Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental, neurochemical, and behavioral analyses of ErbB4 Cyt‐1 knockout mice

Neuregulins (NRGs) and their cognate neuronal receptor ERBB4, which is expressed in GABAergic and dopaminergic neurons, regulate numerous behaviors in rodents and have been identified as schizophrenia at‐risk genes. ErbB4 transcripts are alternatively spliced to generate isoforms that either include (Cyt‐1) or exclude (Cyt‐2) exon 26, which encodes a cytoplasmic domain that imparts ErbB4 receptors the ability to signal via the phosphoinositide 3‐kinase (PI3K)/protein kinase B (Akt) pathway. Although ErbB4 Cyt‐1/2 isoforms have been studied in transfected cultured cells, their functions in vivo remain unknown. Here, we generated ErbB4‐floxed (ErbB4‐Cyt1fl/fl) mice to investigate the effects of germline (constitutive) and conditional (acute) deletions of the Cyt‐1 exon. Overall receptor mRNA levels remain unchanged in germline ErbB4 Cyt‐1 knockouts (Cyt‐1 KOs), with all transcripts encoding Cyt‐2 variants. In contrast to mice lacking all ErbB4 receptor function, GABAergic interneuron migration and number are unaltered in Cyt‐1 KOs. However, basal extracellular dopamine (DA) levels in the medial prefrontal cortex are increased in Cyt‐1 heterozygotes. Despite these neurochemical changes, Cyt‐1 heterozygous and homozygous mice do not manifest behavioral abnormalities previously reported to be altered in ErbB4 null mice. To address the possibility that Cyt‐2 variants compensate for the lack of Cyt‐1 during development, we microinjected an adeno‐associated virus expressing Cre‐recombinase (AAV‐Cre) into the DA‐rich ventral tegmental area of adult ErbB4‐Cyt1fl/fl mice to acutely target exon 26. These conditional Cyt‐1 KOs were found to exhibit behavioral abnormalities in the elevated plus maze and startle response, consistent with the idea that late exon 26 ablations may circumvent compensation by Cyt‐2 variants. Taken together, our observations indicate that ErbB4 Cyt‐1 function in vivo is important for DA balance and behaviors in adults.
Three-dimensional multilayer concentric bipolar electrodes restrict spatial activation in optic nerve stimulation

Objective. Intraneural nerve interfaces often operate in a monopolar configuration with a common and distant ground electrode. This configuration leads to a wide spreading of the electric field. Therefore, this approach is suboptimal for intraneural nerve interfaces when selective stimulation is required. Approach. We designed a multilayer electrode array embedding three-dimensional concentric bipolar (CB) electrodes. First, we validated the higher stimulation selectivity of this new electrode array compared to classical monopolar stimulation using simulations. Next, we compared them in-vivo by intraneural stimulation of the rabbit optic nerve and recording evoked potentials in the primary visual cortex. Main results. Simulations showed that three-dimensional CB electrodes provide a high localisation of the electric field in the tissue so that electrodes are electrically independent even for high electrode density. Experiments in-vivo highlighted that this configuration restricts spatial activation in the visual cortex due to the fewer fibres activated by the electric stimulus in the nerve. Significance. Highly focused electric stimulation is crucial to achieving high selectivity in fibre activation. The multilayer array embedding three-dimensional CB electrodes improves selectivity in optic nerve stimulation. This approach is suitable for other neural applications, including bioelectronic medicine.
Analysis of combined clinical and diffusion basis spectrum imaging metrics to predict the outcome of chronic cervical spondylotic myelopathy following cervical decompression surgery.

