Miracle-dz/UniFAR-FTUs huggingface dataset:
Absence of Sirt3 aggravates cisplatin nephrotoxicity via enhanced renal tubular apoptosis and inflammation

Cisplatin-based chemotherapy is commonly used in the treatment of solid tumors; however, this agent is limited by its adverse effects on normal tissues, including the kidneys, ears and peripheral nerves. Mechanisms of cisplatin nephrotoxicity are proposed to involve oxidative stress, inflammation, cellular apoptosis and cell cycle regulation. Sirtuin 3 (Sirt3) is a member of the sirtuin family of NAD+-dependent enzymes with homology to Saccharomyces cerevisiae gene silent information regulator 2. Sirt3 is located in mitochondria and is involved in mitochondrial energy metabolism and function; however, the role of Sirt3 in cisplatin nephrotoxicity remains unclear. In the present study, whether Sirt3 has anti-inflammatory and anti-apoptotic effects on cisplatin-induced nephrotoxicity was investigated in mice. Sirt3 knockout mice (Sirt3(−/−)) and corresponding wild type mice were employed in the present study. Cisplatin nephrotoxicity was induced by intraperitoneal injection of cisplatin (20 mg/kg). After 3 days following cisplatin treatment, blood and kidney tissues were harvested. Renal function and histology were evaluated. Tubular apoptosis, cell adhesion molecule expression, and inflammatory cells were evaluated by immunohistochemistry and western blot analysis. Following the induction of cisplatin nephrotoxicity, renal function was significantly aggravated in Sirt3 knockout (KO) mice. Tubular injury and inflammatory cell infiltration were significantly increased in Sirt3KO mice compared with wild type mice. Terminal deoxynucleotidyl transferase-mediated dUTP nick-end label-positive tubular cells and renal monocyte chemoattractant protein-1 expression levels were increased in Sirt3KO mice compared with in wild type mice. In summary, the absence of Sirt3 aggravated in renal injury by increasing renal inflammation and tubular apoptosis. The results of the present study suggested that Sirt3 may have an important role in cisplatin-induced nephrotoxicity.
Deep Survival : The Deep Cox Proportional Hazards Network

Different neural network architectures have been effective in modeling survival datasets in which patients’ death times are unknown, i.e. right-censored. However, these neural networks have rarely been shown to outperform their linear counterparts, such as the Cox proportional hazards model. In this paper, we run simulated experiments and use real survival data to build upon the risk-regression architecture proposed by Faraggi-Simon. We demonstrate that a Deep Cox proportional hazards model not only works as well, but also outperforms the standard linear Cox proportional hazards model in predictive ability on survival datasets with non-linear proportional risks. We then show that the neural network can also function as a recommender system by including a categorical variable representing a treatment group. The results of our study suggest, that with modern techniques, neural networks can successfully model Cox regression and, furthermore, explain the interactions of a patient’s factors with their calculated risk.
CMOS-Compatible Tunable Vernier Ring Laser using Erbium Doped Waveguide on a Silicon Photonics Platform

We demonstrate the first silicon photonic tunable laser with integrated erbium-doped Al<inf>2</inf>O<inf>3</inf> waveguides. The laser is designed to have Vernier ring structure for wide tuning operation. It has a 0.23cm<sup>2</sup> footprint and 1.6mW output power.
Multi-Owner Scheduling for Cascade Hydro Power Using Multi-Objective Optimization Technique

The optimal scheduling of hydro power can increase the power generation and other benefits without increasing the existing equipment and investment. Most of the existing reservoir dispatching is aimed at several unified power stations in the same river basin, and it is difficult to carry out joint scheduling for those who belong to different owner of power stations in the same basin. In view of the above challenges, with the analysis of the coupling relationship among the owners in the basin, the idea of multi-objective optimization is adopted to handle this issue. With the goal of maximizing the power benefits in the whole basin, an optimal scheduling model of multi-owner is proposed, in which multiple owners are optimized simultaneously as the objectives. Taking some reservoirs and power stations in the Lushuihe River in Jiangxi Province as a case study, the simulation results show that the proposed model and algorithm have certain application value, which can better solve the optimal dispatching of multi-owners in the basin with the increasing the power benefit, and can even achieve storage and peak regulation without loss of power generation. It provides a new idea for cascade joint optimization.
Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1

