Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis and comparison of genome editing using CRISPResso2

Genome editing technologies are rapidly evolving, and analysis of deep sequencing data from target or off-target regions is necessary for measuring editing efficiency and evaluating safety. However, no software exists to analyze base editors, perform allele-specific quantification or that incorporates biologically-informed and scalable alignment approaches. Here, we present CRISPResso2 to fill this gap and illustrate its functionality by experimentally measuring and analyzing the editing properties of six genome editing agents.
Microsatellite analysis of genetic diversity and structure of Bruguiera gymnorrhiza and Kandelia obovate

Microsatellite loci were used for estimating genetic diversity and structure for three populations of B. gymnorrhiza and K. obovata (Rhizophoracea) in Okinawa, Japan. Thirty propagules of individual samples representing the population of both species were genotyped at five microsatellites. The level of observed heterozygosity (HO) was observed for several population, overall loci, ranged 0.422-0.800 with an average 0.627 for B. gymnorrhiza and 0.477-0.822 with an average 0.665 for K. obovata, indicating both species had relatively low genetic diversity. Both species showed low levels of allelic diversity, 3-5 and 3-5 alleles per locus, respectively. Gene diversitywas also maintained within populations (HS: 0.741 and 0.954). Additionally, an analysis of molecular variance (AMOVA) based on the immeasurable alleles model (F-statistics), for B. gymnorrhiza and K. obovata found that most of the variation resided within individuals in the total populations, i.e. 79.78 % and 69.90 % respectively, and among individuals within populations, i.e.14.30 % and 27.95 % respectively. There was little variation between populations, i.e. 5.92 % and 2.15 % for B. gymnorrhiza and K. obovata, respectively. The high-level genetic differentiation within individuals and populations both species may be due to the geographic range of the species, mating system, and environmental factors.
Symmetric-Key Cryptographic Routine Detection in Anti-Reverse Engineered Binaries Using Hardware Tracing

Software uses cryptography to provide confidentiality in communication and to provide authentication. Additionally, cryptographic algorithms can be used to protect software against cracking core algorithms in software implementation. Recently, malware and ransomware have begun to use encryption to protect their codes from analysis. As for the detection of cryptographic algorithms, previous works have had demerits in analyzing anti-reverse engineered binaries that can detect differences in analysis environments and normal execution. Here, we present a new symmetric-key cryptographic routine detection scheme using hardware tracing. In our experiments, patterns were successfully generated and detected for nine symmetric-key cryptographic algorithms. Additionally, the experimental results show that the false positive rate of our scheme is extremely low and the prototype implementation successfully bypasses anti-reversing techniques. Our work can be used to detect symmetric-key cryptographic routines in malware/ransomware with anti-reversing techniques.
The Influence of Water and Nitrogen Availability on the Expression of End-Use Quality Parameters of Spring Wheat

Wheat (Triticum aestivum L.) grain quality is determined by multiple physical and chemical attributes. However, previous studies mainly focused on protein quantity and composition, which may not be adequate for understanding grain quality, especially end-use quality. Field experiments were conducted at two locations for two years to better understand how and to what extent water and nitrogen (N) availability affect flour end-use quality. Four drought stress levels (i.e., mild, moderate, severe, and well-watered) and four N rates (i.e., zero, low, medium, and high) were applied to two spring wheat cultivars (i.e., Dayn and Egan). Evaluated end-use quality traits, including milling quality, mixograph parameters, flour protein and gluten contents, solvent retention capacity (SRC), and baking quality. Most end-use quality parameters were not significantly different between the well-watered treatment and mild drought stress in both cultivars. Nitrogen availability above the low rate (168 kg N ha−1) failed to further improve most end-use quality traits in either cultivar. Among all the end-use quality traits, lactic acid SRC may be a reliable indicator of flour end-use quality. These results indicate that mild drought stress (i.e., a 25% reduction in irrigation throughout the growing season) may not negatively affect end-use quality and excessive N fertilization offers minimal improvement in end-use quality. Such information could facilitate the development of irrigation and fertilization guidelines targeting at grain quality.
The first complete chloroplast genome of Coptis chinensis var. brevisepala, with implication for the phylogeny of Ranunculaceae

