Miracle-dz/UniFAR-FTUs huggingface dataset:
GPU Based Parallel Ising Computing for Combinatorial Optimization Problems in VLSI Physical Design.

In VLSI physical design, many algorithms require the solution of difficult combinatorial optimization problems such as max/min-cut, max-flow problems etc. Due to the vast number of elements typically found in this problem domain, these problems are computationally intractable leading to the use of approximate solutions. In this work, we explore the Ising spin glass model as a solution methodology for hard combinatorial optimization problems using the general purpose GPU (GPGPU). The Ising model is a mathematical model of ferromagnetism in statistical mechanics. Ising computing finds a minimum energy state for the Ising model which essentially corresponds to the expected optimal solution of the original problem. Many combinatorial optimization problems can be mapped into the Ising model. In our work, we focus on the max-cut problem as it is relevant to many VLSI physical design problems. Our method is inspired by the observation that Ising annealing process is very amenable to fine-grain massive parallel GPU computing. We will illustrate how the natural randomness of GPU thread scheduling can be exploited during the annealing process to create random update patterns and allow better GPU resource utilization. Furthermore, the proposed GPU-based Ising computing can handle any general Ising graph with arbitrary connections, which was shown to be difficult for existing FPGA and other hardware based implementation methods. Numerical results show that the proposed GPU Ising max-cut solver can deliver more than 2000X speedup over the CPU version of the algorithm on some large examples, which shows huge performance improvement for addressing many hard optimization algorithms for practical VLSI physical design.
Non-Local Low-Rank Cube-Based Tensor Factorization for Spectral CT Reconstruction

Spectral computed tomography (CT) reconstructs material-dependent attenuation images from the projections of multiple narrow energy windows, which is meaningful for material identification and decomposition. Unfortunately, the multi-energy projection datasets usually have lower signal-noise ratios (SNR). Very recently, a spatial-spectral cube matching frame (SSCMF) was proposed to explore the non-local spatial-spectral similarities for spectral CT. This method constructs a group by clustering up a series of non-local spatial-spectral cubes. The small size of spatial patches for such a group makes the SSCMF fail to fully encode the sparsity and low-rank properties. The hard-thresholding and collaboration filtering in the SSCMF also cause difficulty in recovering the image features and spatial edges. While all the steps are operated on 4-D group, the huge computational cost and memory load might not be affordable in practice. To avoid the above limitations and further improve the image quality, we first formulate a non-local cube-based tensor instead of group to encode the sparsity and low-rank properties. Then, as a new regularizer, the Kronecker-basis-representation tensor factorization is employed into a basic spectral CT reconstruction model to enhance the capability of image feature extraction and spatial edge preservation, generating a non-local low-rank cube-based tensor factorization (NLCTF) method. Finally, the split-Bregman method is adopted to solve the NLCTF model. Both numerical simulations and preclinical mouse studies are performed to validate and evaluate the NLCTF algorithm. The results show that the NLCTF method outperforms the other state-of-the-art competing algorithms.
Buffalo oocyte‐secreted factors promote cumulus cells apoptosis and the rate of cGMP production but not steroidogenesis

