Miracle-dz/UniFAR-FTUs huggingface dataset:
An Off-the-Shelf Approach for the Production of Fc Fusion Proteins by Protein Trans-Splicing towards Generating a Lectibody In Vitro

Monoclonal antibodies, engineered antibodies, and antibody fragments have become important biological therapeutic platforms. The IgG format with bivalent binding sites has a modular structure with different biological roles, i.e., effector and binding functions, in different domains. We demonstrated the reconstruction of an IgG-like domain structure in vitro by protein ligation using protein trans-splicing. We produced various binding domains to replace the binding domain of IgG from Escherichia coli and the Fc domain of human IgG from Brevibacillus choshinensis as split-intein fusions. We showed that in vitro protein ligation could produce various Fc-fusions at the N-terminus in vitro from the independently produced domains from different organisms. We thus propose an off-the-shelf approach for the combinatorial production of Fc fusions in vitro with several distinct binding domains, particularly from naturally occurring binding domains. Antiviral lectins from algae are known to inhibit virus entry of HIV and SARS coronavirus. We demonstrated that a lectin could be fused with the Fc-domain in vitro by protein ligation, producing an IgG-like molecule as a “lectibody”. Such an Fc-fusion could be produced in vitro by this approach, which could be an attractive method for developing potential therapeutic agents against rapidly emerging infectious diseases like SARS coronavirus without any genetic fusion and expression optimization.
On the Accurate Description of Photoionization Dynamical Parameters.

Calculation of dynamical parameters for photoionization requires an accurate description of both initial and final states of the system, as well as of the outgoing electron. We here show, that using a linear-combination-of-atomic-orbitals (LCAO) B-spline density functional (DFT) method to describe the outgoing electron, in combination with correlated equation-of-motion coupled-cluster singles and double (EOM-CCSD) Dyson orbitals, gives good agreement with experiment and outperforms other simpler approaches, like plane and Coulomb waves, used to describe the photoelectron. Results are presented for cross sections, angular distributions and dichroic parameters in chiral molecules, as well as for photoionization from excited states. We also present a comparison with the results obtained using Hartree-Fock (HF) and density-functional theory molecular orbitals selected according to Koopmans' theorem for the bound states.
The Effect of Early Postoperative Swelling on Change in Upper Eyelid Position After External Levator Resection and Blepharoplasty

Purpose: To determine if early postoperative swelling has an effect on change in the upper eyelid position after external levator resection (ELR) or blepharoplasty. Methods: In this observational cohort study, patients >18 years old who underwent ELR or upper blepharoplasty were identified. Digital photographs in primary position were obtained at the preoperative, early postoperative week one, and late postoperative month 3 visits. Marginal reflex distance 1 (MRD1) was measured digitally. Swelling was graded on a previously validated scale from 0 to 3. Photographs were evaluated by 26 experts/professional image graders. Primary outcome measure was changed in MRD1 from preoperative to late postoperative visits. Secondary outcome measure was change in MRD1 from early to late postoperative visits. The effect of early postoperative swelling on each outcome was assessed using linear regression models. Results: The sample contained 54 patients (25 ELR and 29 blepharoplasty). The model regressing change in MRD1 from preoperative to late postoperative visits with early postoperative swelling as the predictor was significant for ELR (R2 = 0.165, p = 0.044) but not blepharoplasty (R2 = 0.016, p = 0.515). However, the model controlling for preoperative MRD1 was not significant for ELR (B = 0.423, p = 0.354). The model regressing change in MRD1 from early to late postoperative follow up utilizing early postoperative swelling as the sole predictor was not significant for ELR (R2 = 0.010, p = 0.627) but was significant for blepharoplasty (R2 = 0.207, p = 0.013), with increased swelling associated with greater change in MRD1. Conclusions: Early postoperative swelling does not affect the final MRD1 outcome of ELR or upper blepharoplasty; however, blepharoplasty patients with early postoperative swelling may experience greater increase in MRD1 over follow up. Early postoperative swelling does not affect the final MRD1 outcome of external levator resection or upper blepharoplasty.
Linking the bacterial community in pea aphids with host‐plant use and natural enemy resistance

