Miracle-dz/UniFAR-FTUs huggingface dataset:
Catalytic-site mapping of pyruvate formate lyase

Pyruvate formate-lyase of Escherichia coli cells, a homodimeric protein of 2 x 85 kDa, is distinguished by the property of containing a stable organic free radical (g = 2.0037) in its resting state. The enzyme (E-SH) achieves pyruvate conversion to acetyl-CoA via two distinct half-reactions (E-SH + pyruvate in equilibrium E-S-acetyl + formate; E-S-acetyl + CoA in equilibrium E-SH + acetyl-CoA), the first of which has been proposed to involve reversible homolytic carbon-carbon bond cleavage [J. Knappe et al. (1984) Proc. Natl Acad. Sci. USA 81, 1332-1335]. Present studies identified Cys-419 as the covalent-catalytic cysteinyl residue via CNBr fragmentation of E-S-[14C]acetyl and radio-sequencing of the isolated peptide CB-Ac (amino acid residues 406-423). Reaction of the formate analogue hypophosphite with E-S-acetyl was investigated and found to produce 1-hydroxyethylphosphonate with a thioester linkage to the adjacent Cys-418. The structure was determined from the chymotryptic peptide CH-P (amino acid residues 415-425), using 31P-NMR spectroscopy (delta = 44 ppm) and by chemical characterisation through degradation into 1-hydroxyethylphosphonate with phosphodiesterase or bromine. This novel P-C-bond synthesis involves the enzyme-based free radical and is proposed to resemble the physiological C-C-bond synthesis (pyruvate production) from formate and E-S-acetyl. These findings are interpreted as proof of a radical mechanism for the action of pyruvate formate-lyase. The central Cys-418/Cys-419 pair of the active site shows a distinctive thiolate property even in the inactive (nonradical) form of the enzyme, as determined using an iodoacetate probe.
A substitution method for nanoscale capacitance calibration using scanning microwave microscopy

This paper presents a calibration method and an uncertainty budget for capacitance measurements performed on micrometric size capacitors at microwave frequencies and nanometric resolution using a scanning microwave microscopy (SMM). The method applies the classical one-port vector network analyzer calibration for SMM using three known capacitance standards. These standards are established from a commercial calibration kit placed close to the microcapacitors in order to be calibrated. The calibration kit is composed of a large number of Metal-Oxide-Semiconductor (MOS) microcapacitors with capacitance values C ranging from 0.1 fF to 8.6 fF. Diligent selection criteria were established for the choice of the three capacitors. Their capacitance values were calculated from the AFM measured values of the area of the top electrodes and the dielectric thickness and considering the contribution of fringing fields. The combined type uncertainty on these calculated values amounts between 5% and 14% in relative value (uncertainty given at one standard deviation). The comparison between the capacitance values measured on calibration kit capacitors using the calibrated SMM and the calculated values show a good agreement for capacitances higher than 0.8 fF within uncertainties varying between 6% and 9%. For smaller capacitances, most of the observed deviations are not significant at two standard deviations. The uncertainties are mostly dominated by dimensional measurements and less importantly by unwanted capacitance effects. Based on these results, capacitances of two sets of microcapacitors were calibrated. The combined uncertainties vary from 14% to 7% for capacitances ranging from 0.1 fF to 3.1 fF respectively. The permittivity values of the dielectric layer of the two samples have been determined. They are found equal to 4.0 and 4.1 with a standard uncertainty of 0.6 and correlate with the expected value of 3.9.
Bioinformatics For Dummies

Introduction. Part I: Getting Started in Bioinformatics. Chapter 1: Finding Out What Bioinformatics Can Do for You. Chapter 2: How Most People Use Bioinformatics. Part II: A Survival Guide to Bioinformatics. Chapter 3: Using Nucleotide Sequence Databases. Chapter 4: Using Protein and Specialized Sequence Databases. Chapter 5: Working with a Single DNA Sequence. Chapter 6: Working with a Single Protein Sequence. Part III: Becoming a Pro in Sequence Analysis. Chapter 7: Similarity Searches on Sequence Databases. Chapter 8: Comparing Two Sequences. Chapter 9: Building a Multiple Sequence Alignment. Chapter 10: Editing and Publishing Alignments. Part IV: Becoming a Specialist: Advanced Bioinformatics Techniques. Chapter 11: Working with Protein 3-D Structures. Chapter 12: Working with RNA. Chapter 13: Building Phylogenetic Trees. Part V: The Part of Tens. Chapter 14: The Ten (Okay, Twelve) Commandments for Using Servers. Chapter 15: Some Useful Bioinformatics Resources. Index.
Ecological Niches and Geographic Distributions

