Miracle-dz/UniFAR-FTUs huggingface dataset:
Progress and challenges in bioinformatics approaches for enhancer identification

Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.
Tapping out a mechanical code for T cell triggering

Mechanical forces play increasingly recognized roles in T cell receptor (TCR) signal transduction. Hu and Butte (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201511053) demonstrate that actin is required for T cells to generate forces at the TCR and that exogenous application of force can emulate these cytoskeletal forces and trigger T cell activation.
Bacterial biofilm shows persistent resistance to liquid wetting and gas penetration

Most of the world’s bacteria exist in robust, sessile communities known as biofilms, ubiquitously adherent to environmental surfaces from ocean floors to human teeth and notoriously resistant to antimicrobial agents. We report the surprising observation that Bacillus subtilis biofilm colonies and pellicles are extremely nonwetting, greatly surpassing the repellency of Teflon toward water and lower surface tension liquids. The biofilm surface remains nonwetting against up to 80% ethanol as well as other organic solvents and commercial biocides across a large and clinically important concentration range. We show that this property limits the penetration of antimicrobial liquids into the biofilm, severely compromising their efficacy. To highlight the mechanisms of this phenomenon, we performed experiments with mutant biofilms lacking ECM components and with functionalized polymeric replicas of biofilm microstructure. We show that the nonwetting properties are a synergistic result of ECM composition, multiscale roughness, reentrant topography, and possibly yet other factors related to the dynamic nature of the biofilm surface. Finally, we report the impenetrability of the biofilm surface by gases, implying defense capability against vapor-phase antimicrobials as well. These remarkable properties of B. subtilis biofilm, which may have evolved as a protection mechanism against native environmental threats, provide a new direction in both antimicrobial research and bioinspired liquid-repellent surface paradigms.
Quantum transport, quantum effects and circuit functionality of nanostructured electronic circuits

This paper presents a discussion of the impact of quantum effects to classical circuits. We will provide you with a brief introduction to our developed numerical tools to simulate electron tunnelling and energy discretization in MOS structures. Regarding these results a few arguments for simulating circuits including these effects will be given. Copyright © 2004 John Wiley & Sons, Ltd.
Radial Basis Functions for High-Dimensional Visualization

— High-dimensional visualization is usually connected with large data processing. Because of dimensionality, it is nearly impossible to make a tessellation, like the Delaunay tessellation in E d , followed by data interpolation. One possibility of data interpolation is the use of the Radial Basis Functions (RBF) interpolation. The RBF interpolation supports the interpolation of scattered data in d -dimensional space. The computational cost of the RBF interpolation is higher but does not increase significantly with the data dimensionality. It increases with the number of values to be processed non-linearly. In this paper, the RBF interpolation properties will be discussed as well as how to process data incrementally. Incremental computation decreases computational complexity and decreases RBF computational cost for the given data set significantly, especially for the visualization purposes, when the interpolated/approximated data are used many times. As the proposed approach is based on a solution of a system of linear equations, the RBF interpolation is convenient especially for data sets processing using matrix-vector or GPU architectures.
Mating Patterns and Breeding Success in the Larus Glaucescens-occidentalis Complex, Protection Island, Washington

Glaucous-winged gulls (Larus glaucescens) and Western gulls (Larus occidentalis) are found along the Pacific Coast. Where their breeding ranges overlap in Oregon and Washington they hybridize, producing a continuum of phenotypic variation. Whereas most colonies containing these hybrids are found on islands along the coast, several, including a large colony on Protection Island National Wildlife Refuge, WA, are located in the Salish Sea. In 2010 I scored the henotypes of 81 gull pairs at the Protection Island cology using an index based on plumage melanism and bare-part coloration. Gulls from the entire range of phenotypes in the L. glaucescens-occidentalis complex, from putatively pure L. glaucescens to putatively pure L. occidentalis, bred on the colony, although most gulls appeared more like L. glaucescens. Significant assortative mating based on phenotype occured on the colony, but a small number of L. occidentalis-type pairs appeared primarily responsible for this trend. Although the mass of the third egg in the clutch was significantly less for pairs with increasingly L. occidentalis-like males, I observed no significant difference in hatching success or clutch size across the range of phenotypes.
Locomotive Control of a Wearable Lower Exoskeleton for Walking Enhancement

