Miracle-dz/UniFAR-FTUs huggingface dataset:
Episodic β‐cell death and dedifferentiation during diet‐induced obesity and dysglycemia in male mice

Loss of functional islet '‐cell mass through cellular death or dedifferentiation is thought to lead to dysglycemia during the βrogression from obesity to ty'e 2 diabetes. To assess these 'rocesses in a mouse model of obesity, we performed measures of circulating cell‐free differentially methylated insulin II (Ins2) DNA as a bio marker of β‐cell death and aldehyde dehydrogenase 1 family member A3 (ALDH1A3) and forkhead box 01 (Foxol) immunostaining as markers ofβ‐cell dedifferentiation. Eight‐week‐old, C57BL/6J mice were fed a low‐fat diet (LFD; 10% kcal from fat) or a high‐fat diet (HFD; 60% kcal from fat) and were followed longitudinally for up to 13 wk to measure glycemic control and β‐cell mass, death, and dedifferentiation. Compared with LFD controls, β‐cell mass increased during the feeding period in HFD animals, and statistically greater β‐cell death (unmethylated Ins2) was detectable at 2 and 6 wk after diet initiation. Those times correspond to periods when significant step increases in fasting glucose and glucose intolerance, respectively, were detected. ALDH1A3 and Foxo1 immunostaining of the pancreas revealed evidence of β‐cell dedifferentiation by 13 wk when fed an HFD, but not in LFD controls. In conclusion, early episodic β‐cell death may be a feature of cellular turnover correlated with changes in glycemia during β‐cell mass accrual in obesity, whereas β‐cell dedifferentiation may be a feature seen later in established disease. —Tersey, S. A. , Levasseur, E. M. , Syed, F. , Farb, T. B. , Orr, K. S. , Nelson, J. B. , Shaw, J. L. , Bokvist, K. , Mather, K. J., Mirmira, R. G. Episodic β‐cell death and dedifferentiation during diet‐induced obesity and dysglycemia in male mice. FASEB J. 32, 6150–6158 (2018). www.fasebj. org
Generating multivariate continuous data via the notion of nearest neighbors

Taylor and Thompson [15] introduced a clever algorithm for simulating multivariate continuous data sets that resemble the original data. Their approach is predicated upon determining a few nearest neighbors of a given row of data through a statistical distance measure, and subsequently combining the observations by stochastic multipliers that are drawn from a uniform distribution to generate simulated data that essentially maintain the original data trends. The newly drawn values are assumed to come from the same underlying hypothetical process that governs the mechanism of how the data are formed. This technique is appealing in that no density estimation is required. We believe that this data-based simulation method has substantial potential in multivariate data generation due to the local nature of the generation scheme, which does not have strict specification requirements as in most other algorithms. In this work, we provide two R routines: one has a built-in simulator for finding the optimal number of nearest neighbors for any given data set, and the other generates pseudo-random data using this optimal number.
Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma

Genomic instability contributes to the neoplastic phenotype by deregulating key cancer-related genes, which in turn can have a detrimental effect on patient outcome. DNA amplification of the 8p11-p12 genomic region has clinical and biological implications in multiple malignancies, including breast carcinoma where the amplicon has been associated with tumor progression and poor prognosis. However, oncogenes driving increased cancer-related death and recurrent genetic features associated with the 8p11-p12 amplicon remain to be identified. In this study, DNA copy number and transcriptome profiling data for 229 primary invasive breast carcinomas (corresponding to 185 patients) were evaluated in conjunction with clinicopathological features to identify putative oncogenes in 8p11-p12 amplified samples. Illumina paired-end whole transcriptome sequencing and whole-genome SNP genotyping were subsequently performed on 23 samples showing high-level regional 8p11-p12 amplification to characterize recurrent genetic variants (SNPs and indels), expressed gene fusions, gene expression profiles and allelic imbalances. We now show previously undescribed chromothripsis-like patterns spanning the 8p11-p12 genomic region and allele-specific DNA amplification events. In addition, recurrent amplification-specific genetic features were identified, including genetic variants in the HIST1H1E and UQCRHL genes and fusion transcripts containing MALAT1 non-coding RNA, which is known to be a prognostic indicator for breast cancer and stimulated by estrogen. In summary, these findings highlight novel candidate targets for improved treatment of 8p11-p12 amplified breast carcinomas.
HCCL at SemEval-2018 Task 8: An End-to-End System for Sequence Labeling from Cybersecurity Reports