This book provides a first synthetic view of an emerging area of ecology and biogeography, linking individual- and population-level processes to geographic distributions and biodiversity patterns. Problems in evolutionary ecology, macroecology, and biogeography are illuminated by this integrative view. The book focuses on correlative approaches known as ecological niche modeling, species distribution modeling, or habitat suitability modeling, which use associations between known occurrences of species and environmental variables to identify environmental conditions under which populations can be maintained. The spatial distribution of environments suitable for the species can then be estimated: a potential distribution for the species. This approach has broad applicability to ecology, evolution, biogeography, and conservation biology, as well as to understanding the geographic potential of invasive species and infectious diseases, and the biological implications of climate change. The authors lay out conceptual foundations and general principles for understanding and interpreting species distributions with respect to geography and environment. Focus is on development of niche models. While serving as a guide for students and researchers, the book also provides a theoretical framework to support future progress in the field.
Generation and Selection of Promoter Trap Lines for the Investigation of Shoot Development in Arabidopsis

T-DNA-mediated transformation is a common method for generating transgenic plants with insertional mutagenesis. In order to identify important genes involved in shoot development, a system of promoter trap insertional mutagenesis was employed in Arabidopsis thaliana. For this system, an efficient promoter trap vector, pFGL561 was developed. The pFGL561 includes a basta-resistant gene, an intron with multiple splicing donor and acceptor sites, and a promoter-less GFP reporter gene. Using floral-dipping method, we made total 300 T₁ promoter-trap lines which were screened for GFP expression. GFP signals in the T₁ plants were detected with high frequency, 26.7%, and the signals were reconfirmed in T₂ plants. To isolate the genes that are involved in shoot development, phenotypes were analyzed in T₂ plants of the 19 T₁ lines that had GFP signals in shoot apex, and 6 T₁ lines were selected that had abnormal shoot development. These lines will be very useful for the investigation of shoot development.
Participant perceptions of the faculty development Educational Research Series

Interest in the Scholarship of Teaching and Learning (SoTL) is driven in part by the need to provide systematic academic development for faculty anchored in evidence-based practice such as the introduction of quality assurance frameworks. This article reports on a mixedmethod evaluation of one institution’s grassroots multidisciplinary faculty development program, called the Educational Research Series, to determine if it met the needs of its faculty, graduate student, and staff participants. Conducted at one mid-sized university in southern Ontario and framed, as was the program design and implementation, by both adult learning theory and constructivism, the evaluation collected data from session exit surveys, attendee interviews, and facilitator focus groups. The data analysis revealed that reasons for participating included increasing levels of understanding, receiving individual support, and learning about colleagues’ research interests. The major strengths of the program included individual learning, resources, facilitator expertise, interactive sessions, and the multidisciplinary focus. The main challenges centered on depth versus breadth of the sessions, time, and educational language and theory. Participants recommended additional resources, communication among facilitators, institutional recognition, and increased depth of content. As a result of this evaluation, an Advanced Educational Research Series is being offered at the institution. This article will inform other institutions wishing to build SoTL as a field within their institutions.
Optimized Implementation of SIKE Round 2 on 64-bit ARM Cortex-A Processors

In this work, we present the first highly-optimized implementation of Supersingular Isogeny Key Encapsulation (SIKE) submitted to NIST’s second round of post quantum standardization process, on 64-bit ARMv8 processors. To the best of our knowledge, this work is the first optimized implementation of SIKE round 2 on 64-bit ARM over SIKEp434 and SIKEp610. The proposed library is explicitly optimized for these two security levels and provides constant-time implementation of the SIKE mechanism on ARMv8-powered embedded devices. We adapt different optimization techniques to reduce the total number of underlying arithmetic operations on the field level. In particular, benchmark results on embedded processors equipped with ARM Cortex-A55@1.766GHz and ARM Cortex-A75@2.803GHz show that the entire SIKE round 2 Key Encapsulation Mechanism (KEM) takes only 98.6 ms and 85.3ms at NIST’s security level 1, respectively. We also evaluated the compressed version of NIST’s security level 1, which requires 134.7 ms and 113.7 ms for Cortex-A55 and Cortex-A75, respectively. Considering SIKE’s extremely small key size in comparison to other post-quantum cryptography candidates, our result implies that SIKE is one of the promising candidates for key encapsulation mechanism on embedded devices in the quantum era.
Asymptotic Models for Tropical Intraseasonal Oscillations and Geostrophic Balance

