Miracle-dz/UniFAR-FTUs huggingface dataset:
A divalent cation-dependent variant of the glmS ribozyme with stringent Ca2+ selectivity co-opts a preexisting nonspecific metal ion-binding site

Ribozymes use divalent cations for structural stabilization, as catalytic cofactors, or both. Because of the prominent role of Ca2+ in intracellular signaling, engineered ribozymes with stringent Ca2+ selectivity would be important in biotechnology. The wild-type glmS ribozyme (glmSWT) requires glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. Previously, a glmS ribozyme variant with three adenosine mutations (glmSAAA) was identified, which dispenses with GlcN6P and instead uses, with little selectivity, divalent cations as cofactors for site-specific RNA cleavage. We now report a Ca2+-specific ribozyme (glmSCa) evolved from glmSAAA that is >10,000 times more active in Ca2+ than Mg2+, is inactive in even 100 mM Mg2+, and is not responsive to GlcN6P. This stringent selectivity, reminiscent of the protein nuclease from Staphylococcus, allows rapid and selective ribozyme inactivation using a Ca2+ chelator such as EGTA. Because glmSCa functions in physiologically relevant Ca2+ concentrations, it can form the basis for intracellular sensors that couple Ca2+ levels to RNA cleavage. Biochemical analysis of glmSCa reveals that it has co-opted for selective Ca2+ binding a nonspecific cation-binding site responsible for structural stabilization in glmSWT and glmSAAA. Fine-tuning of the selectivity of the cation site allows repurposing of this preexisting molecular feature.
Digestive and bacterial enzyme activities in broilers fed diets supplemented with Lactobacillus cultures.

A study was carried out to investigate the effects of adherent Lactobacillus cultures on 1) amylolytic, lipolytic, and proteolytic enzyme activities in the contents of the small intestine (from the distal end of the duodenum to the ileocecal junction) and 2) bacterial beta-glucuronidase and beta-glucosidase activities in the intestinal contents and feces of broiler chickens. Three dietary treatments were randomly assigned to three groups of chicks, i.e., basal diet only (control group), basal diet + 0.1% dried culture of Lactobacillus acidophilus, and basal diet + 0.1% dried culture of a mixture of 12 Lactobacillus strains. The results showed that supplementation of the adherent Lactobacillus cultures to chickens, either as a single strain of L. acidophilus or as a mixture of 12 Lactobacillus strains, increased significantly (P < 0.05) the levels of amylase in the small intestine. However, the proteolytic and lipolytic activities in the small intestine were not affected by addition of either of the adherent Lactobacillus cultures. Addition of either L. acidophilus or a mixture of 12 Lactobacillus strains was also found to reduce significantly (P < 0.05) the intestinal and fecal beta-glucuronidase and fecal beta-glucosidase but not the intestinal beta-glucosidase at 40 d of feeding.
On Compaction Utilizing Inter and Intra-Correlation of Unknown States

Unknown (X) states are increasingly often identified as having potential for rendering semiconductor tests useless. One of the key requirements for a reliable test response compactor is, therefore, to preserve observability of any scan cell for a wide range of X-profiles while maintaining very high-compaction ratios, providing ability to detect a variety of failures found in real silicon, and assuring design simplicity. We have proposed a fully X-tolerant test response compaction scheme which is based on a flexible scan chain selection mechanism. This new approach delivers extremely high compression of test results by observing that X states are typically not randomly distributed in test responses. Identical or similar patterns of correlated X states let the proposed scheme reduce the size of a scan chain selector and the amount of test data used to control it. It handles, moreover, a wide range of unknown state profiles such that all X states, including those being clustered and of high density, are suppressed in a per-cycle mode without compromising the test quality.
Control of Cascaded DC–DC Converter-Based Hybrid Battery Energy Storage Systems—Part I: Stability Issue

There is an emerging application, which uses a mixture of batteries within an energy storage system. These hybrid battery solutions may contain different battery types. A dc-side cascaded boost converters along with a module-based distributed power sharing strategy has been proposed to cope with variations in battery parameters such as, state-of-charge (SOC) and/or capacity. This power sharing strategy distributes the total power among the different battery modules according to these battery parameters. Each module controller consists of an outer voltage-loop with an inner current-loop where the desired control reference for each control-loop needs to be dynamically varied according to battery parameters to undertake this sharing. As a result, the designed control bandwidth (BW) or stability margin of each module control-loop may vary in a wide range, which can cause a stability problem within the cascaded converter. This paper reports such a unique issue and thoroughly investigates the stability of the modular converter under the distributed sharing scheme. The paper shows that a cascaded PI control-loop approach cannot guarantee the system stability throughout the operating conditions. A detailed analysis of the stability issue and the limitations of the conventional approach are highlighted. Finally in-depth experimental results are presented to prove the stability issue using a modular hybrid battery energy storage system prototype under various operating conditions.
Disunited Nations? A Multiplex Network Approach to Detecting Preference Affinity Blocs using Texts and Votes