Abstract Coptis is one of the most important medicinal plant genera in eastern Asia. To better understand the evolution of this genus, the complete chloroplast genome of C. chinensis var. brevisepala was obtained by next-generation sequencing. The plastome of C. chinensis var. brevisepala is 155,426 bp in length, and consists of large (LSC, 84,488 bp) and small (SSC, 17,402bp) single-copy regions, separated by pair of inverted repeat regions (IRs, 26,768 bp). It harbours 111 unique genes, including 78 protein-coding genes, 29 transfer RNA genes, and four ribosomal RNA genes. Rps19 and ycf1 were pseudogenized due to incomplete duplication in IR regions. The nucleotide composition is asymmetric (30.5% A, 19.4% C, 18.7% G, and 31.3% T) with an overall G + C content of 38.2%. The phylogeny of Ranunculaceae based on 75 CDSs of 27 taxa showed that Ranunculoideae is paraphyletic and thus needs redefinition.
Growth-related changes in salt gland mass in gentoo and chinstrap penguin chicks

The salt gland is a well-developed osmoregulation organ in marine birds, and its relative size often reflects an individual’s feeding environment and osmoregulation capability. The development and functions of salt glands have been described for the Adelie penguin (Pygoscelis adeliae), but this information has been poorly documented in the other two pygoscelid species: gentoo (P. papua) and chinstrap penguins (P. antarcticus). To describe the growth-related changes in salt gland masses in relation to chick growth, we measured the wet mass of the salt glands collected from dead gentoo and chinstrap chicks during the early breeding period. The mass of the salt glands was linearly proportional to their body measurements, especially to body mass, in both species, and no significant difference was detected between the two species. Penguins are obligate marine dwellers throughout their life cycle, and the development of the salt gland in penguin chicks suggests that their ability to regulate dietary osmotic stress begins at an early stage of development after hatching. Furthermore, the linear relationship between the gland mass and body mass also suggests that the osmoregulation capability may continue to develop as penguin chicks grow. This descriptive note provides novel and quantitative information on the early developmental pattern of salt glands in gentoo and chinstrap penguins.
Flexible backbone assembly and refinement of symmetrical homomeric complexes

Symmetrical homomeric proteins are ubiquitous in every domain of life, and information about their structure is essential to decipher function. The size of these complexes often makes them intractable to high-resolution structure determination experiments. Computational docking algorithms offer a promising alternative for modeling large complexes with arbitrary symmetry. Accuracy of existing algorithms, however, is limited by backbone inaccuracies when using homology-modeled monomers. Here, we present Rosetta SymDock2 with a broad search of symmetrical conformational space using a six-dimensional coarse-grained score function followed by an all-atom flexible-backbone refinement, which we demonstrate to be essential for physically-realistic modeling of tightly packed complexes. In global docking of a benchmark set of complexes of different point symmetries — staring from homology-modeled monomers — we successfully dock (defined as predicting three near-native structures in the five top-scoring models) 19 out of 31 cyclic complexes and 5 out of 12 dihedral complexes. Highlights SymDock2 is an algorithm to assemble symmetric protein structures from monomers Coarse-grained score function discriminates near-native conformations Flexible backbone refinement is necessary to create realistic all-atom models Results improve six-fold and outperform other symmetric docking algorithms Graphical Abstract
S-Box Implementation for Security Algorithms in IOT

Internet of Things (IoT) is dominant technology for real time applications because it is integrated with various sensors, software and hardware. Security is the primary concern for IoT because of many ways of threats from different components. Typical encryption algorithms have less complexity and easy to decrypt thereby requiring highcomplexity security algorithm. The improved security algorithm must be less in size and power hence compatible to IoT based applications. This paper is used an Elliptic Curve Cryptography (ECC) to generate Substitution box (S-box) hence proposing 128-bit block cipher based on feistel network.
The Effect of Antimicrobial Photodynamic Therapy Using Chlorophyllin–Phycocyanin Mixture on Enterococcus faecalis: The Influence of Different Light Sources