In the tropics, rainfall is coupled with waves in the form of, for example, convectively coupled equatorial waves (CCEWs) and the Madden–Julian oscillation (MJO). In perhaps the simplest viewpoint of CCEWs, the effects of moisture and convective adjustment can predict the basic aspects of their propagation and structure: reduced propagation speeds and reduced meridional length scales. Here, a similar simple viewpoint is investigated for the MJO’s propagation and structure. To do this investigation, budget analyses of a model MJO are first presented to illustrate and motivate the asymptotic scaling assumptions. Asymptotic models are then derived for the MJO. In brief, the structure of the asymptotic MJO is described by a tropical geostrophic balance, and the slow propagation arises from the dynamics of moist static energy. To be specific, if the moist static energy has a background vertical gradient that is asymptotically weak (i.e., a moist stability that is nearly neutral), then it supports a slowly propagating wave. Beyond these main aspects, other processes also have an influence, such as eddy diffusion of moisture. In comparing the simple viewpoints of CCEWs and the MJO, one main difference is in the propagation speeds: relative to a dry wave speed of 50 m s−1, the MJO has a speed of 5 m s−1, resulting from a reduction factor of 0.1 related to moist stability, whereas the basic CCEW speed is 15 m s−1, resulting from a reduction factor of the square root of 0.1, related to the square root of the moist stability.
Requirement of young pigs for apparent ileal digestible tryptophan

In 5 growth trials with a total of 420 pigs, tryptophan requirements from 20 to 40 kg liveweight were estimated. L-Tryptophan 0, 0.15, 0.30, 0.45 and 0.60 g/kg was added to a basal diet containing tapioca, barley and maize, with CP 162 g/kg and tryptophan 1.65 g/kg. The control diet was supplemented with lysine, methionine plus cystine, threonine, isoleucine, valine and histidine to assure that only tryptophan was limiting pig performance. Diets were freely given as pellets. Total tryptophan was about 2.10 g/kg for optimal weight gain and feed conversion efficiency in a diet containing NE 9.5 MJ/kg, corresponding with apparent ileally digestible tryptophan 1.77 g/kg.
Tracer‐Aided Modeling in the Low‐Relief, Wet‐Dry Tropics Suggests Water Ages and DOC Export Are Driven by Seasonal Wetlands and Deep Groundwater

Our understanding of how wet‐dry tropical catchments process water and solutes remains limited. In this study, we attempt to gain understanding of water and dissolved organic carbon (DOC) transport, storage, and mixing in a 126 km2 catchment of northern Australia. We developed a coupled, tracer‐aided, conceptual rainfall‐runoff model (SAVTAM) that simultaneously calculates water, isotope, and DOC‐based processes at a daily time step. The semidistributed model can account for the marked hydrological distinction between savanna woodlands and adjacent seasonal wetlands. Using the calibrated model, we tracked the fluxes and derived the age of water in fluxes and storages. Model output matched the seasonal variability, controlled by seasonal rainfall, which switched on and off water and carbon flow pathways from the savanna to seasonal wetlands and ultimately to the perennial river. Such hydrological connectivity is modulated by the karst aquifer system that continuously contributes older waters (decades to century old) to maintain relatively stable and older streamflow during the dry season (average stream water age = 9.7 to 16.2 years). Such older waters occur despite a rapid, monsoon‐driven streamflow response. The DOC fluxes were largely sourced from the wetland and riparian forest that transported DOC in the order of 1.9 t C km−2 year−1 to the stream, which was on average 90% of the total simulated DOC exports of 2 t C·km−2·year−1. We conclude that coupled simulation of water and biogeochemistry is necessary to generate a more complete picture of catchment functioning, particularly in the tropics.
Functional analysis of the non-coding regions of RNA segments and the nucleocapsid protein of the Uukuniemi virus

