sets is a reliable tool for the detection of growth in small pulmonary nodules.
An Auto-Calibrating Knee Flexion-Extension Axis Estimator Using Principal Component Analysis with Inertial Sensors

Inertial measurement units (IMUs) have been demonstrated to reliably measure human joint angles—an essential quantity in the study of biomechanics. However, most previous literature proposed IMU-based joint angle measurement systems that required manual alignment or prescribed calibration motions. This paper presents a simple, physically-intuitive method for IMU-based measurement of the knee flexion/extension angle in gait without requiring alignment or discrete calibration, based on computationally-efficient and easy-to-implement Principle Component Analysis (PCA). The method is compared against an optical motion capture knee flexion/extension angle modeled through OpenSim. The method is evaluated using both measured and simulated IMU data in an observational study (n = 15) with an absolute root-mean-square-error (RMSE) of 9.24∘ and a zero-mean RMSE of 3.49∘. Variation in error across subjects was found, made emergent by the larger subject population than previous literature considers. Finally, the paper presents an explanatory model of RMSE on IMU mounting location. The observational data suggest that RMSE of the method is a function of thigh IMU perturbation and axis estimation quality. However, the effect size for these parameters is small in comparison to potential gains from improved IMU orientation estimations. Results also highlight the need to set relevant datums from which to interpret joint angles for both truth references and estimated data.
Focused Hierarchical RNNs for Conditional Sequence Processing

Recurrent Neural Networks (RNNs) with attention mechanisms have obtained state-of-the-art results for many sequence processing tasks. Most of these models use a simple form of encoder with attention that looks over the entire sequence and assigns a weight to each token independently. We present a mechanism for focusing RNN encoders for sequence modelling tasks which allows them to attend to key parts of the input as needed. We formulate this using a multi-layer conditional sequence encoder that reads in one token at a time and makes a discrete decision on whether the token is relevant to the context or question being asked. The discrete gating mechanism takes in the context embedding and the current hidden state as inputs and controls information flow into the layer above. We train it using policy gradient methods. We evaluate this method on several types of tasks with different attributes. First, we evaluate the method on synthetic tasks which allow us to evaluate the model for its generalization ability and probe the behavior of the gates in more controlled settings. We then evaluate this approach on large scale Question Answering tasks including the challenging MS MARCO and SearchQA tasks. Our models shows consistent improvements for both tasks over prior work and our baselines. It has also shown to generalize significantly better on synthetic tasks as compared to the baselines.
Frequency-dependent antidromic activation in thalamocortical relay neurons: effects of synaptic inputs

Objective. Deep brain stimulation (DBS) generates action potentials (APs) in presynaptic axons and fibers of passage. The APs may be antidromically propagated to invade the cell body and/or orthodromically transmitted to downstream structures, thereby affecting widespread targets distant from the electrode. Activation of presynaptic terminals also causes trans-synaptic effects, which in turn alter the excitability of the post-synaptic neurons. Our aim was to determine how synaptic inputs affect the antidromic invasion of the cell body. Approach. We used a biophysically-based multi-compartment model to simulate antidromic APs in thalamocortical relay (TC) neurons. We applied distributed synaptic inputs to the model and quantified how excitatory and inhibitory inputs contributed to the fidelity of antidromic activation over a range of antidromic frequencies. Main results. Antidromic activation exhibited strong frequency dependence, which arose from the hyperpolarizing afterpotentials in the cell body and its respective recovery cycle. Low-frequency axonal spikes faithfully invaded the soma, whereas frequent failures of antidromic activation occurred at high frequencies. The frequency-dependent pattern of the antidromic activation masked burst-driver inputs to TC neurons from the cerebellum in a frequency-dependent manner. Antidromic activation also depended on the excitability of the cell body. Excitatory synaptic inputs improved the fidelity of antidromic activation by increasing the excitability, and inhibitory inputs suppressed antidromic activation by reducing soma excitability. Stimulus-induced depolarization of neuronal segments also facilitated antidromic propagation and activation. Significance. The results reveal that synaptic inputs, stimulus frequency, and electrode position regulate antidromic activation of the cell body during extracellular stimulation. These findings provide a biophysical basis for interpreting the widespread inhibition/activation of target nuclei during DBS.
Differential physiological and metabolic response to low temperature in two zoysiagrass genotypes native to high and low latitude