Significance DNA methylation and histone posttranslational modifications are key epigenetic marks that contribute to the fine-tuned regulation of gene expression and other chromatin-templated biological processes. Here, we build artificial chromatin templates and reveal key chromatin structural features and epigenetic marks that coordinately regulate the binding and enzymatic activity of the DNA methylation regulator UHRF1. Studying activities of epigenetic regulators in the context of defined chromatin templates, particularly for multidomain histone and DNA binding proteins such as UHRF1, is critical for understanding molecular mechanisms of epigenetic crosstalk and mechanics regulating epigenetic signaling, and for determining how epigenetic dysregulation contributes to human disease. Mitotic inheritance of DNA methylation patterns is facilitated by UHRF1, a DNA- and histone-binding E3 ubiquitin ligase that helps recruit the maintenance DNA methyltransferase DNMT1 to replicating chromatin. The DNA methylation maintenance function of UHRF1 is dependent on its ability to bind chromatin, where it facilitates monoubiquitination of histone H3 at lysines 18 and 23, a docking site for DNMT1. Because of technical limitations, this model of UHRF1-dependent DNA methylation inheritance has been constructed largely based on genetics and biochemical observations querying methylated DNA oligonucleotides, synthetic histone peptides, and heterogeneous chromatin extracted from cells. Here, we construct semisynthetic mononucleosomes harboring defined histone and DNA modifications and perform rigorous analysis of UHRF1 binding and enzymatic activity with these reagents. We show that multivalent engagement of nucleosomal linker DNA and dimethylated lysine 9 on histone H3 directs UHRF1 ubiquitin ligase activity toward histone substrates. Notably, we reveal a molecular switch, stimulated by recognition of hemimethylated DNA, which redirects UHRF1 ubiquitin ligase activity away from histones in favor of robust autoubiquitination. Our studies support a noncompetitive model for UHRF1 and DNMT1 chromatin recruitment to replicating chromatin and define a role for hemimethylated linker DNA as a regulator of UHRF1 ubiquitin ligase substrate selectivity.
Optimal Algorithms for Ridge and Lasso Regression with Partially Observed Attributes

We consider the most common variants of linear regression, including Ridge, Lasso and Support-vector regression, in a setting where the learner is allowed to observe only a fixed number of attributes of each example at training time. We present simple and efficient algorithms for these problems: for Lasso and Ridge regression they need the same total number of attributes (up to constants) as do full-information algorithms, for reaching a certain accuracy. For Support-vector regression, we require exponentially less attributes compared to the state of the art. By that, we resolve an open problem recently posed by Cesa-Bianchi et al. (2010). Experiments show the theoretical bounds to be justified by superior performance compared to the state of the art.
A Quasi-Planar  $H$ -Plane Waveguide Power Divider With Full Bandwidth

A quasi-planar <inline-formula> <tex-math notation="LaTeX">${H}$ </tex-math></inline-formula>-plane waveguide power divider/ combiner with full bandwidth is proposed in this letter. The proposed waveguide power divider is composed of three <inline-formula> <tex-math notation="LaTeX">${H}$ </tex-math></inline-formula>-plane rectangular waveguide ports, located in the horizontal plane, a vertical port at the bottom, and a coupling region. The coupling region, all the three <inline-formula> <tex-math notation="LaTeX">${H}$ </tex-math></inline-formula>-plane ports, and the entire waveguide section share the same upper plane, which makes the proposed power divider a quasi-plane structure. Based on the optimized simulation results, a prototype of the waveguide power divider was fabricated and tested. The measured results show that the return loss for all <inline-formula> <tex-math notation="LaTeX">${H}$ </tex-math></inline-formula>-plane ports is lower than −20 dB, the overall insertion loss is lower than 0.15 dB, and the isolation between the two output ports is higher than 20 dB. The measured amplitude and phase difference are less than 0.1 dB and 1°, respectively.
Dietary fats modify vascular fat composition, eNOS localization within lipid rafts and vascular function in obesity