The purpose of this study was to evaluate the in vitro effect of the chlorophyllin–phycocyanin mixture (Photoactive+) as a photosensitizer (PS) during antimicrobial photodynamic therapy (aPDT) on the count of Enterococcus faecalis (E. faecalis) using different light sources. The antimicrobial effect of aPDT with chlorophyllin–phycocyanin mixture using different light sources including diode laser (λ = 660 nm), diode laser (λ = 635 nm), LED (λ = 450 ± 30 nm) alone or in combination was assessed using microbial cell viability assay against E. faecalis. In addition, the cell cytotoxicity of Photoactive+ was assessed on human gingival fibroblast (HuGu) cells by MTT assay; E. faecalis growth when treated by both red wavelengths (635 nm, 660 nm) and combination of LED (420–480 nm) and red wavelengths (635 nm, 660 nm), significantly reduced compared to the control group (p < 0.05). There was no significant reduction in the number of viable cells exposed to Photoactive+ compared to the control group (p < 0.05). This study shows that the application of chlorophyllin–phycocyanin mixture and irradiation with emission of red light achieved a better result for bacterial count reduction, compared to a control. This component can be applied safely due to very negligible cytotoxicity.
The Role of Surface-Charge Transport in Electrohydrodynamics and Electromechanics of a Dielectric Sphere

To simulate the electrokinetic processes in weakly-conducting dielectric media, the Taylor– Melcher leaky-dielectric model is widely used, though its applicability conditions are unknown. To define them, the electric-potential distributions inside and outside a dielectric sphere placed in an electric field are determined, by assuming the sphere and the environment are weakly conducting and by considering the electric and diffusion interfacial currents and the surface-charge decay. Earlier, an electric-field characteristic of a dielectric sphere, for example, the real part of the Clausius–Mossotti factor found for a direct current (DC) field was commonly thought to be a single-valued function of two parameters, the conductivities of the sphere and the environment. Now, it depends on a larger number of parameters and, in the dc case, can range from the perfect-dielectric to perfect-conductor values even for a particle of a good insulator. Using the proposed theory, a variety of the experimental results on the electrohydrodynamic (EHD) fluid circulation and dielectrophoretic (DEP) motion of microparticles in the dielectric drops are explained for the first time or in a new way. The dielectrophoretic inflection and cross-over frequencies are defined allowing for the decay of the surface charge. A dependence of the effective conductivity of a sphere on the angular field distribution is predicted for the first time.
Assessment Postpartum Glucose Status among Women with Gestational Diabetes: Experience of a Sub-Saharan African Endocrinology Department

Background: Women with gestational diabetes mellitus (GDM) have a significantly increased risk for developing type 2 diabetes after delivery. The purpose of this study was to determine the postpartum glycemic status among women with GDM in an Endocrinology-Diabetology department in Sub-Saharan Area. Methods: It was a prospective cohort study conducted between January 1, 2013, and July 31, 2018 (over period of 5 years and 7 months) at Pikine National Hospital, Dakar, Senegal. Postpartum glucose status was evaluated at least 6 weeks post-partum among women with history of GDM according to IADPSG criteria. The glycemic status after delivery was pointed referring to 2006 WHO criteria. Results: Overall 53 patients were included in this study. Fasting plasma glucose was performed as a screening test in 94% of the cases. A type 2 diabetes after GDM as diagnosed in 6 patients, accounting for a prevalence of 11.32%. An Impaired Fasting Glucose (IFG) was revealed in 5 patients (9.43%). The patients underwent a screening test in the first year after delivery in 54.70% of the cases, over a half of whom during the post-partum period range from the 6th to the 12th week. Insulin usage during pregnancy was statistically correlated with the occurrence of postpartum diabetes. Conclusion: Diabetes prevention and early diagnosis require a glycemic status monitoring among women with history of GDM.
Nanobody-antigen catch-bond reveals NK cell mechanosensitivity