Low temperature is one of the important limiting factors for growing season and geographical distribution of plants. Zoysiagrass (Zoysia Willd) is one of the widely used warm-season turfgrass that is distribute in many parts of the world. Zoysaigrass native to high latitude may have evolved higher cold tolerance than the ones native to low latitude. The objective of this study was to investigate the cold stress response in zoysiagrass native to diverse latitude at phenotypic, physiological and metabolic levels. Two zoysiagrass (Z. japonica) genotypes, Latitude-40 (higher latitude) and Latitude-22 (lower latitude) were subjected to four temperature treatments (optimum, 30/25°C, day/night; suboptimum, 18/12°C; chilling, 8/2°C; freezing, 2/-4°C) progressively in growth chambers. Low temperature (chilling and freezing) increased leaf electrolyte leakage (EL) and reduced plant growth, turf quality, chlorophyll (Chl) content, photochemical efficiency (Fv/Fm) and photosynthesis (Pn, net photosynthetic rate; gs, stomatal conductance; intercellular CO2; Tr, transpiration rate) in two genotypes, with more rapid changes in Latitude-22. Leaf carbohydrates content (glucose, fructose, sucrose, trehalose, fructan, starch) increased with the decreasing of temperature, to a great extend in Latitude-40. Leaf abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA) content increased, while indole-3-acetic acid (IAA), gibberellic acid (GA3) and trans-zeatin ribside (t-ZR) content decreased with the reduction of temperature, with higher content in Latitude-40 than in Latitude-22. Chilling and freezing induced the up-regulation of C-repeat binding factor (ZjCBF), late embryogenesis abundant (ZjLEA3) and dehydration-responsive element binding (ZjDREB1) transcription factors in two genotypes, whereas those genes exhibited higher expression levels in Latitude-40, particularly under freezing temperature. These results suggested that zoysiagrass native to higher latitude exhibited higher freezing tolerance may attribute to the higher carbohydrates serving as energy reserves and stress protectants that stabilize cellular membranes. The phytohormones may serve signals in regulating plant growth, development and adaptation to low temperature as well as inducing the up-regulated ZjCBF, ZjLEA3 and ZjDREB1 expressions thus result in a higher cold tolerance.
A 5‐step framework to promote nursing community inclusivity: The example of nurses with disabilities

AIMS AND OBJECTIVES To provide a five-step conceptual framework to promote community inclusivity among nurses and nursing students, using the example of nursing student with a disability. BACKGROUND The value of cultural diversity, including characteristics such as socioeconomic status, ability/disability, sexual affection and ethnicity and/or race, is integrated into bachelor's nursing programmes. Yet, often the focus centres on patient care rather than to fellow nursing students or registered nurses. DESIGN Discursive paper describing a five-step health promotion course framework to promote inclusion for students with disabilities into the nursing community. METHODS Using the health promotion course platform, this framework demonstrates the integration of important issues such as well-being to those of cultural diversity, inclusivity and feeling belonging to a community, which are essential prerequisites towards achieving cultural competence. FINDINGS Health promotion courses provide an optimal platform to teach students about the social environment, well-being and inclusivity, and gives students the opportunity to reflect on the impact of their attitudes and behaviours on social inclusivity in their student community, and later, on their nursing community. CONCLUSIONS Using the example of nursing students with disabilities, the five-step framework incorporates the concepts of social well-being, health and community inclusivity. Nursing students belong to a culturally diverse community including individuals with disabilities. A single course on community inclusivity is insufficient; the approach of inclusivity must be woven throughout the nursing curriculum. RELEVANCE TO CLINICAL PRACTICE As approximately 15% of the world's population has a disability, nurses must possess an understanding of individuals with a disability as an aspect of cultural diversity. It is the responsibility of programmes to instil in nursing students, the ability to appreciate and work with culturally diverse student and registered nurses. Such goals not only reflect nursing goals, but also strengthen the cohesion and inclusivity of the nursing community.
Gene–environment interactions in case–control studies with silent disease

Genome‐wide association studies (GWAS) often measure gene–environment interactions (G × E). We consider the problem of accurately estimating a G × E in a case–control GWAS when a subset of the controls have silent, or undiagnosed, disease and the frequency of the silent disease varies by the environmental variable. We show that using case–control status without accounting for misdiagnosis can lead to biased estimates of the G × E. We further propose a pseudolikelihood approach to remove the bias and accurately estimate how the relationship between the genetic variant and the true disease status varies by the environmental variable. We demonstrate our method in extensive simulations and apply our method to a GWAS of prostate cancer.
Cutting the Cord: Designing a High-quality Untethered VR System with Low Latency Remote Rendering

This paper introduces an end-to-end untethered VR system design and open platform that can meet virtual reality latency and quality requirements at 4K resolution over a wireless link. High-quality VR systems generate graphics data at a data rate much higher than those supported by existing wireless-communication products such as Wi-Fi and 60GHz wireless communication. The necessary image encoding, makes it challenging to maintain the stringent VR latency requirements. To achieve the required latency, our system employs a Parallel Rendering and Streaming mechanism to reduce the add-on streaming latency, by pipelining the rendering, encoding, transmission and decoding procedures. Furthermore, we introduce a Remote VSync Driven Rendering technique to minimize display latency. To evaluate the system, we implement an end-to-end remote rendering platform on commodity hardware over a 60Ghz wireless network. Results show that the system can support current 2160x1200 VR resolution at 90Hz with less than 16ms end-to-end latency, and 4K resolution with 20ms latency, while keeping a visually lossless image quality to the user.
Preoperative Prostate MRI: A Road Map for Surgery.

OBJECTIVE MRI of the prostate is widely used in prostate cancer for local staging. The purpose of this article is to show how preoperative prostate MRI findings may be used as a road map for surgery to preserve the neurovascular bundle, identify risk factors associated with positive surgical margins, and evaluate findings associated with intraoperative complications and functional recovery after surgery. CONCLUSION Knowledge of surgically relevant imaging findings can increase radiologists' confidence in reporting them to our colleagues.