The objectives of this study were to investigate the effect of buffalo oocyte-secreted factors (OSFs) on cumulus cells (CCs) functions, apoptosis and cGMP generation, and whether the direct contact between oocyte and CCs is essential for oocyte-mediated regulation of CCs functions. Buffalo CCs were cultured during IVM within three groups: (a) intact cumulus-oocyte complexes (COCs), (b) CCs cocultured with denuded oocytes (DOs) (CCs + DOs) and (c) CCs monolayer cultured alone (CCsM). After 24 hr of IVM, CCs were harvested for evaluation of the relative mRNA abundance of the genes encoding gap junction (GJA1), glycolysis (PFKP and LDHA), apoptosis (CASPASE-3 and BCL-2) and steroidogenesis (ER-β and PGR) by QRT-PCR, and CASPASE-3 proteins, using western blot. Intracellular cGMP content was also assessed by ELISA. Results showed that the relative abundance of LDHA, PFKP and BCL-2 significantly increased (p < 0.05) in COCs, whereas GJA1 and CASPASE-3 exhibited lower expression (p < 0.05) compared to CCs + DOs and CCsM groups. However, the expression levels of CASPASE-3, both mRNA and protein, were significantly (p < 0.05) downregulated in CCs + DOs compared to CCsM. There was no significant difference in the expression level of PGR and ER-β between the groups. The intracellular content of cGMP was notably (p < 0.05) higher in COCs compared to CCs + DOs and CCsM groups. In conclusion, this study demonstrated, for the first time, that buffalo OSFs protect CCs against apoptosis and stimulate their cGMP production; however, the regulation of cumulus glycolysis and gap junction is confined to those in close contact with the oocyte. Neither OSFs from COCs nor those from DOs have any effect on CCs steroidogenesis.
The effect of beetroot juice supplementation on repeat-sprint performance in hypoxia

ABSTRACT This investigation assessed the effect of dietary nitrate (NO3−) supplementation, in the form of beetroot juice (BR), on repeat-sprint performance in normoxia and normobaric hypoxia. 12 male team-sport athletes (age 22.3 ± 2.6 y, VO2peak 53.1 ± 8.7 mL.kg−1.min−1) completed three exercise trials involving a 10 min submaximal warm-up and 4 sets of cycling repeat-sprint efforts (RSE; 9 × 4 s) at sea level (CON), or at 3000 m simulated altitude following acute supplementation (140 mL) with BR (HYPBR; 13 mmol NO3−) or NO3–depleted BR placebo (HYPPLA). Peak (PPO) and mean (MPO) power output, plus work decrement were recorded during the RSE task, while oxygen consumption (VO2) was measured during the warm-up. There were no significant differences observed between HYPBR and HYPPLA for PPO or MPO; however, work decrement was reduced in the first RSE set in HYPBR compared with HYPPLA. There was a moderate effect for VO2 to be lower following BR at the end of the 10 min warm-up (ES = 0.50 ± 0.51). Dietary NO3− may not improve repeat-sprint performance in hypoxia but may reduce VO2 during submaximal exercise. Therefore, BR supplementation may be more effective for performance improvement during predominantly aerobic exercise.
Major bleeding with apixaban in atrial fibrillation: patient characteristics, management, and outcomes

ABSTRACT Objectives: To identify patient characteristics, bleed management, and bleed outcomes in patients experiencing an apixaban major bleeding event and to identify opportunities to improve the safe use of apixaban. Methods: This retrospective single health-system study identified apixaban patients experiencing a major bleeding event between January 2013 and May 2016 through electronic medical record review. Patient characteristics, bleed management, and outcomes were extracted in those with a confirmed major bleed assessed by the International Society on Thrombosis and Haemostasis criteria. Results: Fifty major bleeding events occurred in 49 patients (79 ± 9.8 years). Patient characteristics included history of hypertension (94%), anemia (68%), and concomitant antiplatelet use (68%). Gastrointestinal bleeding occurred in 72% of patients and intracranial hemorrhage in 14% of patients. Packed red blood cells (PRBCs) were utilized in 82% of patients and reversal agents were administered to 6% of patients. Mortality during the hospital admission for the bleed was 0%. Anticoagulation was held at discharge in 64% of patients and remained held at 30 days in the majority of patients. Of those on concurrent aspirin therapy, an appropriate indication was not found in 64.7% of patients. Conclusions: Patients with major bleeding were elderly and frequently on inappropriate concomitant antiplatelet therapy. The majority of patients were managed with PRBC transfusion. More than half of patients had anticoagulation therapy held at discharge. Concerns with prescribing and patient management were identified leading to recommendations for improving the safe use of apixaban therapy.
Intravascular Schistosoma mansoni Cleave the Host Immune and Hemostatic Signaling Molecule Sphingosine-1-Phosphate via Tegumental Alkaline Phosphatase