This paper describes HCCL team systems that participated in SemEval 2018 Task 8: SecureNLP (Semantic Extraction from cybersecurity reports using NLP). To solve the problem, our team applied a neural network architecture that benefits from both word and character level representaions automatically, by using combination of Bi-directional LSTM, CNN and CRF (Ma and Hovy, 2016). Our system is truly end-to-end, requiring no feature engineering or data preprocessing, and we ranked 4th in the subtask 1, 7th in the subtask2 and 3rd in the SubTask2-relaxed.
Sea Surface Radar Scattering at L-Band Based on Numerical Solution of Maxwell’s Equations in 3-D (NMM3D)

Radar scattering from ocean surfaces is investigated by 3-D numerical solution of Maxwell’s equations [numerical Maxwell’s model in 3-D (NMM3D)] using the ocean surface profiles stochastically generated from a 3-D Durden–Vesecky ocean spectrum. The surface integral equations (SIEs) are formulated for dielectric surfaces using Green’s functions of the air and the ocean permittivities with the surface tangential electric and magnetic fields as the unknowns. In solving the SIEs using the method of moment, a fast matrix solver of the sparse matrix canonical grid is used in conjunction with Rao–Wilton–Glisson basis functions. The computation has been implemented on a high-performance parallel computing cluster for problems with up to six million surface unknowns. Unlike the two-scale model (TSM) approximation, NMM3D does not require division of the surface spectrum into large- and small-scale ocean waves. The results of backscattering simulations are compared to Aquarius satellite radar measurements for wind speeds of 5, 8, and 10 m/s and for incidence angles of 29°, 39°, and 46°. The results show that NMM3D ocean backscattering solutions at L-band are in good agreement with Aquarius satellite radar data for co-polarized VV, HH, and cross-polarized VH returns as well as for the VV/HH ratio. The azimuthal dependence of L-band backscatter is also assessed. Finally, NMM3D results are compared to TSM solutions and are shown to lie close to Aquarius data in observed VV/HH ratio, and their azimuthal dependencies.
Creep feeding beef calves

Preweaning supplementing, or “creep feeding,” is the nutrient supplementation of nursing beef calves. Supplements can include creep feeding with concentrated feeds or creep grazing with high quality forage. Milk production in beef females typically peaks about 2 months after calving. Milk from a lactating beef cow offers only about half the nutrients that a 3to 4month-old calf needs for maximum growth. Calves need extra nutrients to perform to their genetic potential. Pastures with low nutrient quality, which is most common in late summer, or low nutrient quantity, which is common in winter or during drought, cannot meet calves’ nutritional needs for maximum growth. While many warm-season perennial grasses in Mississippi pastures are often plentiful in quantity, they do not maximize calf gains even when considered high quality for the forage species. For example, both average daily gains and weaning weights increase for calves that have access to legume creep grazing on high quality bermudagrass pastures. These production impacts indicate a need to supplement calves’ diets with highquality feed before weaning. High quality grazing is usually the most economical source of additional nutrients for nursing calves. Calves raised in production conditions that would otherwise result in high weaning weights (such as on high quality, abundant forage) usually do not benefit much from additional creep feeding. Typically, creep access to supplemental feed or forage uses creep feeders or gates that restrict access to the supplement by larger or more mature cattle while allowing calves to feed on or graze supplementation at will. Creep feeding “gates” can be created with a single strand of electrified polywire strategically attached to T-posts and placed around creep supplement. Wires should be 36 to 42 inches above the ground so calves can pass under but mature cattle cannot. Creep gates are also commercially available and can be placed on self-feeders or stand-alone creep feeders (Figure 1). Creep entrance slots should be 18 inches wide. Creep Feeding Beef Calves
Local apoptotic-like mechanisms underlie complement-mediated synaptic pruning

Significance Synaptic pruning is dominant in early ontogenesis when a large number of unnecessary synapses are eliminated, and it maintains synaptic plasticity in the mature healthy brain, e.g., in memory processes. Its malfunction is involved in degenerative diseases such as Alzheimer’s disease. C1q, a member of the immune complement system, plays a central role in the selective pruning of synapses by microglial phagocytosis. Understanding the molecular aspects of complement-mediated synapse elimination is of high importance for developing effective therapeutic interventions in the future. Our analysis on C1q-tagged synaptosomes revealed that C1q label-based synaptic pruning is linked to local apoptotic-like processes in synapses. C1q, a member of the immune complement cascade, is implicated in the selective pruning of synapses by microglial phagocytosis. C1q-mediated synapse elimination has been shown to occur during brain development, while increased activation and complement-dependent synapse loss is observed in neurodegenerative diseases. However, the molecular mechanisms underlying C1q-controlled synaptic pruning are mostly unknown. This study addresses distortions in the synaptic proteome leading to C1q-tagged synapses. Our data demonstrated the preferential localization of C1q to the presynapse. Proteomic investigation and pathway analysis of C1q-tagged synaptosomes revealed the presence of apoptotic-like processes in C1q-tagged synapses, which was confirmed experimentally with apoptosis markers. Moreover, the induction of synaptic apoptotic-like mechanisms in a model of sensory deprivation-induced synaptic depression led to elevated C1q levels. Our results unveiled that C1q label-based synaptic pruning is triggered by and directly linked to apoptotic-like processes in the synaptic compartment.
Emission-aware stochastic resource planning scheme for data center microgrid considering batch workload scheduling and risk management

