Miracle-dz/UniFAR-FTUs huggingface dataset:
Regional random mutagenesis driven by multiple sgRNAs and diverse on-target genome editing events to identify functionally important elements in non-coding regions

Functional regions that regulate biological phenomena are interspersed throughout eukaryotic genomes. The most definitive approach for identifying such regions is to confirm the phenotype of cells or organisms in which specific regions have been mutated or removed from the genome. This approach is invaluable for the functional analysis of genes with a defined functional element, the protein-coding sequence. In contrast, no functional analysis platforms have been established for the study of cis-elements or microRNA cluster regions consisting of multiple microRNAs with functional overlap. Whole-genome mutagenesis approaches, such as via N-ethyl-N-nitrosourea (ENU) and gene trapping, have greatly contributed to elucidating the function of coding genes. These methods almost never induce deletions of genomic regions or multiple mutations within a narrow region. In other words, cis-elements and microRNA clusters cannot be effectively targeted in such a manner. Herein, we established a novel region-specific random mutagenesis method named CRISPR-& Transposase-based RegionaL Mutagenesis (CTRL-Mutagenesis). We demonstrated that CTRL-mutagenesis randomly induces diverse mutations within target regions in murine embryonic stem cells. Comparative analysis of mutants harbouring subtly different mutations within the same region would facilitate the further study of cis-element and microRNA clusters. GRAPHICAL ABSTRACT
ATP burst is the dominant driver of antibiotic lethality in Mycobacteria

Antibiotic-tolerant bacteria, due to their unique physiology, are refractory to antimicrobial killing and pose challenges for infection control. Incomplete knowledge of how bactericidal antibiotics work limits our understanding of partial resistance from phenotypic tolerance in mycobacteria, a driver for developing genetic resistance. Using proteomics, 13C isotopomer analysis, and biochemical assays, we investigated the physiological response of M.smegmatis challenged with aminoglycoside and fluoroquinolone antibiotics. Two distinct classes of antibiotics elicited remarkably similar responses and increased flux through the TCA cycle, causing enhanced respiration, ROS generation, and ATP burst. We found that ATP burst drives cidality through metal ion chelation, which was rescued by exogenous supplementation with divalent metals. 13C isotope tracing indicated TCA cycle flux deviation from its oxidative arm as a bacterial adaptive mechanism, which also included activated intrinsic resistance and a higher propensity to develop antibiotic resistance. Our study provides a new understanding of the intricate mechanisms of antibiotic-induced cell death and expands the current paradigm for antibiotic action.
In Silico Analysis of Drug Off-Target Effects on Diverse Isoforms of Cervical Cancer for Enhanced Therapeutic Strategies

Cervical cancer is a severe medical issue as 500,000 new cases of cervical cancer are identified in the world every year. The selection and analysis of the suitable gene target are the most crucial in the early phases of drug design. The emphasis at one protein while ignoring its several isoforms or splice variations may have unexpected therapeutic or harmful side effects. In this work, we provide a computational analysis of interactions between cervical cancer drugs and their targets that are influenced by alternative splicing. By using open-accessible databases, we targeted 45 FDA-approved cervical cancer drugs targeting various genes having more than two distinct protein-coding isoforms. Binding pocket interactions revealed that many drugs do not have possible targets at the isoform level. In terms of size, shape, electrostatic characteristics, and structural analysis have shown that various isoforms of the same gene with distinct ligand-binding pocket configurations. Our results emphasized the risks of ignoring possibly significant interactions at the isoform level by concentrating just on the canonical isoform and promoting consideration of the impacts of cervical cancer drugs on- and off-target at the isoform level to further research.
ENHANCED EFFICIENCY OF RNA-GUIDED CAS12a VERSUS CAS9 TRANSGENE KNOCK-IN AND ACTIVITY AT A SCHISTOSOMA MANSONI GENOME SAFE HARBOR