This paper contributes to an emerging literature that models votes and text in tandem to better understand polarization of expressed preferences. It introduces a new approach to estimate preference polarization in multidimensional settings, such as international relations, based on developments in the natural language processing and network science literatures -- namely word embeddings, which retain valuable syntactical qualities of human language, and community detection in multilayer networks, which locates densely connected actors across multiple, complex networks. We find that the employment of these tools in tandem helps to better estimate states' foreign policy preferences expressed in UN votes and speeches beyond that permitted by votes alone. The utility of these located affinity blocs is demonstrated through an application to conflict onset in International Relations, though these tools will be of interest to all scholars faced with the measurement of preferences and polarization in multidimensional settings.
Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation

Bamboo-eating giant panda (Ailuropoda melanoleuca) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.
Non‐invasive optical assessment of viscosity of middle ear effusions in otitis media

Eustachian tube dysfunction can cause fluid to collect within the middle ear cavity and form a middle ear effusion (MEE). MEEs can persist for weeks or months and cause hearing loss as well as speech and learning delays in young children. The ability of a physician to accurately identify and characterize the middle ear for signs of fluid and/or infection is crucial to provide the most appropriate treatment for the patient. Currently, middle ear infections are assessed with otoscopy, which provides limited and only qualitative diagnostic information. In this study, we propose a method utilizing cross‐sectional depth‐resolved optical coherence tomography to noninvasively measure the diffusion coefficient and viscosity of colloid suspensions, such as a MEE. Experimental validation of the proposed technique on simulated MEE phantoms with varying viscosity and particulate characteristics is presented, along with some preliminary results from in vivo and ex vivo samples of human MEEs. In vivo Optical Coherence Tomography (OCT) image of a human tympanic membrane and Middle Ear Effusion (MEE) (top), with a CCD image of the tympanic membrane surface (inset). Below is the corresponding time‐lapse M‐mode OCT data acquired along the white dotted line over time, which can be analyzed to determine the Stokes–Einstein diffusion coefficient of the effusion.
Theoretical and Empirical Analysis of a Spatial EA Parallel Boosting Algorithm

Many real-world problems involve massive amounts of data. Under these circumstances learning algorithms often become prohibitively expensive, making scalability a pressing issue to be addressed. A common approach is to perform sampling to reduce the size of the dataset and enable efficient learning. Alternatively, one customizes learning algorithms to achieve scalability. In either case, the key challenge is to obtain algorithmic efficiency without compromising the quality of the results. In this article we discuss a meta-learning algorithm (PSBML) that combines concepts from spatially structured evolutionary algorithms (SSEAs) with concepts from ensemble and boosting methodologies to achieve the desired scalability property. We present both theoretical and empirical analyses which show that PSBML preserves a critical property of boosting, specifically, convergence to a distribution centered around the margin. We then present additional empirical analyses showing that this meta-level algorithm provides a general and effective framework that can be used in combination with a variety of learning classifiers. We perform extensive experiments to investigate the trade-off achieved between scalability and accuracy, and robustness to noise, on both synthetic and real-world data. These empirical results corroborate our theoretical analysis, and demonstrate the potential of PSBML in achieving scalability without sacrificing accuracy.
Pulsed Electric Current Sintering of Transparent Alumina Ceramics

Aluminum oxide (Al2O3) commonly referred as to alumina is one of the most widely used as engineering oxide ceramics. From crystalline structure difference, there are many forms of Al2O3 (α, χ, η, δ, θ, γ and ρ), with α-Al2O3 being thermodynamically the most stable form. An example of α phase of Al2O3 is corundum or sapphire [1]. In the present chapter, α-Al2O3 is discussed and described as Al2O3. With a high melting temperature, chemical stability, Al2O3 is leading to applications as high-temperature components, catalyst substrates and biomedical implants. Al2O3 has excellent optical transparency and along with additives such as chromium and titanium, it is important as a sodium lamp (sapphire), a gem stone (sapphire and ruby) and a laser host (ruby).
FINITE ELEMENT SIMULATION OF METAL CUTTING CONSIDERING CHIP BEHAVIOR AND TEMPERATURE DISTRIBUTION