Abstract. 1. Pea aphids, Acyrthosiphon pisum, harbour a range of facultative accessory bacteria (secondary symbionts), including those informally known as PASS (R‐type), PAR, PABS (T‐type), and PAUS (U‐type).
Evidence-based investment selection: Prioritizing agricultural development investments under climatic and socio-political risk using Bayesian networks

Agricultural development projects have a poor track record of success mainly due to risks and uncertainty involved in implementation. Cost-benefit analysis can help allocate resources more effectively, but scarcity of data and high uncertainty makes it difficult to use standard approaches. Bayesian Networks (BN) offer a suitable modelling technology for this domain as they can combine expert knowledge and data. This paper proposes a systematic methodology for creating a general BN model for evaluating agricultural development projects. Our approach adapts the BN model to specific projects by using systematic review of published evidence and relevant data repositories under the guidance of domain experts. We evaluate a large-scale agricultural investment in Africa to provide a proof of concept for this approach. The BN model provides decision support for project evaluation by predicting the value—measured as net present value and return on investment—of the project under different risk scenarios.
Minimally Invasive Glaucoma Surgery: Where Is the Evidence?

Purpose: The last decade has witnessed an unprecedented growth in glaucoma treatment options through the introduction of minimally invasive glaucoma surgeries (MIGS). The aim of the present review is to provide an understanding of the currently available MIGS and to examine what data are currently available to guide treatment choice. Design: Meta-analysis and systematic review of randomized and non-randomized control trials. Methods: Out of 2567 articles identified, a total of 77 articles were retained for analysis, including 28 comparative studies and 12 randomized control trials. Overall, 7570 eyes were included. When data permitted, the weighted mean difference in intraocular pressure reduction was calculated for comparison purposes. Results: Weighted mean intraocular pressure reductions from all analyzed studies were: 15.3% (iStent), 29.1% (iStent inject), 36.2% (ab interno canaloplasty), 34.4% (Hydrus), 36.5% (gonioscopically-assisted transluminal trabeculotomy), 24.0% (trabectome), 25.1% (Kahook dual blade), 30.2% (Cypass), 38.8% (XEN), and 50.0% (Preserflo). Conclusions: One of the advantages of the heterogenous range of available MIGS options is the chance to tailor therapy in an individualized manner. However, high-quality data are required to make this choice more than an educated guess. Overall, this review confirms the efficiency of assessed MIGS compared with standalone phacoemulsification, but it highlights that only few studies compare different MIGS techniques and even fewer assess MIGS against criterion standard treatments. Current evidence, while non-negligible, is mostly limited to heterogenous nonrandomized studies and uncontrolled retrospective comparisons, with few quality randomized control trials. We suggest that future research should be comparative and include relevant comparators, standardized to report key outcome features, long-term to assess sustainability and late complications, and ideally randomized.
The bioaccumulation and biotransformation of cis, trans‐cypermethrin in the rat

The disposition of the pyrethroid insecticide cypermethrin, (RS)-a-cyano-3-phenoxybenzyl (1RS)-cis, trans-3-(2,2-dichlorovinly)-2, 2-dimethylcyclopropane-carboxylate, has been studied in male and female rats following a single toxic oral dose (200mg kg−1) of two radiolabelled forms ([14C-benzyl] and [14C-cyclopropyl]) of the insecticide. The bioaccumulation and elimination of 14C-benzyl-labelled cypermethrin, following repeated administration at a sub-toxic dose (2mg kg−1), has also been studied in male and female rats. Although, at the toxic dose, radioactivity from the two radiolabelled forms was rapidly eliminated in urine and faeces, the increased excretion in the faeces, over that for low doses, was evidence that absorption was incomplete. The major pathways of metabolism involved cleavage of the ester bond, with subsequent hydroxylation and glucuronidation of the cyclopropyl acid moieties, together with hydroxylation and sulphation of the 3-phenoxybenzyl moiety. The absence of sex- or dose-dependent changes was reflected by the constant proportions of these metabolites found in the urine. Constant levels of radioactivity in tissues were achieved rapidly, generally within the first week of repeated administration. Elimination was rapid on the cessation of dosing, although less rapid from the fat and skin. The material in the fat was mainly the cis-isomers of cypermethrin, which were eliminated with a mean half-life of 18.2 days, compared with 3.4 days for the trans-isomers.
Genetic mutation analysis of hereditary spastic paraplegia