Recently, we reported programmed Cas9 mediated insertion of a reporter gene into a gene safe harbor site, GSH1, of Schistosoma mansoni via homology-directed repair (HDR) using overlapping guide RNAs. Here, we report efficient and precise CRISPR/Cas12a-mediated homology directed insertion (knockin, KI) of a 5’ C6-PEG10-modified double-stranded transgene bearing microhomology arms, 50 nt in length, at GSH1. At the outset, we undertook bioinformatic and computational analysis following by experimental verification of the regulatory activity of endogenous schistosome ubiquitin (SmUbi) promoter and terminator, to drive strong reporter gene expression. Green fluorescent protein activity driven by SmUbi followed electroporation-mediated transfection of schistosome eggs. HDR induced by RNA-guided CRISPR/Cas12a, which releases overhanging DNA strands of 18-24, delivered more efficient KI than CRISPR/Cas9. In this non-model pathogen, programmed KI facilitated precise chromosomal integration of the reporter-gene with at GSH1. The approach advances schistosome transgenesis field and may also advance functional genomics and transfection methods in related parasitic and non-parasitic helminths, which hitherto lack these tools. Author summary Genome editing (CRISPR) technology is revolutionizing advances in biology, medicine, and agriculture. Transgenesis approaches are integral in diverse applications including gene therapy, biotherapeutics, deciphering host-pathogen interactions, and enhancements in agricultural production. Parasitic worms that are responsible for infectious diseases including neglected tropical diseases (NTDs), which cause substantial morbidity and mortality. NTDs mainly occur in the Global South, and they are responsible for a disease burden that exceeds that caused by malaria and tuberculosis. Infections with parasitic helminths also are responsible for immense economic burden in the agriculture. Tools for functional genomics in parasitic helminths are limited. Access to CRISPR-based approaches can be expected to hasten development of drug and/or vaccine targets for these diseases. Here, we focused on the helminth Schistosoma mansoni, a water borne parasite of humans, and which is endemic in Africa, and northeastern South America. To advance the state of the art in laboratory techniques currently used to study the biology and pathogenesis of this and related pathogens, we evaluated a spectrum of technological approaches aimed at improved current lab practice in this field. The findings demonstrated that specific technical and chemical modifications, including deploying a DNA cutting enzyme termed Cas12a along with a transgene with chemically modified short flanking sequences (homology arms) provided improved gene editing efficiency for this schistosome.
Implications for crustal accretion at fast spreading ridges from observations in Jurassic oceanic crust in the western Pacific

Downhole logging data and basement stratigraphy interpretations are used to determine the spreading environment and crustal accretion history of the ocean basement cored at ODP Hole 801C located in the Jurassic Magnetic Quiet Zone of the western Pacific. High‐resolution microresistivity data obtained with the Formation MicroScanner are used to measure the dip of the extrusive layers and indicate a 10°–30° increase in dip down the drill hole with lava flow contacts dipping back toward the original ridge axis. This structural pattern and the high proportion of massive flows relative to pillow units are consistent with prevailing crustal accretion models proposed for faster spreading ridges (e.g., >60 km/m.y., full‐rate). A detailed analysis of the age data, basement lithology, related geochemistry, and structural attitudes suggest the shallowest 100 m of the drilled section (e.g., Sequences I–III) were emplaced just off the ridge (Sequence III) or significantly farther off‐axis up to 5–15 m.y. later (Sequences I and II). The remainder of the drilled section (e.g., Sequences IV–VIII) has geochemical, lithological and physical trends that are assumed to be representative of crust created at faster spreading ridges. The pattern of dipping lava flow contacts from this deeper section of the drill hole suggests lava flows emanating from the ridge axis are limited to 1–2 km off‐axis. Our results suggest ocean crust drilled at Hole 801C was created at faster spreading rates; however, caution should be used when incorporating Sequences I–III into geochemical reference sections for faster spreading ridges.
The Effects of Vegetation on the Dynamic State of the Ground