We tested whether dietary fatty acids alter membrane composition shifting localization of signaling pathways within caveolae to determine their role in vascular function. Wild type (WT) and caveolin‐1‐deficient mice (cav‐1 KO), required for vascular caveolae formation, were fed low fat (LF), high saturated fat (HF, 60% kcal from lard), or high‐fat diet with 50:50 lard and n‐3 polyunsaturated fatty acid‐enriched menhaden oil (MO). HF and MO increased body weight and fat in WT but had less effect in cav‐1 KO. MO increased unsaturated fatty acids and the unsaturation index of aorta from WT and cav‐1 KO. In LF WT aorta, endothelial nitric oxide synthase (eNOS) was localized to cav‐1‐enriched low‐density fractions which shifted to actin‐enriched high‐density fractions with acetylcholine (ACh). HF and MO shifted eNOS to high‐density fractions in WT aorta which was not affected by ACh. In cav‐1 KO aorta, eNOS was localized in low‐density non‐caveolar fractions but not shifted by ACh or diet. Inducible NOS and cyclooxygenase 1/2 were not localized in low‐density fractions or affected by diet, ACh or genotype. ACh‐induced dilation of gracilis arteries from HF WT was similar to dilation in LF but the NOS component was reduced. In WT and cav‐1 KO, dilation to ACh was enhanced by MO through increased role for NOS and cyclooxygenase. We conclude that dietary fats affect vascular fatty acid composition and membrane localization of eNOS but the contribution of eNOS and cyclooxygenase in ACh‐mediated vascular responses is independent of lipid rafts.
Low Cost Si-Less RDL Interposer Package for High Performance Computing Applications

A new concept of Si-less redistribution layer (RDL) platform was proposed for server/HPC application with advantages of packaging cost reduction, warpage control, and enhanced reliability. In this paper, RDL interposer package with size larger than 3000mm2 was fabricated. Warpage behavior, electrical performance and reliability of the RDL interposer package were evaluated. In order to predict warpage behavior of RDL interposer, the critical factors were defined. The electrical performance between Si interposer and RDL interposer was analyzed using electrical simulation and finally joint reliability was also compared in terms of predicted joint stress.
On the Achievable Error Region of Physical Layer Authentication Techniques over Rayleigh Fading Channels

For a physical layer message authentication procedure based on the comparison of channel estimates obtained from the received messages, we focus on an outer bound on the type I/II error probability region. Channel estimates are modelled as multivariate Gaussian vectors, and we assume that the attacker has only some side information on the channel estimate, which he does not know directly. We derive the attacking strategy that provides the tightest bound on the error region, given the statistics of the side information. This turns out to be a zero mean, circularly symmetric Gaussian density whose correlation matrices may be obtained by solving a constrained optimization problem. We propose an iterative algorithm for its solution: Starting from the closed form solution of a relaxed problem, we obtain, by projection, an initial feasible solution; then, by an iterative procedure, we look for the fixed point solution of the problem. Numerical results show that for cases of interest the iterative approach converges, and perturbation analysis shows that the found solution is a local minimum.
c‐MPL Is a Candidate Surface Marker and Confers Self‐Renewal, Quiescence, Chemotherapy Resistance, and Leukemia Initiation Potential in Leukemia Stem Cells