OBJECTIVE Cervical spondylotic myelopathy (CSM) is the most common cause of chronic spinal cord injury, a significant public health problem. Diffusion tensor imaging (DTI) is a neuroimaging technique widely used to assess CNS tissue pathology and is increasingly used in CSM. However, DTI lacks the needed accuracy, precision, and recall to image pathologies of spinal cord injury as the disease progresses. Thus, the authors used diffusion basis spectrum imaging (DBSI) to delineate white matter injury more accurately in the setting of spinal cord compression. It was hypothesized that the profiles of multiple DBSI metrics can serve as imaging outcome predictors to accurately predict a patient's response to therapy and his or her long-term prognosis. This hypothesis was tested by using DBSI metrics as input features in a support vector machine (SVM) algorithm. METHODS Fifty patients with CSM and 20 healthy controls were recruited to receive diffusion-weighted MRI examinations. All spinal cord white matter was identified as the region of interest (ROI). DBSI and DTI metrics were extracted from all voxels in the ROI and the median value of each patient was used in analyses. An SVM with optimized hyperparameters was trained using clinical and imaging metrics separately and collectively to predict patient outcomes. Patient outcomes were determined by calculating changes between pre- and postoperative modified Japanese Orthopaedic Association (mJOA) scale scores. RESULTS Accuracy, precision, recall, and F1 score were reported for each SVM iteration. The highest performance was observed when a combination of clinical and DBSI metrics was used to train an SVM. When assessing patient outcomes using mJOA scale scores, the SVM trained with clinical and DBSI metrics achieved accuracy and an area under the curve of 88.1% and 0.95, compared with 66.7% and 0.65, respectively, when clinical and DTI metrics were used together. CONCLUSIONS The accuracy and efficacy of the SVM incorporating clinical and DBSI metrics show promise for clinical applications in predicting patient outcomes. These results suggest that DBSI metrics, along with the clinical presentation, could serve as a surrogate in prognosticating outcomes of patients with CSM.
The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle

Abstract The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater population size. Currently, populations of the species continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, with some studies predicting its extinction by 2070. Here, using a combination of short and long reads, we generate the first high-quality reference genome for the Balearic shearwater, with a completeness amongst the highest across available avian species. We used this reference genome to study critical aspects relevant to the conservation status of the species and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194–135 ka). Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision, and the development of natriuresis. The reference genome obtained will be the crucial in the future development of genetic tools in conservation efforts for this Critically Endangered species.
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

Abstract Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated 5′GGUC3′ paired to 3′CUGG5′ separately from other 5′GU3′/3′UG5′ stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37°C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.
Engineering Pseudomonas putida for improved utilization of syringyl aromatics

Lignin is a largely untapped source for the bioproduction of value‐added chemicals. Pseudomonas putida KT2440 has emerged as a strong candidate for bioprocessing of lignin feedstocks due to its resistance to several industrial solvents, broad metabolic capabilities, and genetic amenability. Here we demonstrate the engineering of P. putida for the ability to metabolize syringic acid, one of the major products that comes from the breakdown of the syringyl component of lignin. The rational design was first applied for the construction of strain Sy‐1 by overexpressing a native vanillate demethylase. Subsequent adaptive laboratory evolution (ALE) led to the generation of mutations that achieved robust growth on syringic acid as a sole carbon source. The best mutant showed a 30% increase in the growth rate over the original engineered strain. Genomic sequencing revealed multiple mutations repeated in separate evolved replicates. Reverse engineering of mutations identified in agmR, gbdR, fleQ, and the intergenic region of gstB and yadG into the parental strain recaptured the improved growth of the evolved strains to varied extent. These findings thus reveal the ability of P. putida to utilize lignin more fully as a feedstock and make it a more economically viable chassis for chemical production.
Estimation of the COVID‐19 mean incubation time: Systematic review, meta‐analysis, and sensitivity analysis

Providing sensible estimates of the mean incubation time for COVID‐19 is important yet complex. This study aims to provide synthetic estimates of the mean incubation time of COVID‐19 by capitalizing on available estimates reported in the literature and exploring different ways to accommodate heterogeneity involved in the reported studies. Online databases between January 1, 2020 and May 20, 2021 are first searched to obtain estimates of the mean incubation time of COVID‐19, and meta‐analyses are then conducted to generate synthetic estimates. Heterogeneity of the studies is examined via the use of Cochran's Q $Q$ statistic and Higgin's & Thompson's I2 ${I}^{2}$ statistic, and subgroup analyses are conducted using mixed effects models. The publication bias issue is assessed using the funnel plot and Egger's test. Using all those reported mean incubation estimates for COVID‐19, the synthetic mean incubation time is estimated to be 6.43 days with a 95% confidence interval (CI) [5.90, 6.96], and using all those reported mean incubation estimates together with those transformed median incubation estimates, the estimated mean incubation time is 6.07 days with a 95% CI [5.70, 6.45]. The reported estimates of the mean incubation time of COVID‐19 vary considerably due to multiple reasons, including heterogeneity and publication bias. To alleviate these issues, we take different angles to provide a sensible estimate of the mean incubation time of COVID‐19. Our analyses show that the mean incubation time of COVID‐19 between January 1, 2020 and May 20, 2021 ranges from 5.68 to 8.30 days.
Evaluation of Test Method for Solar Collector Efficiency