Schistosomes are parasitic flatworms that infect the vasculature of >200 million people around the world. These long-lived parasites do not appear to provoke blood clot formation or obvious inflammation around them in vivo. Proteins expressed at the host–parasite interface (such as Schistosoma mansoni alkaline phosphatase, SmAP) are likely key to these abilities. SmAP is a glycoprotein that hydrolyses the artificial substrate p-nitrophenyl phosphate in a reaction that requires Mg2+ and at an optimal pH of 9. SmAP additionally cleaves the nucleoside monophosphates AMP, CMP, GMP, and TMP, all with a similar Km (~600–650 μM). Living adult worms, incubated in murine plasma for 1 h, alter the plasma metabolome; a decrease in sphingosine-1-phosphate (S1P) is accompanied by an increase in the levels of its component parts—sphingosine and phosphate. To test the hypothesis that schistosomes can hydrolyze S1P (and not merely recruit or activate a host plasma enzyme with this function), living intravascular life-stage parasites were incubated with commercially obtained S1P and cleavage of S1P was detected. Parasites whose SmAP gene was suppressed using RNAi were impaired in their ability to cleave S1P compared to controls. In addition, recombinant SmAP hydrolyzed S1P. Since extracellular S1P plays key roles in controlling inflammation and platelet aggregation, we hypothesize that schistosome SmAP, by degrading S1P, can regulate the level of this bioactive lipid in the environment of the parasites to control these processes in the worm’s local environment. This is the first report of any parasite being able to cleave S1P.
Awe as a Scientific Emotion

Awe has traditionally been considered a religious or spiritual emotion, yet scientists often report that awe motivates them to answer questions about the natural world, and to do so in naturalistic terms. Indeed, awe may be closely related to scientific discovery and theoretical advance. Awe is typically triggered by something vast (either literally or metaphorically) and initiates processes of accommodation, in which existing mental schemas are revised to make sense of the awe-inspiring stimuli. This process of accommodation is essential for the kind of belief revision that characterizes scientific reasoning and theory change. Across six studies, we find that the tendency to experience awe is positively associated with scientific thinking, and that this association is not shared by other positive emotions. Specifically, we show that the disposition to experience awe predicts a more accurate understanding of how science works, rejection of creationism, and rejection of unwarranted teleological explanations more broadly.
Hello darkness my old friend: preferences for darkness vary by neuroticism and co-occur with negative affect*

ABSTRACT Metaphors frequently link negative affect with darkness and associations of this type have been established in several experimental paradigms. Given the ubiquity and strength of these associations, people who prefer dark to light may be more prone to negative emotional experiences and symptoms. A five study investigation (total N = 605) couches these ideas in a new theoretical framework and then examines them. Across studies, 1 in 4 people preferred the perceptual concept of dark over the perceptual concept of light. These dark-preferring people scored higher in neuroticism (Studies 1 and 2) and experienced greater depressive feelings in daily life (Study 3). Moreover, dark preferences shared a robust relationship with depressive symptoms (Study 4) as well as generalised anxiety symptoms (Study 5). The results provide novel insights into negative affectivity and extend conceptual metaphor theory in a way that is capable of making individual difference predictions.
Microbial anaerobic Fe(II) oxidation – Ecology, mechanisms and environmental implications

