Miracle-dz/UniFAR-FTUs huggingface dataset:
Chitinases A, B, and C1 of Serratia marcescens 2170 Produced by Recombinant Escherichia coli: Enzymatic Properties and Synergism on Chitin Degradation

To discover the individual roles of the chitinases from Serratia marcescens 2170, chitinases A, B, and C1 (ChiA, ChiB, and ChiC1) were produced by Escherichia coli and their enzymatic properties as well as synergistic effect on chitin degradation were studied. All three chitinases showed a broad pH optimum and maintained significant chitinolytic activity between pH 4 and 10. ChiA was the most active enzyme toward insoluble chitins, but ChiC1 was the most active toward soluble chitin derivatives among the three chitinases. Although all three chitinases released (GlcNAc)2 almost exclusively from colloidal chitin, ChiB and ChiC1 split (GlcNAc)6 to (GlcNAc)3, while ChiA exclusively generated (GlcNAc)2 and (GlcNAc)4. Clear synergism on the hydrolysis of powdered chitin was observed in the combination between ChiA and either ChiB or ChiC, and the sites attacked by ChiA on the substrate are suggested to be different from those by either ChiB or ChiC1.
BEAM web server: a tool for structural RNA motif discovery

Motivation: RNA structural motif finding is a relevant problem that becomes computationally hard when working on high‐throughput data (e.g. eCLIP, PAR‐CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. Results: The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre‐processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. Availability and implementation: The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. Contact: marco.pietrosanto@uniroma2.it Supplementary information: Supplementary data are available at Bioinformatics online.
Ru NMR and NQR Studies in CeRu2

Abstract We have carried out Ru NMR and NQR measurements in superconductor CeRu2 having Tc = 6.1 K in the temperature range of 1.3-30 K. From the 99Ru NMR in 10.2 T above Hc2 , T1T = const was found in the measured-T range, and the value of T1TK2 is almost the same as that in the uncorrelated Korringa relation, suggesting that there does not exist the strong spin fluctuation of Ru d-spins. The property of the superconducting state was investigated by using Ru NQR. We observed the Hebel-Slichter peak just below T c and the exponential decrease in 1/T1 indicating that this superconductivity has an ordinary s-wave character. The effect of Al substitution for Ru was also studied by NMR and NQR.
Semantic Web-based policy interaction detection method with rules in smart home for detecting interactions among user policies

The emerging technologies such as the Internet-of-Things, sensors, communication networks, have been or will be introduced to conventional domotics to provide a wide variety of smart home services to facilitate the household appliances or home cares and improve the lifestyles of people. Currently, smart home system are integrated with different features from product line and equipped with various sensors and actuators to meet the requirements of house occupants by specifying their customised user policies. However, the introduction of features and policies may result in undesired behaviours, and this effect is known as feature interactions. In this study, the authors proposed a Semantic Web-based policy interaction detection method with rules to model smart home services and policies with the aids of ontological analysis in the smart home domain, so as to construct a semantic context for inferring the interaction of policies. The authors focus their work on user policies interaction, which are detected by using the Semantic Web rule language in semantic context. The approach is successfully applied to the smart home system and is able to detect 90 interactions among 32 user policies by automated reasoning with tools support as Protege and Jess.
Study on the Spectrum of the One-dimensional Metallodielectric Photonic Crystal

The spectral structure of the one-dimensional metallodielectric photonic crystal is studied.The result shows that the theory about stationary wave can be used to properly explain the relationship between the spectral structure and the thickness of the dielectric material,the index of refraction of the dielectric and metallic materials composed photonic crystal.And the thicker of the metallic material deeper than the skin depth will lead to a lower transmittance and absorption,but the thickness do not affect the position of the peak of transmittance and absorption.
Autonomous citation matching

Advances in computational resources and the communications infrastructure, and the rapid rise of the World Wide Web, have led to the increasingly widespread availability of scientific papers in electronic form. Scientific papers usually contain citations to previous work, and indices of these citations are valuable for literature search , analysis, and evaluation. Current citation indices of the scientific literature are constructed using manual effort and are typically expensive. Part of the reason for using manual effort is the great variability of citation syntax – i t can be difficult to autonomously determine if two citations refer to the same article because citations can be written in many different formats. We present machine learning techniques that identify variant forms of citations to the same paper. A number of algorithms are presented. An algorithm based on word and phrase matching is found to perform best, and is sufficiently accurate for unassisted use in an autonomous citation indexing system. An algorithm based on a string edit distance performs poorly in comparison. A computationally efficient subfield algorithm is also presented. The accuracy and efficiency of all algorithms is quantitatively compared on a number of datasets.
Application of Public Knowledge Discovery Tool (PKDE4J) to Represent Biomedical Scientific Knowledge