The test method of the standard EN12975-2 (European Committee for Standardization, 2004) is used by European test laboratories to determine the efficiency of solar collectors. The aim of this work is to present an evaluation of the test method for a 12.5 m² flat plate solar collector panel from Arcon Solvarme A/S. CFD (Computational Fluid Dynamics) simulations, calculations with a solar collector simulation program SOLEFF and thermal experiments are carried out in the investigation. The influences of the method to determine the mean solar collector fluid temperature, the approximation used to determine the specific heat of the solar collector fluid, the temperature levels used in the tests and the weather conditions on the collector efficiency are elucidated. Based on the investigations, it is recommended that the maximum temperature level used in the tests is not higher than the maximum operation temperature of the collector. Further, if the solar collector efficiency for low flow rates are measured in future test methods there is a need to change the method used to determine the mean solar collector fluid temperature.
Inhibition of human androgen receptor by delta 9‐tetrahydro‐cannabinol and cannabidiol related to reproductive dysfunction: A computational study

There have been conflicting reports on the impact of Cannabis sativa impact on reproductive function. Hence this study was aimed to ascertain the impact of tetrahydrocannabinol (THC) and cannabidiol (CBD) binding affinity on human androgen receptor (AR) via computational molecular dynamic simulation. The human AR coordinate in this study is derived from human AR in complex with the ligand metribolone (R18) (PBD ID: 1E3G) template using (MODELER version. 9.15). CBD (PubChem CID: 644019), and THC (PubChem CID: 16078) 2D structures were retrieved from PubChem and docked (Autodock‐Vina inbuilt in PyMol into the active site of human AR using the coordinates of the co‐crystalized ligand (R18). All atomic representations in this study were created using visual molecular dynamics (VMD) tools. The result revealed that neither CBD nor THC bear significant 2D similarity with R18. Despite the diversity within the chemical space, both CBD and THC poses bond flexibility required to bind avidly to AR with the docking scores comparable to R18. In fully bound state, the three compounds engage the AR pocket hydrophobic residues such as L701, L704, and L707, and aromatic residues such as F764. Polar contacts with T877 observed in R18 bound state is avoided in the THC and CBD bound states. Moreso, the results revealed that CBD has lesser binding energy compared to THC and R18 compound which serves as standard. This study hypothesized that CBD and THC binds complimentarily to the pocket AR, indicating a likely inhibition of reproductive function and prostate cancer progression.
Dynamics of alternating current electric field–assisted non‐Newtonian droplet formation with geometry confinement

Recently, microfluidic techniques have been widely applied for biomaterial droplet manipulations due to their precision and efficiency. Many biosamples such as deoxyribonucleic acid and blood samples are non‐Newtonian fluids with complex rheology, which brings challenges in control over them. The electric field is characterized by fast response and excellent adaptation to control microscale fluid flow. Here, we systematically investigate the alternating current electric field–assisted formation of non‐Newtonian droplet in a flow‐focusing microchannel with different sizes of channel orifice. The dependencies of flow conditions, microchannel geometries and electric parameters on the dynamics of non‐Newtonian droplet formation are thus elucidated. An effective capacitance electric model is developed to reveal and predict the interaction between the fluid flow and the electric field. Furthermore, the flow field of non‐Newtonian droplet formation is captured via the high‐speed microparticle image velocimetry system. The characteristics of the regimes of droplet formation and the influences of the channel orifice are revealed quantitatively. Our work offers elaborate references to the control of non‐Newtonian droplet formation, which benefits a wide range of applications in biology and chemistry.
Design of Simulation System in Tank Farm

At present, with the rapid development of science and technology, the level of automation in every field is improved to high degree. As tank farm is an indispensable and important component of petrochemical industry, its level of automation also needs to be improved. So we begin to develop the simulation system of tank farms. This article introduces the structure and function of the system. During designing the system, we used VC++ to design a calculating program, namely, the simulation engine, which calculates the dynamic parameters of the pipe system in tank farms according to the mathematical models that have been built. At the same time, we also used a kind of industry configuration software, KINGVIEW6.0, to make graphical interfaces, build a database, and then connect the variables of the database and the graphical units of the graphical interfaces. Through updating the database in real time, the simulation engine can drive the graphical interfaces. Although this system is still restricted to teaching now, it will be used in tank farms after the simulation system is applied in teaching successfully.
Innate immune cell response to host-parasite interaction in a human intestinal tissue microphysiological system