Abstract : The Battlespace Terrain Reasoning and Awareness (BTRA) research program edict for the Future Combat System(s) (FCS) is to "provide warfighters with an accurate and timely understanding of the battlespace environment's effect on personnel, platforms, sensors and systems in order to develop improved tactics, techniques, procedures and plans that insure information superiority and situational awareness" (R. Davis, ERDCCRREL, personal communication). BTRA is developing tools which will be embedded in DTSS (Digital Topographic Support System) and CJMTK (Commercial Joint Mapping Tool Kit). These tools will "use measured and forecasted weather to predict weapon sensor performance and weather influences upon on - and offroad mobility; to analyze and predict maneuver options by looking at cover, concealment, defensible positions, etc.; and to perform automated terrain analysis based on enemy doctrine, equipment constraints, operational posture and terrain effects" (M. Powers, ERDC-TEC, personal communication). As part of the BTRA program we developed a dynamic state of the ground model, FASST (Fast All-season Soil STrength) to provide input to mobility (STDMOB) and infrared and acoustic sensor performance overlay algorithms (RSPD and SPEBE respectively). This model predicts the soil moisture, ice content, temperature and strength as well as snow and ice accretion/depletion as a function of meteorological forcing and site characteristics. Recently, a two tier, multilayer vegetation algorithm was added. We will start by briefly discussing the original model followed by details of the new vegetation subroutines. How the vegetation affects the above model outputs will also be presented.
Hunters and gatherers: Strategies for curriculum mapping and data collection for assuring learning

Assurance of learning is a predominant feature in both quality enhancement and assurance in higher education. It involves making program expectations and standards explicit, then systematically gathering, and interpreting evidence to determine how well performance matches those expectations. This benefits the institution, ensuring program aims are evaluated and used for program development, and is important for external scrutiny (AUQA, TEQSA, professional bodies). This project aims to investigate two elements of assurance of learning: (1) mapping graduate attributes throughout a program; and (2) collecting assurance data. It will conduct an audit across disciplines subject to accreditation in Australian universities to evaluate current methods of mapping graduate attributes and their impact on the curriculum, and also the systems used to collect and store data. This information will be critically analysed to develop strategy on curriculum mapping and data collection. It will draw upon the use of existing software packages (e.g., SOS - mapping; ReView, SPARKPLUS collection) to support the efficient and effective implementation strategies.
ResearchOnline@ND ResearchOnline@ND

Background There is a growing interest in the role of disturbed body perception in people with persistent pain problems such as chronic low back pain (CLBP). A questionnaire, the Fremantle Back Awareness Questionnaire (FreBAQ), was recently developed as a simple and quick way of assessing disturbed perceptual awareness of the back in people with CLBP and appears to have acceptable psychometric properties. The aim of the present study was to develop a Japanese version of the FreBAQ (FreBAQ-J) and evaluate its psychometric properties in a sample of Japanese people with low back pain (LBP).
Geodetic constraints on magma movement and withdrawal during the 2006 eruption of Augustine Volcano: Chapter 17 in The 2006 eruption of Augustine Volcano, Alaska