In today’s era of information explosion, extracting entities and their relations in large-scale, unstructured collections of text to better represent knowledge has emerged as a daunting challenge in biomedical text mining. To respond to the demand to automatically extract scientific knowledge with higher precision, the public knowledge discovery tool PKDE4J (Song et al., 2015) was proposed as a flexible text-mining tool. In this study, we propose an extended version of PKDE4J to represent scientific knowledge for literature-based knowledge discovery. Specifically, we assess the performance of PKDE4J in terms of three extraction tasks: entity, relation, and event detection. We also suggest applications of PKDE4J along three lines: 1) knowledge search, 2) knowledge linking, and 3) knowledge inference. We first describe the updated features of PKDE4J and report on tests of its performance. With additional options in the processes of named entity extraction, verb expansion, and event detection, we expect that the enhanced PKDE4J can be utilized for literature-based knowledge discovery.
Measuring Residual Renal Function in Hemodialysis Patients without Urine Collection

Many patients on hemodialysis retain significant residual renal function (RRF) but currently measurement of RRF in routine clinical practice can only be achieved using inter‐dialytic urine collections to measure urea and creatinine clearances. Urine collections are difficult and inconvenient for patients and staff, and therefore RRF is not universally measured. Methods to assess RRF without reliance on urine collections are needed since RRF provides useful clinical and prognostic information and also permits the application of incremental hemodialysis techniques. Significant efforts have been made to explore the use of serum based biomarkers such as cystatin C, β‐trace protein and β2‐microglobulin to estimate RRF. This article reviews blood‐based biomarkers and novel methods using exogenous filtration markers which show potential in estimating RRF in hemodialysis patients without the need for urine collection.
Assessing Brain–Muscle Connectivity in Human Locomotion through Mobile Brain/Body Imaging: Opportunities, Pitfalls, and Future Directions

Assessment of the cortical role during bipedalism has been a methodological challenge. While surface electroencephalography (EEG) is capable of non-invasively measuring cortical activity during human locomotion, it is associated with movement artifacts obscuring cerebral sources of activity. Recently, statistical methods based on blind source separation revealed potential for resolving this issue, by segregating non-cerebral/artifactual from cerebral sources of activity. This step marked a new opportunity for the investigation of the brains’ role while moving and was tagged mobile brain/body imaging (MoBI). This methodology involves simultaneous mobile recording of brain activity with several other body behavioral variables (e.g., muscle activity and kinematics), through wireless recording wearable devices/sensors. Notably, several MoBI studies using EEG–EMG approaches recently showed that the brain is functionally connected to the muscles and active throughout the whole gait cycle and, thus, rejecting the long-lasting idea of a solely spinal-driven bipedalism. However, MoBI and brain/muscle connectivity assessments during human locomotion are still in their fledgling state of investigation. Mobile brain/body imaging approaches hint toward promising opportunities; however, there are some remaining pitfalls that need to be resolved before considering their routine clinical use. This article discusses several of these pitfalls and proposes research to address them. Examples relate to the validity, reliability, and reproducibility of this method in ecologically valid scenarios and in different populations. Furthermore, whether brain/muscle connectivity within the MoBI framework represents a potential biomarker in neuromuscular syndromes where gait disturbances are evident (e.g., age-related sarcopenia) remains to be determined.
Proteomic and Physiological Responses of Kineococcus radiotolerans to Copper

Copper is a highly reactive, toxic metal; consequently, transport of this metal within the cell is tightly regulated. Intriguingly, the actinobacterium Kineococcus radiotolerans has been shown to not only accumulate soluble copper to high levels within the cytoplasm, but the phenotype also correlated with enhanced cell growth during chronic exposure to ionizing radiation. This study offers a first glimpse into the physiological and proteomic responses of K. radiotolerans to copper at increasing concentration and distinct growth phases. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations (0–1.5 mM) in complex medium. Copper uptake coincided with active cell growth and intracellular accumulation was positively correlated with Cu(II) concentration in the growth medium (R2 = 0.7). Approximately 40% of protein coding ORFs on the K. radiotolerans genome were differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Interestingly, the specific activity of superoxide dismutase was repressed by low to moderate concentrations of copper during exponential growth, and activity was unresponsive to perturbation with paraquot. The biochemical response pathways invoked by sub-lethal copper concentrations are exceptionally complex; though integral cellular functions are preserved, in part, through the coordination of defense enzymes, chaperones, antioxidants and protective osmolytes that likely help maintain cellular redox. This study extends our understanding of the ecology and physiology of this unique actinobacterium that could potentially inspire new biotechnologies in metal recovery and sequestration, and environmental restoration.
Electric Field Enhanced Plasmid Delivery to Liver Hepatocellular Carcinomas