Acute myeloid leukemia (AML) is initiated and maintained by a unique, small subset of leukemia cells known as leukemia stem cells (LSCs). Self‐renewal, quiescence, and chemotherapy resistance are key stemness properties of LSCs that are essential for poor clinical responses to conventional therapies. Identifying LSC surface markers and targeting LSCs are important for the development of potential therapies. In this study, application of chemotherapy treatment in AML‐ETO9a (AE9a) leukemia mice led to the enrichment of a chemotherapy‐resistant cell population identified as Lin−c‐Kit+c‐MPL+. In addition, this c‐MPL‐positive cell population within Lin−c‐Kit+ leukemia cells included a high percentage of cells in a quiescent state, enhanced colony formation ability, and increased homing efficiency. Serial transplantation demonstrated that Lin−c‐Kit+c‐MPL+ cells displayed a significantly high potential for leukemia initiation. Furthermore, it was demonstrated that in AML patients, c‐MPL was expressed on the majority of CD34+ leukemia cells and that the proportion of c‐MPL+ cells in CD34+ leukemia cells is associated with poor prognosis. Finally, AMM2, an inhibitor of c‐MPL, was shown to significantly enhance the survival of AE9a leukemia mice when combined with chemotherapeutic agent. These results indicate that c‐MPL is a candidate LSC surface marker that may serve as a therapeutic target for the elimination of LSCs. Stem Cells 2018;36:1685–1696
The pervasive effects of lighting environments on sensory drive in bluefin killifish: an investigation into male/male competition, female choice, and predation

Abstract Sensory drive predicts that the conditions under which signaling takes place have large effects on signals, sensory systems, and behavior. The coupling of an ecological genetics approach with sensory drive has been fruitful. An ecological genetics approach compares populations that experience different environments and asks whether population differences are adaptive and are the result of genetic and/or environmental variation. The multi-faceted effects of signaling environments are well-exemplified by the bluefin killifish. In this system, males with blue anal fins are abundant in tannin-stained swamps that lack UV/blue light but are absent in clear springs where UV/blue light is abundant. Past work indicates that lighting environments shape genetic and environmental variation in color patterns, visual systems, and behavior. Less is known about the selective forces creating the across population correlations between UV/blue light and the abundance of blue males. Here, we present three new experiments that investigate the roles of lighting environments on male competition, female mate choice, and predation. We found strong effects of lighting environments on male competition where blue males were more likely to emerge as dominant in tea-stained water than in clear water. Our preliminary study on predation indicated that blue males may be less susceptible to predation in tea-stained water than in clear water. However, there was little evidence for female preferences favoring blue males. The resulting pattern is one where the effects of lighting environments on genetic variation and phenotypic plasticity match the direction of selection and favor the expression of blue males in swamps.
Dictionary Learning for Sparse Representation Based on Smoothed L_0 Norm

Dictionary learning for sparse representation is a powerful and efficient tool for signal processing applications. Designing a dictionary, which can sparsely represent the training samples is the main target of this work. Most of the current dictionary learning methods minimize the representation error of the training samples, subject to the sparseness of the coefficient matrix. They use a two-steps alternating minimization approach to find the dictionary and the coefficient matrix. The first step is to sparsely approximate the training samples over the current dictionary and the second step is to update the dictionary. The first step is often time-consuming, because it is required to minimize the l_0 (or l_1) norm of the coefficient matrix. In this paper, we propose a new method for dictionary learning based on smoothed l_0 norm, which increases the speed of the sparse decomposition step. We also combine the sparse representation and the dictionary update steps, which helps us expedite convergence of the parameters. Simulation results show that, the proposed algorithm considerably increases the speed of convergence, while providing the same or better performance, particularly in the presence of noise.
Comparing the Data Quality of Global Positioning System Devices and Mobile Phones for Assessing Relationships Between Place, Mobility, and Health: Field Study