This article presents a wearable lower extremity exoskeleton (LEE) designed to augment the ability of a human to walk while carrying payloads. The ultimate goal of the current research is to design and control a wearable power-assisted system that integrates a human’s intellect as the control command. The system in this work consists of an inner exoskeleton and an outer exoskeleton. The inner system measures the movements of the human and controls the outer system, which follows the human movements and supports the payload. A special foot-unit was designed to measure the zero moment points (ZMPs) of the human and the exoskeleton simultaneously. Using the measured human ZMP as the reference, the exoskeleton’s ZMP is controlled by trunk compensation to achieve stable walking. A COTS program, xPC Target, together with toolboxes from MATLAB, were used as a real-time operating system and integrated development environment, and real-time locomotion control of the exoskeleton was successfully implemented in this environment. Finally, some walking experimental results, by virtue of the ZMP control for the inner and outer exoskeletons, show that the stable walking can be achieved.
The Impact of Prenatal Depressive Symptoms, Intimate Partner Relationship, and Immune Status on Postpartum Depression

OF DISSERTATION THE IMPACT OF PRENATAL DEPRESSIVE SYMPTOMS, INTIMATE PARTNER RELATIONSHIP, AND IMMUNE STATUS ON POSTPARTUM DEPRESSION The prevalence of depression during pregnancy in the U. S. is approximately 13%. Poor quality of the intimate partner relationship is significantly correlated with depression during pregnancy. The adverse effects of antenatal depression have been widely documented. The relationship between the intimate partner relationship and depression during pregnancy has not been well delineated in the literature. Little data exist regarding the impact of prenatal immune status on risk for postpartum depression. Due to limited evidence, there is a critical need to examine the relationship among trimester specific cytokines, quality of the intimate partner relationship, and antenatal depressive symptoms on risk for postpartum depression. Examining this relationship is a crucial aspect in understanding the holistic aspects of depression during pregnancy. The purpose of this dissertation was to examine the impact of the quality of the intimate partner relationship and immune status in early pregnancy on risk for postpartum depression. This was done in three ways: a critical review and analysis of the current state of measurement of antenatal depression via four instruments; a psychometric assessment of the Autonomy and Relatedness Inventory (ARI) during pregnancy; and an examination of the impact of trimester specific cytokines on depressive symptoms and the quality of the intimate partner relationship. The critical review and analysis of the current state of measurement of four antenatal instruments measuring depression indicated similar results in detecting depression during pregnancy. The Postpartum Depression and Screening Scale (PDSS) performed more conclusively in detecting true cases of antenatal depression. In the next manuscript, psychometric assessment of the ARI revealed a 6 component model. Further, the ARI was significantly inversely correlated with depressive symptoms in the first trimester. For the final manuscript, first trimester serum MMP-8 levels were significant in predicting depression in the third trimester of pregnancy. The findings of this dissertation study indicate that measuring and predicting pregnancy associated depression continues to be confounded by multitudinous factors. A comprehensive approach is warranted when screening for depression before, during, and after pregnancy. An emphasis on psychosocial, physical, immunological, and behavioral characteristics should be included when examining pregnancy associated depression in future research studies.
Comparison of the design of FIR and IIR filters for a given specification and removal of phase distortion from IIR filters

In digital signal processing both Finite Impulse Response (FIR) and Infinite Impulse Response (IIR) filters can be designed from a given specification. Both these design methods have their respective advantages and disadvantages. This paper takes a given specification to design both FIR and IIR filter. An input signal was passed through both these filters. The two designs were compared w.r. t circuit complexity, group delay, phase distortion and the output response. An equalizer was also designed to remove the phase distortion of the IIR filter. The results are summarized in the concluding section.
Minnow: Lightweight Offload Engines for Worklist Management and Worklist-Directed Prefetching

The importance of irregular applications such as graph analytics is rapidly growing with the rise of Big Data. However, parallel graph workloads tend to perform poorly on general-purpose chip multiprocessors (CMPs) due to poor cache locality, low compute intensity, frequent synchronization, uneven task sizes, and dynamic task generation. At high thread counts, execution time is dominated by worklist synchronization overhead and cache misses. Researchers have proposed hardware worklist accelerators to address scheduling costs, but these proposals often harden a specific scheduling policy and do not address high cache miss rates. We address this with Minnow, a technique that augments each core in a CMP with a lightweight Minnow accelerator. Minnow engines offload worklist scheduling from worker threads to improve scalability. The engines also perform worklist-directed prefetching, a technique that exploits knowledge of upcoming tasks to issue nearly perfectly accurate and timely prefetch operations. On a simulated 64-core CMP running a parallel graph benchmark suite, Minnow improves scalability and reduces L2 cache misses from 29 to 1.2 MPKI on average, resulting in 6.01x average speedup over an optimized software baseline for only 1% area overhead.
Effects of caffeine, sodium bicarbonate, and their combined ingestion on high-intensity cycling performance.