Electric field enhanced molecular delivery for cancer research and treatment is a new technology that has demonstrated its effectiveness in clinical trials using bleomycin or cisplatin (Heller, R., Gilbert, R., Jaroszeski, M. J. Clinical applications of electrocemotherapy. Advanced Drug Delivery Reviews 35, 119–129 (1999)), as chemotherapeutic agents. The technology is being investigated in research applications for applicability as a method to enhance gene expression in a target tumor. Success is predicated on an appropriate effective electric field mediated delivery protocol that triggers significant appropriate gene expression duration and levels. An electric field mediated delivery protocol includes a set of conditions associated with the electric field, the electroporation signature, as well as parameters associated with the plasmid and the electric field applicator. Manipulation of the electrical parameters within the electroporation signature generates different gene expression levels in liver hepatocellular carcinomas. Statistically significant gene expression levels were obtained that differed by an order of magnitude when two different electric field strength and duration conditions were employed.
Thermodynamics and Kinetics of the Three-Way Junction of Phi29 Motor pRNA and its Assembly into Nanoparticles for Therapeutic Delivery to Prostate Cancer

OF DISSERTATION THERMODYNAMICS AND KINETICS OF THE THREE-WAY JUNCTION OF PHI29 MOTOR PRNA AND ITS ASSEMBLY INTO NANOPARTICLES FOR THERAPEUTIC DELIVERY TO PROSTATE CANCER The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles, but has been limited by particle instability. Previously, it was found the three-way junction (3WJ) of the Phi29 DNA packaging motor pRNA was found to be ultra-stable and assemble in solution without the presence of metal ions. The three-way junction is composed of three short oligo RNA strands and proven to be thermodynamically stable. Here the assembly mechanism, thermodynamic and enzymatic stabilities, and kinetics are examined in order to understand the stability behind this unique motif. Thermodynamic and kinetics studies found that the pRNA 3WJ formed out of three components at a rapid rate creating a single-step three component collision with a lack of dimer intermediate formation while being governed by entropy, instead of the commonly seen enthalpy. Furthermore, the pRNA 3WJ proved to be stable at temperatures above 50 °C, concentrations below 100 pM, and produced a free energy of formation well below other studied RNA structures and motifs. With the high stability and folding efficiency of the pRNA 3WJ, it serves as an ideal platform for multi-branched RNA nanoparticles constructed through bottom-up techniques. RNA nanoparticles were constructed for the specific targeting of prostate cancer cells expressing Prostate Specific Membrane Antigen (PSMA) by receptor mediated endocytosis through the addition of an RNA aptamer; and the delivery of anti-miRNA sequences for gene regulation. The resulting nanoparticles remained stable while showing highly specific binding and entry in PSMA positive cells through cell surface receptor endocytosis. Furthermore, the entry of the nanoparticles allowed for the knockdown of against onco-miRNAs. Nanoparticles harboring antimiRNAs led to the upregulation of tumor suppressor genes, and signaling of apoptotic pathways. These findings display RNA nanotechnology can result in the production of stable nanoparticles and result in the specific treatment of cancers, specifically prostate cancer.
Effects of navigated TMS on object and action naming

Transcranial magnetic stimulation (TMS) has been used to induce speech disturbances and to affect speech performance during different naming tasks. Lately, repetitive navigated TMS (nTMS) has been used for non-invasive mapping of cortical speech-related areas. Different naming tasks may give different information that can be useful for presurgical evaluation. We studied the sensitivity of object and action naming tasks to nTMS and compared the distributions of cortical sites where nTMS produced naming errors. Eight healthy subjects named pictures of objects and actions during repetitive nTMS delivered to semi-random left-hemispheric sites. Subject-validated image stacks were obtained in the baseline naming of all pictures before nTMS. Thereafter, nTMS pulse trains were delivered while the subjects were naming the images of objects or actions. The sessions were video-recorded for offline analysis. Naming during nTMS was compared with the baseline performance. The nTMS-induced naming errors were categorized by error type and location. nTMS produced no-response errors, phonological paraphasias, and semantic paraphasias. In seven out of eight subjects, nTMS produced more errors during object than action naming. Both intrasubject and intersubject analysis showed that object naming was significantly more sensitive to nTMS. When the number of errors was compared according to a given area, nTMS to postcentral gyrus induced more errors during object than action naming. Object naming is apparently more easily disrupted by TMS than action naming. Different stimulus types can be useful for locating different aspects of speech functions. This provides new possibilities in both basic and clinical research of cortical speech representations.
System-Level Modeling and Analysis of Thermal Effects in WDM-Based Optical Networks-on-Chip