For the first time in the United States, a modern geodetic network of continuously recording Global Positioning System (GPS) receivers has measured a complete eruption cycle at a stratovolcano, Augustine Volcano in Alaska, from the earliest precursory unrest through the return to background quiescence. The on-island network consisted of five continuously recording, telemetered GPS stations, four continuously recording, nontelemetered stations, and about 10 campaign bench marks. The continuous network recorded several distinct and conspicuous signals over the course of the unrest and eruption, starting with a months-long precursory inflation centered beneath the volcano at around sea level. Nearly coincident with the highest volumetric eruption rates, this inflation gave way to a more deep seated deflation that we interpret as a major withdrawal (approx. 25 million m3 of compressed magma) from a nearly cylindrical magma reservoir centered about 5 km below sea level. Detailed analysis of the geodetic time series reveals additional nuance, including the probable upward propagation of a small dike into the edifice in the 60 days or so before the onset of large-scale explosive activity. Comparisons of the geodetic data and their resulting interpretations with other data, such as earthquake hypocenters and petrologically inferred magma-pressure histories, reveal a kinematic, if not mechanical, account of the 2006 eruption that details the shape and location of the magma source region, the means and velocity of magma transport, and the establishment of a short lived volume(or pressure-) buffering capability held within the magma reservoir. The cumulative deformation over the course of the eruption shows a large signal close in and high on the edifice that decays rapidly with distance. This pattern indicates a small permanent increase in the edifice volume (beyond that added by the surficial lava dome) but also shows that without close-in (<2.5 km from the summit) stations, the eruption might have been invisible to campaign GPS stations alone.
Pengaruh pH pada Penurunan Kadar Ion Sianida secara Elektrokimia dengan Elektroda PbO2/Grafit

Telah dilakukan penelitian mengenai pengaruh pH pada penurunan kadar ion sianida secara elektrokimia dengan elektroda PbO 2 /grafit. Tujuan dari penelitian ini adalah menurunkan kadar sianida dengan metode elektrolisis menggunakan elektroda PbO 2 /grafit dan mengkaji pengaruh pH terhadap penurunan kadar sianida dalam limbah artificial dengan elektroda PbO 2 /grafit. Logam PbO 2 digunakan sebagai anoda dan grafit sebagai katoda. Elektrolisis dilakukan selama 8 jam disertai pengadukan dan variasi pH dengan potensial aplikasi sebesar 5,0 volt. Variasi pH yang digunakan adalah 7, 8, 9, 10, 11, 12, dan 13 yang diatur dengan penambahan H 2 SO 4 atau NaOH. Analisis sianida dilakukan secara kuantitatif dengan metode spoktrofotometri UV-Vis , sedangkan analisis karbonat dan amoniak dilakukan secara kualitatif. Hasil penelitian menunjukkan bahwa metode elektrolisis dengan elektroda PbO 2 /grafit mampu menurunkan kadar sianida sampai 100% dan pada pH basa penurunan kadar sianida cenderung meningkat dengan peningkatan pH. Elektrolisis larutan sianida menghasilkan karbonat dan amoniak.
ONGOING RESEARCH IN HONG KONG HAS LED TO IMPROVED WIND SHEAR AND TURBULENCE ALERTS

SUBTITLE: LOCATED IN AN AREA SUSCEPTIBLE TO WIND SHEAR AND TURBULENCE, THE HONG KONG OBSERVATORY CONTINUES TO REFINE TECHNIQUES FOR DETECTING THESE PHENOMENA AND PROVIDING TIMELY ALERTS TO AIRCRAFT APPROACHING OR DEPARTING HONG KONG INTERNATIONAL AIRPORT.
A global, regional and national developmental status assessment of fishing capacity and fishing effort from 1950 to 2012

Global marine wild capture landings have remained relatively stable over the last twenty years, however, stability cannot be inferred from landings alone without taking into account the quantity of fishing effort required to capture a given quantity of seafood. Thus, it is possible that the observed stability could be due to a combination of increasing fishing effort, the transfer of effort to previously under exploited stocks or inaccurate reporting by some countries.
Computers and Electrical Engineering

The outbreak of novel coronavirus (COVID-19) has extremely shaken the whole world. COVID-19 has increased human distress, damaged the global economy, flipped the lives of many people around the world upside down, and has had a huge effect on the health, economic, environmental, and social sectors. This study aims to determine the social and economic trends in the outbreak of COVID-19 in Pakistan. Machine learning techniques learn patterns from historical data and make predictions on its basis. Furthermore, an online survey has been conducted to collect data and a total of 410 responses are collected. Machine learning techniques have been used to highlight the impact of COVID-19 on daily life. Moreover, sentiment analysis on tweets of Pakistan has also been performed to evaluate the positive and negative sentiments of the people on COVID-19.
Soft started induction motor modeling and heating issues for different starting profiles using a flux linkage ABC-frame of reference