The finite element method was used for simulating orthogonal metal cutting of low-carbon steel. The model predicts chip geometry, behavior of the metal under machining, cutting force values, stress distribution, and temperature distribution along the workpiece and the chip. Separation and the friction action between the chip and tool were simulated using a friction slideline capability. The same technique was applied to the undeformed chip–workpiece interaction zone to simulate the separation between the chip and the workpiece. The model considered the thermal effect and the friction along the tool rake face. Force values predicted from this model were compared with some experimental work for the same material at the same range of cutting speed and show good correlation.
1 REDUCING STEREOTYPE THREAT EFFECTS Creating a Critical Mass Eliminates the Effects of Stereotype Threat on Women

Background: Women in mathematical domains may become attuned to situational cues that signal a discredited social identity, contributing to their lower achievement and underrepresentation. Aim: The current study examined whether heightened ingroup representation alleviates the effects of stereotype threat on women’s mathematical performance. It further investigated whether single-sex testing environments and stereotype threat influenced participants to believe that their ability was fixed (fixed mindset) rather than a trait that could be developed (growth mindset). Sample and Method: One hundred and forty-four female participants were assigned randomly to a self-as-target or group-as-target stereotype threat condition or to a control condition. They completed a modular arithmetic maths test and a mindset questionnaire either alone or in same-sex groups of 3-5 individuals. Results: Participants solved fewer mathematical problems under self-as-target and group-astarget stereotype threat when they were tested alone but these performance deficits were eliminated when they were tested in single-sex groups. Participants reported a weaker growth mindset when they were tested under stereotype threat and in singlesex groups. Moreover, evidence of inconsistent mediation indicated that single-sex testing environments negatively predicted mindset but positively predicted mathematical performance. Conclusions: These findings suggest that single-sex testing environments may represent a practical intervention to alleviate stereotype threat effects but may have a paradoxical effect on mindset.
A Review and Reconsideration of Nonneoplastic Myometrial Pathology

From 1861 to 1962, clinicopathologic research tried to explain the association of abnormal uterine bleeding with uterine enlargement. The etiology was theorized as metropathy, suggesting that myometrial dysfunction may predispose to abnormal uterine bleeding. Research reached a nadir in 1962, when a major review dismissed myometrial hypertrophy as a plausible explanation after prior rejections of the theories of chronic myometritis, fibrosis uteri, and subinvolution as causes of bleeding. Subsequent to this arose a crusade against unnecessary hysterectomies in the 1970s. Although myometrial hyperplasia was proposed in 1868, it is only in the past 25 years that tangible evidence has supported that idea. It now appears that clinically enlarged uteri are due to globoid outward bulging of the uterus, caused by increased intramural pressure—often unrelated to either uterine weight or myometrial thickness. Abnormal (dysfunctional) uterine bleeding may often be due to spontaneous rupture of thrombosed dilated endometrial vessels, due to the combined effects of obstructed venous drainage by increased intramural pressure, and Virchow’s triad. Despite a century-old known association of parity with naturally occurring outer wall myometrial scars (fibrosis uteri with elastosis), it was not previously suggested that these may reflect healing reactions to muscle tears during labor and delivery. We now suggest that smaller, similar inner wall elastotic scars in the nerve-rich inner myometrium may explain many cases of pelvic pain. This review suggests that diverse pressure-related lesions may be present in clinically abnormal uteri that have been called “normal” since the crusade against unnecessary hysterectomy.
Kinetics of Proton Transport into Influenza Virions by the Viral M2 Channel

M2 protein of influenza A viruses is a tetrameric transmembrane proton channel, which has essential functions both early and late in the virus infectious cycle. Previous studies of proton transport by M2 have been limited to measurements outside the context of the virus particle. We have developed an in vitro fluorescence-based assay to monitor internal acidification of individual virions triggered to undergo membrane fusion. We show that rimantadine, an inhibitor of M2 proton conductance, blocks the acidification-dependent dissipation of fluorescence from a pH-sensitive virus-content probe. Fusion-pore formation usually follows internal acidification but does not require it. The rate of internal virion acidification increases with external proton concentration and saturates with a pKm of ∼4.7. The rate of proton transport through a single, fully protonated M2 channel is approximately 100 to 400 protons per second. The saturating proton-concentration dependence and the low rate of internal virion acidification derived from authentic virions support a transporter model for the mechanism of proton transfer.
Aurora: Providing Trusted System Services for Enclaves On an Untrusted System

Intel SGX provisions shielded executions for security-sensitive computation, but lacks support for trusted system services (TSS), such as clock, network and filesystem. This makes \textit{enclaves} vulnerable to Iago attacks~\cite{DBLP:conf/asplos/CheckowayS13} in the face of a powerful malicious system. To mitigate this problem, we present Aurora, a novel architecture that provides TSSes via a secure channel between enclaves and devices on top of an untrusted system, and implement two types of TSSes, i.e. clock and end-to-end network. We evaluate our solution by porting SQLite and OpenSSL into Aurora, experimental results show that SQLite benefits from a \textit{microsecond} accuracy trusted clock and OpenSSL gains end-to-end secure network with about 1ms overhead.
Energy-efficiency based resource allocation for the scalar broadcast channel