Multiprocessor systems-on-chip show a trend toward integration of tens and hundreds of processor cores on a single chip. With the development of silicon photonics for short-haul optical communication, wavelength division multiplexing (WDM)-based optical networks-on-chip (ONoCs) are emerging on-chip communication architectures that can potentially offer high bandwidth and power efficiency. Thermal sensitivity of photonic devices is one of the main concerns about the on-chip optical interconnects. We systematically modeled thermal effects in optical links in WDM-based ONoCs. Based on the proposed thermal models, we developed OTemp, an optical thermal effect modeling platform for optical links in both WDM-based ONoCs and single-wavelength ONoCs. OTemp can be used to simulate the power consumption as well as optical power loss for optical links under temperature variations. We use case studies to quantitatively analyze the worst-case power consumption for one wavelength in an eight-wavelength WDM-based optical link under different configurations of low-temperature-dependence techniques. Results show that the worst-case power consumption increases dramatically with on-chip temperature variations. Thermal-based adjustment and optimal device settings can help reduce power consumption under temperature variations. Assume that off-chip vertical-cavity surface-emitting lasers are used as the laser source with WDM channel spacing of 1 nm, if we use thermal-based adjustment with guard rings for channel remapping, the worst-case total power consumption is 6.7 pJ/bit under the maximum temperature variation of 60°C; larger channel spacing would result in a larger worst-case power consumption in this case. If we use thermal-based adjustment without channel remapping, the worst-case total power consumption is around 9.8 pJ/bit under the maximum temperature variation of 60°C; in this case, the worst-case power consumption would benefit from a larger channel spacing.
ACM SIGIR Student Liaison Program

ACM SIGIR has recently created the Student Liaison Program, a means to connect and stay connected with the student body of the information retrieval (IR) community. This report provides more information about the program, introduces the founding ACM SIGIR student liaisons, and explains past, ongoing, and future activities. We seek suggestions and recommendations on the current plans as well as the new ideas that fit into our mission.
Quantitative Estimates for the Long-Time Behavior of an Ergodic Variant of the Telegraph Process

Motivated by stability questions on piecewise-deterministic Markov models of bacterial chemotaxis, we study the long-time behavior of a variant of the classic telegraph process having a nonconstant jump rate that induces a drift towards the origin. We compute its invariant law and show exponential ergodicity, obtaining a quantitative control of the total variation distance to equilibrium at each instant of time. These results rely on an exact description of the excursions of the process away from the origin and on the explicit construction of an original coalescent coupling for both the velocity and position. Sharpness of the obtained convergence rate is discussed.
Human cytomegalovirus UL23 inhibits transcription of interferon-γ stimulated genes and blocks antiviral interferon-γ responses by interacting with human N-myc interactor protein

Interferon-γ (IFN-γ) represents one of the most important innate immunity responses in a host to combat infections of many human viruses including human herpesviruses. Human N-myc interactor (Nmi) protein, which has been shown to interact with signal transducer and activator of transcription (STAT) proteins including STAT1, is important for the activation of IFN-γ induced STAT1-dependent transcription of many genes responsible for IFN-γ immune responses. However, no proteins encoded by herpesviruses have been reported to interact with Nmi and inhibit Nmi-mediated activation of IFN-γ immune responses to achieve immune evasion from IFN-γ responses. In this study, we show strong evidence that the UL23 protein of human cytomegalovirus (HCMV), a human herpesvirus, specifically interacts with Nmi. This interaction was identified through a yeast two-hybrid screen and co-immunoprecipitation in human cells. We observed that Nmi, when bound to UL23, was not associated with STAT1, suggesting that UL23 binding of Nmi disrupts the interaction of Nmi with STAT1. In cells overexpressing UL23, we observed (a) significantly reduced levels of Nmi and STAT1 in the nuclei, the sites where these proteins act to induce transcription of IFN-γ stimulated genes, and (b) decreased levels of the induction of the transcription of IFN-γ stimulated genes. UL23-deficient HCMV mutants induced higher transcription of IFN-γ stimulated genes and exhibited lower titers than parental and control revertant viruses expressing functional UL23 in IFN-γ treated cells. Thus, UL23 appears to interact directly with Nmi and inhibit nuclear translocation of Nmi and its associated protein STAT1, leading to a decrease of IFN-γ induced responses and an increase of viral resistance to IFN-γ. Our results further highlight the roles of UL23-Nmi interactions in facilitating viral immune escape from IFN-γ responses and enhancing viral resistance to IFN antiviral effects.