Background Mobile devices are increasingly used to collect location-based information from individuals about their physical activities, dietary intake, environmental exposures, and mental well-being. Such research, which typically uses wearable devices or mobile phones to track location, benefits from the growing availability of fine-grained data regarding human mobility. However, little is known about the comparative geospatial accuracy of such devices. Objective In this study, we compared the data quality of location information collected from two mobile devices that determine location in different ways—a global positioning system (GPS) watch and a mobile phone with Google’s Location History feature enabled. Methods A total of 21 chronically ill participants carried both devices, which generated digital traces of locations, for 28 days. A mobile phone–based brief ecological momentary assessment (EMA) survey asked participants to manually report their location at 4 random times throughout each day. Participants also took part in qualitative interviews and completed surveys twice during the study period in which they reviewed recent mobile phone and watch trace data to compare the devices’ trace data with their memory of their activities on those days. Trace data from the devices were compared on the basis of (1) missing data days, (2) reasons for missing data, (3) distance between the route data collected for matching day and the associated EMA survey locations, and (4) activity space total area and density surfaces. Results The watch resulted in a much higher proportion of missing data days (P<.001), with missing data explained by technical differences between the devices as well as participant behaviors. The mobile phone was significantly more accurate in detecting home locations (P=.004) and marginally more accurate (P=.07) for all types of locations combined. The watch data resulted in a smaller activity space area and more accurately recorded outdoor travel and recreation. Conclusions The most suitable mobile device for location-based health research depends on the particular study objectives. Furthermore, data generated from mobile devices, such as GPS phones and smartwatches, require careful analysis to ensure quality and completeness. Studies that seek precise measurement of outdoor activity and travel, such as measuring outdoor physical activity or exposure to localized environmental hazards, would benefit from the use of GPS devices. Conversely, studies that aim to account for time within buildings at home or work, or those that document visits to particular places (such as supermarkets, medical facilities, or fast food restaurants), would benefit from the greater precision demonstrated by the mobile phone in recording indoor activities.
Service Function Chaining Simplified

— Middleboxes have become a vital part of modern networks by providing service functions such as content ﬁltering, load balancing and optimization of network trafﬁc. An ordered sequence of middleboxes composing a logical service is called service chain . Service Function Chaining (SFC) enables us to deﬁne these service chains. Recent optimization models of SFCs assume that the functionality of a middlebox is provided by a single software appliance, commonly known as Virtual Network Function (VNF). This assumption limits SFCs to the throughput of an individual VNF and resources of a physical machine hosting the VNF instance . Moreover, typical service providers offer VNFs with heterogeneous throughput and resource conﬁgurations. Thus, deploying a service chain with custom throughput can be- come a tedious process of stitching heterogeneous VNF instances. In this paper, we describe how we can overcome these limitations without worrying about underlying VNF conﬁgurations and resource constraints. This prospect is achieved by distributed deploying multiple VNF instances providing the functionality of a middlebox and modeling the optimal deployment of a service chain as a mixed integer programming problem. The proposed model optimizes host and bandwidth resources alloca- tion, and determines the optimal placement of VNF instances, while balancing workload and routing trafﬁc among these VNF instances. We show that this problem is NP-Hard and propose a heuristic solution called Kariz . Kariz utilizes a tuning parameter to control the trade-off between speed and accuracy of the solution. Finally, our solution is evaluated using simulations in data-center networks.
21-fs Kerr-lens Mode-locked Yb:CaYAlO4 Laser

We experimentally demonstrated the generation of 5.87-optical-cycle pulses from a Kerr-lens mode-locked Yb:CaYAlO4 (Yb:CYA) laser. Pumped by a 976 nm fiber laser, stable ultrashort pulses with a repetition rate of ∼ 114 MHz were obtained around 1077 nm.
Improving Solder Joint Reliability for PoP Packages in Current Mobile Ecosystem

Package on Package (PoP) has been an ideal choice for high end products in mobile ecosystem due to its high-density bandwidth support and flexibility for the original equipment manufacturers (OEMs) to accommodate required memory integration. Form-factor and performance requirements of high end handsets pushes the envelope of PoP package solutions in recent times and requires chip manufacturers to constantly shift package attributes. These changes often add various thermo-mechanical challenges for the chip manufacturers and end OEMs when integrating into their final system while maintaining high reliability requirement in field. In this paper, the focus will be primarily on addressing various attributes that concern the 2nd level solder interconnect reliability. We will discuss factors that affect both PoP memory BGAs and bottom logic package BGAs especially during temperature cycle (TC) condition. We will demonstrate a few case studies using both testing data and simulation data on how factors such as Memory BGA array, underfill choices and BGA depopulation can impact the board level reliability. We will further provide recommendations and guidelines to improve board level reliability of PoP packages in current ecosystem where OEMs are facing challenges juggling form-factor constraints, performance, functionality and field reliability.