Abstract Hereditary spastic paraplegias are heterogeneous disorders with diversified clinical manifestations, and genetic testing is important for the diagnosis and typing of hereditary spastic paraplegias. Gene panel sequencing containing 55 hereditary spastic paraplegias-related genes was performed to screen the pathogenic genes for hereditary spastic paraplegias. Sanger sequencing was adopted to validate if the family member carried the same pathogenic gene as the proband. Fifteen out of 53 patients carried mutation(s) in the screened hereditary spastic paraplegias-related genes. Among the 23 identified mutations, only one mutation had been previously reported as a pathogenic mutation. In the pedigree of case 6, the proband, his mother and uncle all carried the same novel deletion mutation (c.1459delA) at SPAST gene. Based on the pedigree, the disease was inherited in an AD pattern. In the pedigree of case 53, the family disease may be in an X-linked recessive inheritance pattern. The proband (case 53) carried two novel mutations in ALT1 gene and L1CAM gene (c.2511C>A), respectively. The L1CAM gene is the causative gene for the SPG1 X-linked recessive—hereditary spastic paraplegias. Our data confirm the genetic heterogeneity of hereditary spastic paraplegias, and SPG4/SPAST were the most frequent forms. The pathogenicity of the novel mutations is worth to be further investigated.
Best Practice Standards in Animal-Assisted Interventions: How the LEAD Risk Assessment Tool Can Help

Simple Summary Animal-assisted interventions (AAI) in educational and other settings have steadily increased over the last fifty years. While scientific research on the effects of AAI is still growing, the application in the field has overtaken the science and seen a steep rise in many countries and settings in recent years. Surprisingly, while different organisations provide a range of guidelines, no unified, standardised guidelines exist, nor do easy-to-use risk assessment tools for AAI providers and users exist. With differences in practical application and different policies used by AAI providers worldwide, this means that in practice AAI takes place in an unregulated manner without a gold standard of best practice. To ensure safe AAI worldwide, we provide urgently needed unified guidelines on best practice in relation to risk assessment, safeguarding and animal welfare priorities. We also provide the first comprehensive risk assessment and animal welfare tools to achieve consistent welfare and safety standards for best practice across educational and other settings around the world. Abstract Animal-assisted interventions (AAI) in educational and other settings have steadily increased over the last fifty years and a steep rise in AAI has been observed in many countries and settings in recent years. Surprisingly, while different providers and organisations provide a range of guidelines, no unified, standardised guidelines or risk assessment tools for AAI exist. This means that in practice AAI takes place in an unregulated manner and without a gold standard of best practice. In addition, knowledge of which interventions are effective is still scarce and the mechanisms of successful interventions are not yet fully understood. This is partly due to AAI being a relatively new research field and standards of research and practice have often lacked rigour in the past. Furthermore, knowledge and experience of providers undertaking interventions varies greatly as there is no standardised training either. We address the striking lack of standardised guidelines and procedures. In all AAI, high importance should be placed on safety and welfare of all involved. Children and other AAI participants, staff and animals should be given equal consideration when assessing risks and welfare needs. To ensure safe AAI worldwide, we provide urgently needed guidelines on best practice in relation to risk assessment, safeguarding and animal welfare priorities. The guidelines were developed for a large-scale longitudinal, randomised controlled trial AAI project and are relevant to AAIs within educational and other settings. We also provide the first set of comprehensive risk assessment and animal welfare tools to achieve consistent welfare and safety standards for best practice across educational and other settings around the world.
Short-chain fructo-oligosaccharides supplementation to suckling piglets: Assessment of pre- and post-weaning performance and gut health