9 1. REVIEW OF THE LITERATURE . 11 1.1 TAXONOMY OF VIRUSES . 11 1.2 FAMILY BUNYAVIRIDAE . 12 1.2. 1 Classification. 12 1.2. 2 Epidemiology and transmission. 14 1.2. 3 Diseases caused by bunyaviruses. 14 1.3 GENUS PHLEBOVIRUS. 15 1.3.1 Novel phleboviruses. 17 1.3.2 Discovery of Uukuniemi virus (UUKV). 18 1.4 GENOME ORGANIZATION OF BUNYAVIRUSES . 19 1.4. 1 S segment codes for the N and NSs proteins . 19 1.4. 2 M segment and the glycoproteins Gn and Gc. 21 1.4. 3 L segment and the RNA­dependent RNA polymerase (RdRp). 22 1.5 REPLICATION CYCLE OF BUNYAVIRUSES . 23 1.5. 1 Attachment and entry. 23 1.5. 2 Replication of viral genome and virus assembly. 24 1.6 REVERSE GENETICS SYSTEMS . 27 1.7 THE STRUCTURE AND FUNCTIONS OF NUCLEOCAPSID (N) PROTEIN. 29 1.7. 1 Structure of the virion . 29 1.7. 2 Ribonucleoprotein (RNP) complex. 29 1.7. 3 N protein oligomerization and RNA­binding . 30 1.7. 4 Solved N protein structures of negative­strand RNA viruses . 32 2. AIMS OF THE STUDY.34 3. MATERIALS AND METHODS.35 3.1 MATERIALS. 35 3.1.1 Virus (I, II). 35 3.1.2 Cell lines (I, II, III) . 35 3.1.3 Antibodies and antisera (II, III). 36 3.2 METHODS . 36 3.2. 1 Construction of plasmids (I, II, III) . 36 3.2. 2 Sequencing and sequence analysis (I, II, III). 37 3.2. 3 2D and 3D predictions and analysis of UUKV N and phlebovirus N proteins (II, III) . 38 3.2. 4 RNA secondary structure prediction (I) . 38 3.2. 5 RNA polymerase I minigenome system (I, II, III) . 38 3.2. 6 Virus­like particle (VLP) system for UUKV (II, III) . 41 3.2. 7 Mammalian two­hybrid (M2H) assay (II, III). 41 3.2. 8 Immunofluorescence assay (IFA) and UV microscopy (I, II, III). 41 3.2. 9 Chemical cross­linking (II) . 42 3.2. 10 SDS­PAGE and immunoblotting (I, II, III). 42
A conceptual framework for ex ante valuation of ecosystem services of brownfield greening from a systematic perspective

ABSTRACT Introduction: Although Brownfield greening (BG) can be a crucial solution to green space deficiency in dense urban areas, the potential benefits of different BG initiatives have rarely been quantitatively pre-evaluated. Here, the concept and main features of BG and its costs and benefits are firstly depicted. Next, a conceptual framework is presented which combines ecosystem service (ESS) valuation, economic cost-benefit analysis, and spatial pattern analysis. The framework is used to perform ex ante valuation of the ESS value of BG in Xuhui District, Shanghai. Outcomes: The scenario comparison results show that it can spatially reflect a closer-to-reality value of ESS at the urban scale instead of a theoretical value at the site scale. The ultimate values of ESS (After economic and landscape adjustments) in the composite scenario is more than 21% higher than those in the full-eco scenario, whereas the initial values of ESS (before the adjustments) in the former was 14% lower than those in the latter. These results suggest that a considerable part of brownfield greening projects need to be implemented in the more populated and economically vibrant areas instead of solely in the ecological construction zone, thereby correspondingly providing more cultural and regulation services and forming a better urban green space network. Conclusion: The framework provides a simple, science-based, and feasible tool for making BG decisions from a systematic perspective in dense urban areas. It can help meet the need for applying ESS knowledge to BG-based green space planning and policy making in the context of urban sustainable development.
The Evolution of GSM Technologies into 5G and the Imminent Emergence of Transformative Telemedicine Applications: A Review