PURPOSE To determine the effects of ingesting caffeine (CAFF) and sodium bicarbonate (SB), taken individually and simultaneously, on 3-km cycling time-trial (TT) performance. METHOD Ten well-trained cyclists, age 24.2 ± 5.4 yr, participated in this acute-treatment, double-blind, crossover study that involved four 3-km cycling TTs performed on separate days. Before each TT, participants ingested either 3 mg/kg body mass (BM) of CAFF, 0.3 g · kg⁻¹ · BM⁻¹ of SB, a combination of the two (CAFF+SB), or a placebo (PLAC). They completed each 3-km TT on a laboratory-based cycle ergometer, during which physiological, perceptual, and performance measurements were determined. For statistical analysis, the minimal worthwhile difference was considered ~1% based on previous research. RESULTS Pretrial pH and HCO₃ were higher in SB and CAFF+SB than in the CAFF and PLAC trials. Differences across treatments for perceived exertion and gastric discomfort were mostly unclear. Compared with PLAC, mean power output during the 3-km TT was higher in CAFF, SB, and CAFF+SB trials (2.4%, 2.6%, 2.7% respectively), resulting in faster performance times (-0.9, -1.2, -1.2% respectively). Effect sizes for all trials were small (0.21-0.24). CONCLUSIONS When ingested individually, both CAFF and SB enhance high-intensity cycling TT performance in trained cyclists. However, the ergogenic effect of these 2 popular supplements was not additive, bringing into question the efficacy of coingesting the 2 supplements before short-duration high-intensity exercise. In this study there were no negative effects of combining CAFF and SB, 2 relatively inexpensive and safe supplements.
Human Papillomavirus Assays and Cytology in Primary Cervical Screening of Women Aged 30 Years and Above

In women aged ≥30 years, Human Papillomavirus testing will replace cytology for primary cervical screening. We compared Hybrid Capture 2 (HC2), cobas, CLART, and APTIMA HPV assays with cytology on 2869 SurePath samples from women undergoing routine screening at 30–65 years in Copenhagen, Denmark. Women with cytological abnormalities were managed according to routine recommendations, with 92% completeness. Those with cytology-normal/HPV-positive samples (on any of the four assays) were invited for repeated cytology and HPV testing in 1.5 year, and 58% had additional testing. HPV testing detected more ≥CIN3 than cytology (HC2: 35, cobas, CLART: 37, APTIMA: 34, cytology: 31), although statistically the differences were not significant. Cobas and CLART detected significantly more ≥CIN2 than cytology (cobas, CLART: 49, cytology: 39). The proportion of women with false-positive test results (positive test results without ≥CIN3) varied between 3.3% with cytology and 14.9% with cobas. All HPV assays led to significantly more false-positive tests, whereas compared to HC2 cobas and CLART were associated with a significantly higher and APTIMA with a significantly lower proportion. Detection of CIN1 was particularly increased for the three DNA assays. With APTIMA combined with cytological triage, about 20% more women were referred for colposcopy than with cytology screening. With the three DNA assays, the increase was ≥50%. The number of women with repeated testing was twice as high with APTIMA and almost five times as high with cobas compared to cytology. To our knowledge, Horizon was the only study set in routine practice that compared more than two HPV assays in the same women while also ascertaining the histological status of women with normal cytology/HPV-positive test results. HPV-based screening of Danish women aged 30–65 detected more high-grade CIN but decreased the screening specificity, and increased the demand for additional testing.
How to validate the secret of a Ring Learning with Errors (RLWE) key

We use the signal function from the RLWE key exchange in [26] to derive an efficient zero knowledge authentication protocol to validate an RLWE key p = as + e with secret s and error e in the Random Oracle Model (ROM). With this protocol, a verifier can validate that a key p presented to him by a prover P is of the form p = as + e with s, e small and that the prover knows s. We accompany the description of the protocol with proof to show that it has negligible soundness and completeness error. The soundness of our protocol relies directly on the hardness of the RLWE problem. The protocol is applicable for both LWE and RLWE but we focus on the RLWE based protocol for efficiency and practicality. We also present a variant of the main protocol with a commitment scheme to avoid using the ROM.
An AlAs/germanene heterostructure with tunable electronic and optical properties via external electric field and strain