Protozoan parasites that infect humans are widespread, and lead to varied clinical manifestations, including life-threatening illnesses in immunocompromised individuals. Animal models have provided insight into innate immunity against parasitic infections, however, species-specific differences and complexity of innate immune responses make translation to humans challenging. Thus, there is a need for novel in vitro systems that can elucidate mechanisms of immune control and parasite dissemination. We have developed a human microphysiological system of intestinal tissue to evaluate parasite-immune-specific interactions during infection, which integrates primary intestinal epithelial cells and immune cells to investigate the role of innate immune cells during epithelial infection by the protozoan parasite, Toxoplasma gondii, which affects billions of people worldwide. Our data indicate that epithelial-infection by parasites stimulates a broad range of effector functions in neutrophils and NK cell-mediated cytokine production that play immunomodulatory roles, demonstrating the potential of our system for advancing the study of human-parasite interactions. Teaser Novel engineered model of human intestinal tissue for study of dissemination and immune control of parasitic infections.
Application of developmental regulators to improve in planta or in vitro transformation in plants

Summary Plant genetic transformation is a crucial step for applying biotechnology such as genome editing to basic and applied plant science research. Its success primarily relies on the efficiency of gene delivery into plant cells and the ability to regenerate transgenic plants. In this study, we have examined the effect of several developmental regulators (DRs), including PLETHORA (PLT5), WOUND INDUCED DEDIFFERENTIATION 1 (WIND1), ENHANCED SHOOT REGENERATION (ESR1), WUSHEL (WUS) and a fusion of WUS and BABY‐BOOM (WUS‐P2A‐BBM), on in planta transformation through injection of Agrobacterium tumefaciens in snapdragons (Antirrhinum majus). The results showed that PLT5, WIND1 and WUS promoted in planta transformation of snapdragons. An additional test of these three DRs on tomato (Solanum lycopersicum) further demonstrated that the highest in planta transformation efficiency was observed from PLT5. PLT5 promoted calli formation and regeneration of transformed shoots at the wound positions of aerial stems, and the transgene was stably inherited to the next generation in snapdragons. Additionally, PLT5 significantly improved the shoot regeneration and transformation in two Brassica cabbage varieties (Brassica rapa) and promoted the formation of transgenic calli and somatic embryos in sweet pepper (Capsicum annum) through in vitro tissue culture. Despite some morphological alternations, viable seeds were produced from the transgenic Bok choy and snapdragons. Our results have demonstrated that manipulation of PLT5 could be an effective approach for improving in planta and in vitro transformation efficiency, and such a transformation system could be used to facilitate the application of genome editing or other plant biotechnology application in modern agriculture.
E-Service Quality Evaluation on E-Government Website: Case Study BPJS Kesehatan Indonesia

This research intends to develop a model to evaluate the quality of e-services on e-government. The proposed model consists of seven dimensions: web design, reliability, responsiveness, privacy and security, personalization, information, and ease of use. The model is used to measure the quality of the e-registration of BPJS Kesehatan, an Indonesian government health insurance program. The validation and reliability testing show that of the seven dimensions proposed, only four that suitable for the case study. The result shows that the BPJS Kesehatan e-registration service is good in reliability and responsiveness dimensions, while from web design and ease of use dimensions the e-service still needs to be optimized.
Characterization and modeling of silicon and silicon carbide power devices

Power devices play key roles in the power electronics applications. In order for the power electronics designers to fully utilize the performance advantages of power devices, compact power device models are needed in the circuit simulator (Saber, P-spice, etc.). Therefore, it is very important to get accurate device models. However, there are many challenges due to the development of new power devices with new internal structure and new semiconductor materials (SiC, GaN, etc.). In this dissertation, enhanced power diode model is presented with an improvement in the reverse blocking region. In the current power diode model in the Saber circuit simulator, an empirical approach was used to describe the low-bias reverse blocking region by introducing an effect called “conduction loss,” a parameter that causes a linear relationship between the device voltage and current at low bias voltages with no physics meaning. Furthermore, this term is not sufficient to accurately describe the changes to the device characteristics as the junction temperature is varied. In the enhanced model, an analytical temperature dependent model for the reverse blocking characteristics has been developed for Schottky/JBS diodes by including the thermionic-emission mechanism in the low-bias range. The newly derived model equations have been implemented in Saber