Until recently, link adaptation and resource allocation for communication system relied extensively on the spectral efficiency as an optimization criterion. With the emergence of the energy efficiency (EE) as a key system design criterion, resource allocation based on EE is becoming of great interest. In this paper, we propose an optimal EE-based resource allocation method for the scalar broadcast channel (BC-S). We introduce our EE framework, which includes an EE metric as well as a realistic power consumption model for the base station, and utilize this framework for formulating our EE-based optimization problem subject to a power as well as fairness constraints. We then prove the convexity of this problem and compare our EE-based resource allocation method against two other methods, i.e. one based on sum-rate and one based on fairness optimization. Results indicate that our method provides large EE improvement in comparison with the two other methods by significantly reducing the total consumed power. Moreover, they show that near-optimal EE and average fairness can be simultaneously achieved over the BC-S channel.
ST-CDP: Snapshots in TRAP for Continuous Data Protection

Continuous Data Protection (CDP) has become increasingly important as digitization continues. This paper presents a new architecture and an implementation of CDP in Linux kernel. The new architecture takes advantages of both traditional snapshot technology and recent Timely Recovery to Any Point-in-time (TRAP) architecture [CHECK END OF SENTENCE]. The idea is to periodically insert snapshots within the parity logs of changed data blocks in order to ensure fast and reliable data recovery in case of failures. A mathematical model is developed as a guide to designers to determine when and how to insert snapshots to optimize performance in terms of space usage and recovery time. Based on the mathematical model, we have designed and implemented a CDP module in the Linux system. Our implementation is at block level as a device driver that is capable of recovering data to any point-in-time in case of various failures. Extensive experiments have been carried out to show that the implementation is fairly robust and numerical results demonstrate that the implementation is efficient.
Everyday memory measures in multiple sclerosis: a systematic review

ABSTRACT Everyday memory is one of the most affected cognitive functions in multiple sclerosis (MS). Assessing everyday memory problems is crucial for monitoring the impact of memory deficits on individuals’ day-to-day lives and evaluating the effectiveness of interventions that aim to improve cognitive functions. The aim of this systematic review was to identify the research literature on everyday memory measures used with people with MS, describe the types of measures used, and summarise their psychometric properties. Empirical studies of cognitive function in MS using standardised everyday memory measures were included. Online databases (MEDLINE, PsycINFO, PsycARTICLES, Embase) and Google Scholar were searched. Forty-four studies met the inclusion criteria. A total of 12 measures were identified, with varied uses and administration methods. The majority of papers did not report any psychometric properties for MS populations. The few papers that did, reported that the measures have good reliability and appear to have good face, concurrent, and ecological validity, but these need to be evaluated further. This review presents researchers and clinicians with an overview of the various everyday memory measures used in studies with people with MS, to help them choose the appropriate measure for their evaluations.
A single‐bit continuous‐time delta‐sigma modulator using clock‐jitter and inter‐symbol‐interference suppression technique

This paper presents a technique for mitigating two well‐known DAC non‐idealities in continuous‐time delta‐sigma modulators (CTDSMs), particularly in wide‐band and low over‐sampling‐ratio (OSR) cases. This technique employs a special digital‐to‐analog convertor (DAC) waveform, called modified return‐to‐zero (MRZ), to reduce the time uncertainty effect because of the jittered clock at the sampling time instances and eliminate the effect of inter‐symbol‐interference (ISI) which degrades the modulator performance, especially when non‐return‐to‐zero (NRZ) DAC waveform is chosen in the modulator design. A third‐order single‐bit CTDSM is designed based on the proposed technique and step‐by‐step design procedure at circuit and system levels, considering clock jitter and ISI, is explained. Circuit simulations in 180‐nm CMOS technology show that in the presence of circuit non‐idealities which generate jitter and asymmetrical rise and fall times in the DAC current pulse, signal‐to‐noise‐distortion‐ratio (SNDR) of the proposed modulator is higher than the conventional modulator with NRZ waveform by about 10 dB. In these simulations, clock jitter standard deviation is 0.3% of the sampling period (TS) and the difference between fall/rise times in the DAC current pulse is 4%TS. Simulated at 600‐MHz sampling frequency (fS) with an oversampling ratio (OSR) of 24, SNDR figure of merit (FOMSNDR) of the proposed modulator in 180‐nm CMOS is 300 fj/conversion. Copyright © 2016 John Wiley & Sons, Ltd.