In order to mitigate adverse effects of starting torque transients and high inrush currents in induction motors, a popular method is to use electronically controlled soft starting voltages utilizing series connected silicon controlled rectifiers (SCRs). Investigation of semi-optimum soft starting voltage profiles was implemented using a flux linkage ABC-frame of reference model of a soft started three-phase induction motor. A state-space model of the soft starter thyristor switching sequence for the motor and load was developed and implemented in a time-domain simulation to examine winding heating and shaft stress issues for different starting profiles. Simulation results of line starts and soft starts were compared with measured data through which validation of the model was established. In this paper, different induction machine soft start profiles are shown and comparisons of starting times, torque profiles, and heating losses are made. Discussion of these results and conclusions as to the near-optimum types of profiles are delineated based on peak torque, starting times, and winding heating criteria.
2015 Ieee International Conference on Big Data (big Data) Distributed Frank-wolfe under Pipelined Stale Synchronous Parallelism

—Iterative-convergent algorithms represent an important family of applications in big data analytics. These are typically run on distributed processing frameworks deployed on a cluster of machines. On the other hand, we are witnessing the move towards data center operating systems (OS), where resources are unified by a resource manager and processing frameworks coexist with each other. In this context, different processing framework job tasks can be scheduled on the same machine and slow down a worker (straggler problem). Existing work has shown that an iteration model with relaxed consistency such as the Stale Synchronous Parallel (SSP) model, while still guaranteeing convergence, is able to cope with stragglers. In this paper we propose a model for the integration of the SSP model on a pipelined distributed processing framework. We then apply SSP on a distributed version of the Frank-Wolfe algorithm. We theoretically show its sparsity bounds and convergence under SSP. Finally, we experimentally show that the Frank-Wolfe algorithm applied on LASSO regression under SSP is able to converge faster than its BSP counterpart, especially under load conditions similar to those encountered in a data center OS.
Modeling social influences from call records and mobile web browsing histories

Nowadays, companies are usually strongly interested in discovering the latent social influences among their customers since the information is highly valuable to their marketing strategies. In this paper, we study how to model the influence probabilities among the customers of a telecommunication company by analyzing their call records and mobile web browsing histories. We first construct a directed network using the phone call records. We verify whether the statistical properties of our constructed network follow the commonly known social network properties. Next, we propose several heuristics to measure the influence probabilities between users in the constructed network by analyzing both the call records and the mobile web browsing histories. Finally, we evaluate our proposed measurements by two prediction tasks, including predicting the lengths of a call and estimating the number of common website visits between two users. The results show that our proposed measurements are effective with better prediction accuracy.
Checklist of the reptiles and amphibians of egypt

Abstract : The checklist is based primarily on extensive collections made by the United States Naval Medical Research Unit No. 3 (NAMRU-3) in Egypt. Forms listed are those that are known or expected to occur in Egypt (including Sinai), and those that have been reported from Egypt without further verification. The systematic lists contain original citations, references to major faunal works, and the most recent reviews of each particular group. From the 3.424 specimens obtained, adequate distributional data are now available for most forms in Egypt. Maps showing collecting localities for each species are also presented for use in future sympatric and ecological studies.
Geophysical Data Summary for Fletcher's Ice Island (T-3) May 1962 - October 1974. Part A: Geophysical Data Listings. Part B: Bathymetric, Geomagnetic, and Gravity Profiles. Part C: Seismic Reflection Profiles.

Abstract : Position, depth, gravity and magnetic data collected at Ice Island (T-3) during the period from 1962 to 1974 are presented in tabular form at 12-hour intervals. The station orbited the Canada Basin during this interval. Drift tracks are presented as well as profiles of the geophysical data against time. Seismic reflection profiles over 4000 km of track are shown. (Author)