Iron is the most abundant redox-active metal in the Earth's crust. The one electron transfer between the two most common redox states, Fe(II) and Fe(III), plays a role in a huge range of environmental processes from mineral formation and dissolution to contaminant remediation and global biogeochemical cycling. It has been appreciated for more than a century that microorganisms can harness the energy of this Fe redox transformation for their metabolic benefit. However, this is most widely understood for anaerobic Fe(III)-reducing or aerobic and microaerophilic Fe(II)-oxidizing bacteria. Only in the past few decades have we come to appreciate that bacteria also play a role in the anaerobic oxidation of ferrous iron, Fe(II), and thus can act to form Fe(III) minerals in anoxic settings. Since this discovery, our understanding of the ecology of these organisms, their mechanisms of Fe(II) oxidation and their role in environmental processes has been increasing rapidly. In this article, we bring these new discoveries together to review the current knowledge on these environmentally important bacteria, and reveal knowledge gaps for future research.
Balancing the risk of the evacuation and sheltering-in-place options: a survival study following Japan’s 2011 Fukushima nuclear incident

Objective The decision to evacuate or shelter-in-place is fundamental to emergency response, especially for a vulnerable population. While an elevated risk of mortality due to a hasty, unplanned evacuation has been well documented, there is little research on and knowledge about the health consequences of sheltering-in-place in disaster contexts. We compared hospital mortality in patients who sheltered-in-place (non-evacuees) after the incident with the baseline preincident mortality and articulated postincident circumstances of the hospital while sheltering-in-place. Participants We considered all 484 patients admitted to Takano Hospital (located 22 km South of the Fukushima Daiichi nuclear power plant) from 1 January 2008 to 31 December 2016. Methods Significant differences in mortality rates between preincident baseline and three postincident groups (evacuees, non-evacuees (our major interest) and new admittees) were tested using the Bayesian survival analysis with Weibull multivariate regression and survival probability using the Kaplan-Meier product limit method. All the analyses were separately performed by the internal and psychiatry department. Results After adjusting for covariates, non-evacuees in the internal department had a significantly higher mortality risk with an HR of 1.57 (95% credible intervals 1.11 to 2.18) than the baseline preincident. Of them, most deaths occurred within the first 100 days of the incident. No significant increase in mortality risk was identified in evacuees and new admittees postincident in the department, which were adjusted for covariates. In contrast, for the psychiatry department, statistical difference in mortality risk was not identified in any groups. Conclusions The mortality risk of sheltering-in-place in a harsh environment might be comparable to those in an unplanned evacuation. If sheltering-in-place with sufficient resources is not guaranteed, evacuation could be a reasonable option, which might save more lives of vulnerable people if performed in a well-planned manner with satisfactory arrangements for appropriate transportation and places to safely evacuate.
The effect of nanoemulsified methionine and cysteine on the in vitro expression of casein in bovine mammary epithelial cells

Objective Dairy cattle nutrient requirement systems acknowledge amino acid (AAs) requirements in aggregate as metabolizable protein (MP) and assume fixed efficiencies of MP used for milk protein. Regulation of mammary protein synthesis may be associated with AA input and milk protein output. The aim of this study was to evaluate the effect of nanoemulsified methionine and cysteine on the in-vitro expression of milk protein (casein) in bovine mammary epithelial cells (MAC-T cells). Methods Methionine and cysteine were nonionized using Lipoid S 75 by high-speed homogenizer. The nanoemulsified AA particle size and polydispersity index were determined by dynamic light scattering correlation spectroscopy using a high-performance particle sizer instrument. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was performed to determine the cytotoxicity effect of AAs with and without nanoionization at various concentrations (100 to 500 μg/mL) in mammary epithelial cells. MAC-T cells were subjected to 100% of free AA and nanoemulsified AA concentration in Dulbecco’s modified Eagle medium/nutrient mixture F-12 (DMEM/F12) for the analysis of milk protein (casein) expression by the quantitative reverse transcription polymerase chain reaction method. Results The AA-treated cells showed that cell viability tended to decrease (80%) in proportion to the concentration before nanogenesis, but cell viability increased as much as 90% after nanogenesis. The analysis of the expression of genetic markers related to milk protein indicated that; αs2-casein increased 2-fold, κ-casein increased 5-fold, and the amount of unchanged β-casein expression was nearly doubled in the nanoemulsified methionine-treated group when compared with the free-nanoemulsified methionine-supplemented group. On the contrary, the non-emulsified cysteine-administered group showed higher expression of genetic markers related to milk protein αs2-casein, κ-casein, and β-casein, but all the genetic markers related to milk protein decreased significantly after nanoemulsification. Conclusion Detailed knowledge of factors, such nanogenesis of methionine, associated with increasing cysteine and decreasing production of genetic markers related to milk protein (casein) will help guide future recommendations to producers for maximizing milk yield with a high level of milk protein casein.
Gene therapy for C1 esterase inhibitor deficiency in a Murine Model of Hereditary angioedema