Farmers face difficulties in redeeming their investment in larger litter sizes since this comes with larger litter heterogenicity, lower litter resilience and risk of higher mortality. Dietary oligosaccharides, given to the sow, proved beneficial for the offspring’s performance. However, giving oligosaccharides to the suckling piglet is poorly explored. Therefore, this field trial studied the effect of dietary short-chain fructo-oligosaccharides (scFOS; 1g/day; drenched) supplementation to low (LBW, lower quartile), normal (NBW, two intermediate quartiles) and high (HBW, upper quartile) birth weight piglets from birth until 7 or 21 days of age. Performance parameters, gut microbiome and short-chain fatty acids profile of feces and digesta were assessed at birth (d 0), d 7, weaning (d 21.5) and 2 weeks post-weaning (d 36.5). Additional parameters reflecting gut health (intestinal integrity and morphology, mucosal immune system) were analysed at d 36.5. Most parameters changed with age or differed with the piglet’s birth weight. Drenching with scFOS increased body weight by 1 kg in NBW suckling piglets and reduced the post-weaning mortality rate by a 100%. No clear difference in the IgG level, the microbiota composition and fermentative activity between the treatment groups was observed. Additionnally, intestinal integrity, determined by measuring intestinal permeability and regenerative capacity, was similar between the treatment groups. Also, intestinal architecture (villus lenght, crypt depth) was not affected by scFOS supplementation. The density of intra-epithelial lymphocytes and the expression profiles (real-time qPCR) for immune system-related genes (IL-10, IL-1ß, IL-6, TNFα and IFNγ) were used to assess mucosal immunity. Only IFNγ expression, was upregulated in piglets that received scFOS for 7 days. The improved body weight and the reduced post-weaning mortality seen in piglets supplemented with scFOS support the view that scFOS positively impact piglet’s health and resilience. However, the modes of action for these effects are not yet fully elucidated and its potential to improve other performance parameters needs further investigation.
FairCs—Blockchain-Based Fair Crowdsensing Scheme using Trusted Execution Environment

Crowdsensing applications provide platforms for sharing sensing data collected by mobile devices. A blockchain system has the potential to replace a traditional centralized trusted third party for crowdsensing services to perform operations that involve evaluating the quality of sensing data, finishing payment, and storing sensing data and so forth. The requirements which are codified as smart contracts are executed to evaluate the quality of sensing data in a blockchain. However, regardless of the fact that the quality of sensing data may actually be sufficient, one key challenge is that malicious requesters can deliberately publish abnormal requirements that cause failure to occur in the quality evaluation process. If requesters control a miner node or full node, they can access the data without making payment; this is because of the transparency of data stored in the blockchain. This issue promotes unfair dealing and severely lowers the motivation of workers to participate in crowdsensing tasks. We (i) propose a novel crowdsensing scheme to address this issue using Trusted Execution Environments; (ii) offer a solution for the confidentiality and integrity of sensing data, which is only accessible by the worker and corresponding requester; (iii) and finally, report on the implementation of a prototype and evaluate its performance. Our results demonstrate that the proposed solution can guarantee fairness without a significant increase in overhead.
Comparison of three selectable marker genes for transformation of wheat by microprojectile bombardment

Three selectable marker genes were compared for their efficacy in the production of transgenic wheat plants following microprojectile bombardment of cultured immature embryos. While transformed plants were recovered using the bar (phosphinothricin acetyltransferase) gene in combination with bialaphos, and the aphA (neomycin phosphotransferase) gene in combination with geneticin or paromomycin, no transgenic material was obtained with the hpt (hygromycin phosphotransferase) gene and hygromycin B. Southern analysis revealed single copy as well as multiple copy insertions of the bar and aphA transgenes. Inheritance of these selectable marker genes was demonstrated in the T1 generation progenies.
Prostaglandin F2α Agonists Negatively Modulate the Size of 3D Organoids from Primary Human Orbital Fibroblasts