Internet data centers are booming in the last few years, leading to gigantic amount of energy consumption and greenhouse gas emission. In this paper, a data center microgrid including conventional units, energy storage, and renewable generation is modeled to optimize its electricity bill and carbon footprint. Considering the randomness of electricity price, renewable output and workload distribution, the volatility risk is incorporated to measure the associated operation risk. Then a day-ahead emission-aware stochastic resource planning scheme is formulated to decide the strategy on power procurement, energy storage operation, batch workload allocation and unit commitment of conventional units. Simulation results show the effectiveness of the proposed approach.
An edge optimization method based on segmented surfaces of stone flakes

In our previous research, [3] has put forward a method to extract surfaces of stone flakes. But for reassembling stone flakes, it is necessary to obtain the suitable flake surface. Extracting accurate and smooth edges of stone flake surfaces plays a significant part. The former method extracted the boundary edges of stone flakes based on the density of points. However, some surface boundaries are rough. It is hard to match flake surfaces with these irregular edges. To solve this problem, an effective method is proposed for optimizing edges based on a mesh. According to experiments, results of our optimization method indicate that the boundary edges become smooth, which will make a contribute to stone flake matching.
Pomegranate seed extract reduces ischemia induced anxiety in male rats

Introduction: Ischemia-associated depression and anxiety may occur due to brain damage caused by oxidative stress. A number of reports indicated that treatment with herbal plant extracts with antioxidant properties could lead to a significant reduction in Ischemic complications. The aim of this study was to evaluate the behaviors of ischemic rats through animal models of anxiety and exploratory behavior (open field) to determine the efficiency of pomegranate seed extract (PGSE) as antioxidant.Methods: In this study, 21 male Wistar rats (250 ± 20 g) were randomly divided into 3 groups with 7 in each: 1) Control; 2) Ischemic; 3) Ischemic plus PGSE (14 days). In order to create ischemia/hypoperfusion, carotid arteries were ligatured and cut bilaterally. Then, plus maze and open-field tests were used for the measurement.Results: Ischemic rats showed a significant increase in anxiety or decrease approach and reduction locomotor activity compared to control group. Fourteen days administration of PGSE significantly improved the immobilization and ischemia-induced anxiety.Conclusion: PGSE exhibits therapeutic potential for anxiety and depression, which is most likely related, at least in part, to its antioxidant and free radical scavenging actions.
Title The four Cs of HIV prevention with African Americans : Crisis , condoms , culture , and community Permalink

HIV/AIDS continues to be a devastating epidemic with African American communities carrying the brunt of the impact. Despite extensive biobehavioral research, current strategies have not resulted in significantly decreasing HIV/ AIDS cases among African Americans. The next generation of HIV prevention and risk reduction interventions must move beyond basic sex education and condom use and availability. Successful interventions targeting African Americans must optimize strategies that integrate sociocultural factors and address institutional and historical barriers that hinder or support HIV risk reduction behaviors. Community-based participatory research to decrease the HIV/AIDS disparity by building community capacity and infrastructure and advocating for and distributing equitably, power and resources, must be promoted. Recommendations for paradigm shifts in using innovative theories and conceptual frameworks and for training researchers, clinicians, grant and journal reviewers, and community members are made so that culturally congruent interventions may be tested and implemented at the community level.
VM processes state detection by hypervisor tracing

The diagnosis of performance issues in cloud environments is a challenging problem, due to the different levels of virtualization, the diversity of applications and their interactions on the same physical host. Moreover, because of privacy, security, ease of deployment and execution overhead, an agent-less method, which limits its data collection to the physical host level, is often the only acceptable solution. In this paper, a precise host-based method, to recover wait state for the processes inside a given Virtual Machine (VM), is proposed. The virtual Process State Detection (vPSD) algorithm computes the state of processes through host kernel tracing. The state of a virtual Process (vProcess) is displayed in an interactive trace viewer (Trace Compass) for further inspection. Our proposed VM trace analysis algorithm has been open-sourced for further enhancements and for the benefit of other developers. Experimental evaluations were conducted using a mix of workload types (CPU, Disk, and Network), with different applications like Hadoop, MySQL, and Apache. vPSD, being based on host hypervisor tracing, brings a lower overhead (around 0.03%) as compared to other approaches.
A Low Contact Resistance 4-Terminal Mems Relay: Theoretical Analysis, Design, and Demonstration