Hereditary angioedema (HAE) is a life‐threatening, autosomal dominant disorder characterized by unpredictable, episodic swelling of the face, upper airway, oropharynx, extremities, genitalia, and gastrointestinal tract. Almost all cases of HAE are caused by mutations in the SERPING1 gene resulting in a deficiency in functional plasma C1 esterase inhibitor (C1EI), a serine protease inhibitor that normally inhibits proteases in the contact, complement, and fibrinolytic systems. Current treatment of HAE includes long‐term prophylaxis with attenuated androgens or human plasma‐derived C1EI and management of acute attacks with human plasma‐derived or recombinant C1EI, bradykinin, and kallikrein inhibitors, each of which requires repeated administration. As an approach to effectively treat HAE with a single treatment, we hypothesized that a one‐time intravenous administration of an adeno‐associated virus (AAV) gene transfer vector expressing the genetic sequence of the normal human C1 esterase inhibitor (AAVrh.10hC1EI) would provide sustained circulating C1EI levels sufficient to prevent angioedema episodes.
Connected Components at Scale via Local Contractions

As a fundamental tool in hierarchical graph clustering, computing connected components has been a central problem in large-scale data mining. While many known algorithms have been developed for this problem, they are either not scalable in practice or lack strong theoretical guarantees on the parallel running time, that is, the number of communication rounds. So far, the best proven guarantee is $\Oh(\log n)$, which matches the running time in the PRAM model. In this paper, we aim to design a distributed algorithm for this problem that works well in theory and practice. In particular, we present a simple algorithm based on contractions and provide a scalable implementation of it in MapReduce. On the theoretical side, in addition to showing $\Oh(\log n)$ convergence for all graphs, we prove an $\Oh(\log \log n)$ parallel running time with high probability for a certain class of random graphs. We work in the MPC model that captures popular parallel computing frameworks, such as MapReduce, Hadoop or Spark. On the practical side, we show that our algorithm outperforms the state-of-the-art MapReduce algorithms. To confirm its scalability, we report empirical results on graphs with several trillions of edges.
CUPSMAN: Control User Plane Separation Based Routing in Ad-hoc Networks

Separation of user (data) plane from the control plane in networks helps scale resources independently, increase the quality of service and facilitate autonomy by employing software-defined networking techniques. Clustering introduces hierarchy in ad hoc networks where control functions can be carried out by some designated cluster heads. It is also an effective solution to handle challenges due to lack of centralized controllers and infrastructure in ad-hoc networks. Clustered network topologies gain a significant amount of scalability and reliability in comparison to flat topologies. Different roles that nodes have in a clustered network can be effectively used for routing as well. In this paper, we propose a novel plane-separated routing algorithm, Cluster-based Hybrid Routing Algorithm (CHRA). In CHRA, we take advantage of the hierarchical clustered structure through control and user plane separation (CUPS) in mobile ad-hoc networks. In the cluster neighborhood with a particular size, a link-state routing is used to minimize delay, control overhead, and also utilize energy consumption. For facilitating the communication with distant nodes, we form a routing backbone that is responsible for both control and data messages. The results show that CHRA outperforms its opponents in terms of fair energy consumption and end-to-end delay.