Purpose To elucidate the molecular etiology of deepening of the upper eyelid sulcus (DUES) induced by prostaglandin (PG) analogs, a three-dimensional (3D) tissue culture system was employed using human orbital fibroblasts (HOFs). Methods During adipogenesis, changes in HOF 3D organoid sizes, as well as their lipids stained by BODIPY and expression of the extracellular matrix (ECM) by immunolabeling and/or quantitative PCR, were studied in the presence or absence of either 100-nM bimatoprost acid or 100-nM prostaglandin F2α. Results The size of the 3D organoids increased remarkably during adipogenesis, but such increases were significantly inhibited by the presence of PG analogs. Staining intensities by BODIPY and mRNA expression of peroxisome proliferator-activated receptor gamma were significantly increased upon adipogenesis but were not influenced by the presence of PG analogs. Unique changes in ECM expression observed with or without adipogenic differentiation were significantly modified by the presence of PG analogs. Conclusions Our present study indicates that PG analogs have the potential to modulate the ECM network within HOF 3D organoids. Thus, a 3D tissue culture system may be a suitable strategy for understanding the disease etiology of DUES.
Sylvatic Mosquito Diversity in Kenya—Considering Enzootic Ecology of Arboviruses in an Era of Deforestation

As new and re-emerging vector-borne diseases are occurring across the world, East Africa represents an interesting location, being the origin of several arboviruses with a history of urbanization and global spread. Rapid expansion of urban populations and alteration of natural habitats creates the opportunity for arboviruses to host-switch from wild, sylvatic hosts or vectors into urban transmission affecting human populations. Although mosquito surveillance regularly takes place in urban areas of Kenya, for example identifying vectors of dengue virus or malaria viruses, little work has been carried out to determine the distribution and abundance of sylvatic vectors. Here, we describe the mosquito vector species and diversity collected at twelve forest habitats of rural Kenya. We conducted arbovirus screening of over 14,082 mosquitoes (47 species, 11 genera) as 1520 pools, and detected seven viruses (six bunyaviruses, and one flavivirus-bunyavirus co-infection) isolated from pools of Aedes dentatus, Anopheles funestus, Culex annulioris, and Cx. vansomereni. Awareness of sylvatic vector species and their location is a critical part of understanding the ecological foci and enzootic cycling of pathogens that may be of concern to public, animal or wildlife health. As natural ecosystems come under anthropogenic pressures, such knowledge can inform us of the One Health potential for spillover or spillback leading to outbreaks, and assist in vector control strategies.
Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae

Understanding the functional connection that occurs for the three nuclear RNA polymerases to synthesize ribosome components during the ribosome biogenesis process has been the focal point of extensive research. To preserve correct homeostasis on the production of ribosomal components, cells might require the existence of proteins that target a common subunit of these RNA polymerases to impact their respective activities. This work describes how the yeast prefoldin-like Bud27 protein, which physically interacts with the Rpb5 common subunit of the three RNA polymerases, is able to modulate the transcription mediated by the RNA polymerase I, likely by influencing transcription elongation, the transcription of the RNA polymerase III, and the processing of ribosomal RNA. Bud27 also regulates both RNA polymerase II-dependent transcription of ribosomal proteins and ribosome biogenesis regulon genes, likely by occupying their DNA ORFs, and the processing of the corresponding mRNAs. With RNA polymerase II, this association occurs in a transcription rate-dependent manner. Our data also indicate that Bud27 inactivation alters the phosphorylation kinetics of ribosomal protein S6, a readout of TORC1 activity. We conclude that Bud27 impacts the homeostasis of the ribosome biogenesis process by regulating the activity of the three RNA polymerases and, in this way, the synthesis of ribosomal components. This quite likely occurs through a functional connection of Bud27 with the TOR signaling pathway.