Antibodies are key tools in biomedical research and medicine. Their binding properties are classically measured in solution and characterized by an affinity. However, in physiological conditions, antibodies can bridge an immune effector cell and an antigen presenting cell, implying that mechanical forces apply to the bonds. For example, in antibody-dependent cell cytotoxicity, a major mode of action of therapeutic monoclonal antibodies, the Fab domains bind the antigens on the target cell, while the Fc domain binds to the activating receptor CD16 (also known as FcgRIII) of an immune effector cell, in a quasi bi-dimensional environment (2D). Therefore, there is a strong need to investigating antigen/antibody binding under force (2D), to better understand and predict antibody activity in vivo. We used two anti-CD16 nanobodies targeting two different epitopes and laminar flow chamber assay to measure the association and dissociation of single bonds formed between microsphere-bound CD16 antigens and surface-bound anti-CD16 nanobodies (or single domain antibodies), simulating 2D encounters. The two nanobodies exhibit similar 2D association kinetics, characterized by a strong dependence on the molecular encounter duration. However, their 2D dissociation kinetics strongly differ as a function of applied force: one exhibits a slip bond behaviour where off-rate increases with force; the other exhibits a catch bond behaviour with off-rate decreasing with force. This is the first time, to our knowledge, that catch bond behaviour was reported for antigen-antibody bond. We further exploit this property to show how Natural Killer cells spread differentially on surfaces coated with these molecules, revealing NK cells mechanosensitivity. Our results may also have strong implications for the design of efficient bispecific antibodies for therapeutic applications.
The Effect of Ownership Structure on Earnings Management Practices Toward Achieving the Real Comprehensive Income “An Applied Study on the Listed Companies in Libyan Stock Market”

Due to the importance of presenting an integrated model to disclose the real comprehensive income, to measure the management performance fairly and to take rational decisions related to dividends away from earnings management practices, this study aimed to identify the effect of the combination of ownership structure on earnings management practices in the listed companies in the Libyan stock market, as an addition and evidence of the emerging economies like the Libyan one. The study has stated the main following hypothesis: the ownership structure has a significant effect on earnings management practices in the listed companies in the Libyan stock market. As a result, relying on a multiple regression technique, which has been used to examine the five subhypotheses of the main one, the study became able to state that the ownership structure of enormous stockholders does not have a significant effect on earnings management practices in the listed companies in the Libyan stock market, while each of the managerial ownership structure; institutional ownership structure and foreign ownership structure, has a positive significant effect on earnings management practices in the listed companies in the Libyan stock market. On the other hand, the public ownership structure has a negative significant effect on earnings management practices in the listed companies in the Libyan stock market.
Elderliness and Obesity

Dunya gittikce daha yasli hale geliyor ve obezite sikligi artiyor. Geriatrik bireylerde obezite sikligi yuksek oldugu gibi bircok hastalikla iliskilidir ve yasam kalitesinde dusmeye ve malulluge sebep olmaktadir. Bu calismanin amaci, geriatrik obez ve obez olmayan hastalarin Kapsamli Geriatrik Degerlendirme Kriterleri Indekslerini karsilastirmaktir. Calismaya 39 normal kilolu ve cesitli nedenlerle Geriatri klinigine basvuran 41 obez hasta dahil edildi. Kapsamli Geriatrik Degerlendirme, Gunluk Yasamin Temel Aktiviteleri, Gunluk Yasam Enstrumantal Aktiviteleri, Tinetti Dengesi ve Yuruyus Degerlendirmesi, Zamanli kalkma ve yurume, Mini Mental Degerlendirme, Mini Beslenme Degerlendirmesi, Yesevage Geriatrik Depresyon ve Pittsburgh Uyku Kalitesi Endeksi testleri uygulandi ve her hastanin yurume hizi ve el kavrama gucu tespit edildi. Sonuc olarak, yasli obez hastalarin yuruyus ve denge, kas gucu, bazi gunluk yasam aktiviteleri ve ruh hali ve uyku kalitesi gibi gunluk yasami surdurmek icin gerekli olan bazi fiziksel yetenek ve islevlerde normal kiloya gore kotulestigi goruldu.
Aurora A ligand complex

Loss-of-function mutations in the retinoblastoma gene RB1 are common in several treatment-refractory cancers such as small-cell lung cancer and triple-negative breast cancer. To identify drugs synthetic lethal with RB1 mutation (RB1mut), we tested 36 cell-cycle inhibitors using a cancer cell panel profiling approach optimized to discern cytotoxic from cytostatic effects. Inhibitors of the Aurora kinases, AurA and AurB, showed the strongest RB1 association in this assay. LY3295668, an AurA inhibitor with over 1000-fold selectivity versus AurB, is distinguished by minimal toxicity to bone marrow cells at concentrations active against RB1mut cancer cells and leads to durable regression of RB1mut tumor xenografts at exposures that are well tolerated in rodents. Genetic suppression screens identified enforcers of the spindle assembly checkpoint (SAC) as essential for LY3295668 cytotoxicity in Rb-deficient cancers and suggest a model in which a primed SAC creates a unique dependency on AurA kinase for mitotic exit and survival.
Participação comunitária na gestão de recursos pesqueiros na Reserva Extrativista Marinha de Soure, Amazônia Marajoara (PA)