Telemedicine is the delivery of health care services over a distance by health care providers using electronic technologies for the diagnosis, information exchange, treatment and disease prevention, injuries prevention, research and evaluation, and for continuing education for the health care provider. Telemedicine has been in existence since the 1960s, through telephone and video technologies. Over several decades, wireless broadband technology has become better with advancement with internet speed becoming almost ubiquitous. According to a telemedicine study by World Health Organization, 114 countries, that is, (59%) of member states, revealed that teleradiology has the highest rate of established service provision globally at (33%). Close to 70% of the countries indicated the need to know the cost and cost-effectiveness of telemedicine solutions, and above 50% needed to know about the infrastructure needed for telemedicine implementation while 60% needed clarification on clinical uses. With the evolution of Global System for Mobile (GSM) Communication services into 5G, it is the objective of this study to demonstrate how a combination of faster communication at lower latencies can be used to provide clinical support that overcomes geographical barriers using Information and Communication Technologies (ICT), with a goal of transforming healthcare service provision. A resultant prototype telemedicine application capable of medical diagnosis using artificial intelligence techniques demonstrates with the highest accuracy at 93.68% match. The medical similarity index of pathogens is captured from digital sources such as USB microscopes and scanners as medical images or specimens.
On Divergence Approximations for Unsupervised Training of Deep Denoisers Based on Stein’s Unbiased Risk Estimator

Recently, there have been several works on unsupervised learning for training deep learning based denoisers without clean images. Approaches based on Stein’s unbiased risk estimator (SURE) have shown promising results for training Gaussian deep denoisers. However, their performance is sensitive to hyper-parameter selection in approximating the divergence term in the SURE expression. In this work, we briefly study the computational efficiency of Monte-Carlo (MC) divergence approximation over recently available exact divergence computation using backpropagation. Then, we investigate the relationship between smoothness of nonlinear activation functions in deep denoisers and robust divergence term approximations. Lastly, we propose a new divergence term that does not contain hyper-parameters. Both unsupervised training methods yield comparable performance to supervised training methods with ground truth for denoising on various datasets. While the former method still requires roughly tuned hyper parameter selection, the latter method removes the necessity of choosing one.
Nanoscale NMR Spectroscopy Using Nanodiamond Quantum Sensors

While conventional nuclear magnetic resonance (NMR) spectroscopy is widely used for chemical analysis of macroscopic sample volumes, quantum NMR sensors based on nitrogen-vacancy (N-V) centers in bulk diamond have brought NMR spectroscopy to the nanoscale, demonstrating single-nucleus sensitivity and chemical structure determination. However, the detection volume for existing nanoscale N-V NMR devices extends only nanometers above a bulk diamond chip, which prevents measurements in thicker structures, such as cells. Here, we introduce N-V NMR devices based on nanodiamonds and use them to detect and distinguish multiple nuclear species in a sample volume of about ${20}^{3}\phantom{\rule{0.1em}{0ex}}\mathrm{n}{\mathrm{m}}^{3}$. We describe how analyte concentrations can be measured in situ using nuclear spins on the nanodiamond surface for calibration. The nanodiamond host provides a small size (\ensuremath{\sim}30 nm diameter), low toxicity, and opportunities for surface functionalization, which makes these devices promising for intracellular applications. These results mark an important step toward feasible and reliable nanoscale NMR measurements inside living cells.
Tunnel Magnetoresistance-Based Short-Circuit and Over-Current Protection for IGBT Module

This article presents a short-circuit and over current protection method using a new current sensor—tunnel magnetoresistance (TMR). The resistance of TMR changes with the magnetic flux density and a Wheatstone bridge circuit-based TMR can be used for current measurement. A toroid TMR current sensor is first proposed to measure the IGBT current, and the measured current is compared to references for protection. A prototype based on a 1200-V/200-A IGBT module is constructed to test the TMR sensor. A 120 A over-current can be detected in 604 ns. The measured current is also utilized to estimate the dc bus capacitance, experimental results show the maximum estimation error is 0.26%. Next, the TMR sensors are integrated into an IGBT module to expand the application scenario. The Calculation method and finite element method (FEM) are proposed to find optimal install locations of the TMR inside a 62-mm IGBT module. A differential TMR sensor circuit is employed to suppress the interference of the adjacent magnetic field. Experimental results based on a commercial IGBT with an integrated TMR sensor have been provided. The reaction time of the integrated TMR sensor is 530 ns and the maximum measurement error for the dc current is 0.85%. The detection and protection time for a 280-A short-circuit fault is 677 ns and 1.23 μs, respectively.