By means of comprehensive first-principles calculations, we investigate the stability, electronic and optical properties of an AlAs/germanene heterostructure. In particular, electric field and strain are used to tailor its electronic band gap and dielectric function. The binding energy and interlayer distance indicate that germanene and AlAs monolayers in the AAI pattern are bound together via van der Waals interaction with a maximum indirect-gap of 0.494 eV, which is expected to have potential application in the field of field-effect transistors. Under a negative E-field and compressive strain, the bandgaps of the AAI-stacking show a near-linear and linear decrease behavior, respectively, whereas the response of the bandgaps to a positive E-field and tensile strain displays a dramatic and monotonous decrease relationship. The work function of the AAI-stacking is calculated to be 4.35 eV smaller than that of individual monolayers. Besides, the optical properties are also calculated. The imaginary parts of the dielectric function of the germanene/AlAs heterobilayer exhibit a significant enhancement in comparison with the considered monolayers, indicating the improvement of the capability of absorbing photons. In particular, the imaginary part of the dielectric function of the heterostructure is enhanced with the increase of E-field and mechanical strain, which suggests that the optical properties of the heterostructure can be improved by E-field and mechanical strain. Simultaneously, a red-shift or blue-shift can be observed with the changes in E-field and mechanical strain. All these nontrivial and tunable properties endow the AlAs/germanene nanocomposite with great potential for FETs, strain sensors, photocatalysis, field emission, energy harvesting, and photonic devices.
Reduced power consumption in wireless sensor networks using queue based approach

Technological advancements in low power integrated circuits and wireless communications have made it possible to use efficient, low cost, low power small devices in remote sensing applications. This has led to the feasibility of using a network of sensors to be used for the collection, processing, analysis and distribution of important information, collected in a wide variety of environments. Sensor nodes in a wireless sensor network transmit data in single or multi-hop to a central node called the base station. A very important issue in wireless sensor networks is the scarcity of power and hence optimal use of available power is of prime importance. It is seen that in any sensor node, switching from idle to busy state and vice versa takes up a major portion of the power. We study and analyze a technique that aims to reduce the number of these in order to reduce the consumption of power. In this technique the radio of the sensor node is switched on only when the number of packets in a queue exceed a certain threshold as opposed to the general tendency of transmitting a packet as soon as it is available for transmission. We analyze the performance of this system with respect to the power consumption. The simulations performed show that the simulation results are close to the theoretical results thus indicating the validity of the technique studied.
Values and Limitations of Targeting lncRNAs in Diabetic Nephropathy

Deep RNA sequencing of mammalian transcriptomes during the past two decades has unveiled more than 100,000 different RNAs, far more than the estimated 20,000 protein-coding genes, suggesting that the protein-coding potential of the mammalian genome is very limited and the majority of these RNA sequences are indeed noncoding (1–3). Although once considered “evolutionary junk” or “transcriptional noise,” more recent observations have shown that noncoding RNAs (ncRNAs) participate in diverse biological activities of the cell by interacting with RNA, DNA, or proteins to modulate the expression of protein-coding genes. Generally, ncRNAs are divided into two major subclasses (long or short), depending on their size. The long ncRNAs (lncRNAs) are arbitrarily defined as transcripts longer than 200 nucleotides that are produced by RNA polymerase II and lack protein-coding potential, thus separating them from the other subclass of small ncRNAs that range from a few to 200 nucleotides and include microRNAs (miRNAs), small nuclear RNAs, circular RNAs, and small nucleolar RNAs (4). Compared with messenger RNAs (mRNAs), lncRNAs are usually less evolutionarily conserved, less abundant, and more tissue specific (5). Cumulative research has revealed that lncRNAs exert a wide variety of biological functions and their aberrant expression has been associated with diverse pathologies including cancer and cardiac, neurological, and metabolic diseases (6–8). Mechanisms underlying the broad functions of lncRNAs are still emerging. It has recently …
Egg cannibalism in a gull colony increases with sea surface temperature

ABSTRACT Cannibalism occurs regularly across a broad range of taxa with a variety of ecological and evolutionary consequences. Rises in sea surface temperature (SST) have been linked to increased cannibalism in some species, including polar bears (Ursus maritimus), Peruvian anchovy (Engraulis ringens), and Peruvian hake (Merluccius gayi peruanus), and might be expected in birds that depend on marine food webs for sustenance. Increased SSTs are associated with lowered ocean thermoclines and weakened upwellings. These changes, in turn, lead to decreased productivity in surface water and movement of surviving forage fish to deeper water, thereby food-stressing surface feeders such as gulls, diminishing energy intake and lengthening foraging bouts. While controlling for a suite of other environmental factors, we tested whether egg cannibalism and hatching success were independent of rises in local SST at a colony of Glaucous-winged Gulls (Larus glaucescens) and Glaucous-winged × Western Gull (L. glaucescens × occidentalis) hybrids during 2006–2011 on Protection Island, Washington, USA. Cannibalism increased and hatching success decreased with rises in SST. It is unclear if rises in SST impact overall population trends. Gulls are multiyear breeders; if they experience reproductive failure during one or several El Niño-Southern Oscillation–related events, they typically have other opportunities to breed. With rising SSTs associated with climate change, however, increasing levels of cannibalism could lead to declining populations in the absence of compensatory adaptive modifications or range shifts.