A 4-terminal microelectromechanical systems (MEMS) relay has long been sought for signal switching applications because it allows de-coupling of the actuation (body and gate) and signal (source and drain) components unlike a 3-terminal MEMS relay. However, the contact resistance still remains a serious problem in current 4-terminal MEMS relays compared with the 3-terminal MEMS relays. In this paper, using theoretical analysis, we first determined that the two-contact design, which was the most common design in the 4-terminal MEMS relay, was the origin of the high contact resistance. We subsequently developed a 4-terminal MEMS relay with a novel single-contact design. The fabricated 4-terminal MEMS relay with the single-contact design exhibited a contact resistance of 18 <inline-formula> <tex-math notation="LaTeX">$\text{m}\Omega $ </tex-math></inline-formula>. To the best of our knowledge, this result is the lowest value among 4-terminal MEMS relays. In addition, we demonstrated that the two-contacts are the origin of the high contact resistance using measurement. The relay operated up to <inline-formula> <tex-math notation="LaTeX">$1.1\times 10^{6}$ </tex-math></inline-formula> cycles at 1 V / 50 mA in air and hot switching conditions. Finally, the proposed 4-terminal MEMS relay was hermetically packaged for use in commercial applications. [2017-0183]
Tempo-Lexical Context Driven Word Embedding for Cross-Session Search Task Extraction

Task extraction is the process of identifying search intents over a set of queries potentially spanning multiple search sessions. Most existing research on task extraction has focused on identifying tasks within a single session, where the notion of a session is defined by a fixed length time window. By contrast, in this work we seek to identify tasks that span across multiple sessions. To identify tasks, we conduct a global analysis of a query log in its entirety without restricting analysis to individual temporal windows. To capture inherent task semantics, we represent queries as vectors in an abstract space. We learn the embedding of query words in this space by leveraging the temporal and lexical contexts of queries. Embedded query vectors are then clustered into tasks. Experiments demonstrate that task extraction effectiveness is improved significantly with our proposed method of query vector embedding in comparison to existing approaches that make use of documents retrieved from a collection to estimate semantic similarities between queries.
Coarse Lexical Frame Acquisition at the Syntax–Semantics Interface Using a Latent-Variable PCFG Model

We present a method for unsupervised lexical frame acquisition at the syntax–semantics interface. Given a set of input strings derived from dependency parses, our method generates a set of clusters that resemble lexical frame structures. Our work is motivated not only by its practical applications (e.g., to build, or expand the coverage of lexical frame databases), but also to gain linguistic insight into frame structures with respect to lexical distributions in relation to grammatical structures. We model our task using a hierarchical Bayesian network and employ tools and methods from latent variable probabilistic context free grammars (L-PCFGs) for statistical inference and parameter fitting, for which we propose a new split and merge procedure. We show that our model outperforms several baselines on a portion of the Wall Street Journal sentences that we have newly annotated for evaluation purposes.
Cnn-Based Detection of Generic Contrast Adjustment with Jpeg Post-Processing

Detection of contrast adjustments in the presence of JPEG post processing is known to be a challenging task. JPEG post processing is often applied innocently, as JPEG is the most common image format, or it may correspond to a laundering attack, when it is purposely applied to erase the traces of manipulation. In this paper, we propose a CNN-based detector for generic contrast adjustment, which is robust to JPEG compression. The proposed system relies on a patch-based Convolutional Neural Network (CNN), trained to distinguish pristine images from contrast adjusted images, for some selected adjustment operators of different nature. Robustness to JPEG compression is achieved by training the CNN with JPEG examples, compressed over a range of Quality Factors (QFs). Experimental results show that the detector works very well and scales well with respect to the adjustment type, yielding very good performance under a large variety of unseen tonal adjustments.
Applicability of large-ion lithophile and high field strength element basalt discrimination diagrams

ABSTRACT Basalt discriminant diagrams have been used to identify the tectonic setting of basaltic magmatism since the 1970s and have played an important role in reconstructing paleotectonic environments. However, the significant increase in the availability of geochemical data has led to a reassessment of these diagrams, suggesting that some of the tectonic settings indicated by these diagrams are not accurate. Here, we use a database of global ocean island basalt (OIB), mid-ocean ridge basalt (MORB), and island arc basalt (IAB) geochemistry to propose a series of new tectonic discriminant diagrams based on the ratios of large-ion lithophile elements (LILEs) to high field strength elements (HFSEs). These new diagrams indicate that the LILE can be used to differentiate OIB, MORB, and IAB samples, meaning that LILE/HFSE ratios can discriminate between these basalts that form in different tectonic settings. Our new diagrams can correctly assign samples to OIB, MORB, and IAB categories more than 85% of the time, with the discrimination between OIB and MORB having an accuracy of slightly less than 85%.