As politicas ambientais brasileiras criadas no final do seculo XX influenciaram significativamente o manejo dos recursos naturais no pais. Elas possibilitaram novos tipos de gestao ambiental e a criacao de areas protegidas, atualmente gerenciadas por meio de dispositivos de governanca que envolvem a esfera institucional e os arranjos locais. O Sistema Nacional de Unidades de Conservacao (SNUC), especificamente as Reservas Extrativistas Marinhas (Resex), sao exemplos-chave para pensar em como a governanca territorial e ambiental, atraves de novos instrumentos, permite a gestao inovadora dos recursos naturais de modo sustentavel, equitativo e compartilhado. Com base nessa premissa, o objetivo deste texto foi o de analisar a participacao comunitaria na gestao dos recursos pesqueiros na Reserva Extrativista Marinha de Soure, Marajo (PA). Para atingir esse objetivo, pesquisas de campo ocorreram entre 2015 e 2019 com base na perspectiva metodologica do estudo de caso e de metodos qualitativos de pesquisa, focados em geografia. Foram aplicadas entrevistas semiestruturadas e observacao participante a pescadores artesanais e funcionarios do Instituto Chico Mendes de Conservacao da Biodiversidade (ICMBio) e houve participacao em reunioes internas dos comunitarios e do Conselho Deliberativo. Abstract COMMUNITY PARTICIPATION IN THE MANAGEMENT OF THE FISHING RESOURCES IN SOURE MARINE EXTRACTIVE RESERVE, IN MARAJOARA AMAZON (PA) Brazilian environmental policies created at the end of the twentieth century have significantly influenced the management of natural resource in the country. They have made possible new types of environmental management and the creation of protected areas that are currently managed through governance devices involving the institutional sphere and local arrangements. The National System of Conservation Units, specifically, Marine Extractive Reserves, are key examples for thinking about how environmental governance, through new instruments, allows for innovative sustainable resource management, which is at once sustainable, equitable and shared. Based on this premise, this paper aims to analyze the community participation in the management of the fishing resources in the Soure Marine Extractive Reserve, Marajo (PA). To achieve this end, field researchs took place between 2015 and 2019 by using a case study methodological perspective and qualitative research methods, focused in geography. Moreover, I have applied semi structured interviews and participant observation with locals and Chico Mendes Institute for Biodiversity Conservation’s (ICMBio) staff and there was participation in the internal meetings of the locals and the Deliberative Council.
Endothelial Regulation of Drug Transport in a 3D Vascularized Tumor Model

Drug discovery and efficacy in cancer treatments are limited by the inability of pre‐clinical models to predict successful outcomes in humans. Limitations remain partly due to their lack of a physiologic tumor microenvironment (TME), which plays a considerable role in drug delivery and tumor response to therapy. Chemotherapeutics and immunotherapies rely on transport through the vasculature, via the smallest capillaries and stroma to the tumor, where passive and active transport processes are at play. Here, a 3D vascularized tumor on‐chip is used to examine drug delivery in a relevant TME within a large bed of perfusable vasculature. This system demonstrates highly localized pathophysiological effects of two tumor spheroids (Skov3 and A549), which cause significant changes in vessel density and barrier function. Paclitaxel (Taxol) uptake is examined through diffusivity measurements, functional efflux assays, and accumulation of the fluorescent‐conjugated drug within the TME. Due to vascular and stromal contributions, differences in the response of vascularized tumors to Taxol (shrinkage and CD44 expression) are apparent compared with simpler models. This model specifically allows for examination of spatially resolved tumor‐associated endothelial dysfunction, likely improving the representation of in vivo drug distribution, and has potential for development into a more predictable model of drug delivery.