Miracle-dz/UniFAR-FTUs huggingface dataset:
Aerodynamic effects on an emulated hovering passerine with different wing-folding amplitudes

Bird flight involves complicated wing kinematics, especially during hovering flight. The detailed aerodynamic effects of wings with higher degrees of freedom (DOFs) remain to be further investigated. Therefore, we designed a novel multiarticulate flapping-wing robot with five DOFs on each wing. Using this robot we aimed to investigate the more complicated wing kinematics of birds, which are usually difficult to test and analyze. In this study the robot was programmed to mimic the previously observed hovering motion of passerines, and force measurements and particle image velocimetry experiments. We experimented with two different wing-folding amplitudes: one with a larger folding amplitude, similar to that of real passerines, and one with only half the amplitude. The robot kinematics were verified utilizing direct linear transformation, which confirmed that the wing trajectories had an acceptable correlation with the desired motion. According to the lift force measurements, four phases of the wingbeat cycle were characterized and elaborated through camera images and flow visualization. We found that the reduction in folding amplitude caused a higher negative force during upstrokes and also induced a greater positive force at the initial downstroke through ‘wake capture’. This could increase the vertical oscillation while hovering despite a minor increase in average force production. This phenomenon was not observed during forward flight in previous studies. Our results provide a critical understanding of the effect of wing folding which is required for designing the wing kinematics of future advanced flapping-wing micro aerial vehicles.
Dose-area product ratio in external small-beam radiotherapy: beam shape, size and energy dependencies in clinical photon beams

In small-field radiotherapy (RT), a significant challenge is to define the amount of radiation dose absorbed in the patient where the quality of the beam has to be measured with high accuracy. The properties of a proposed new beam quality specifier, namely the dose-area-product ratio at 20 and 10 cm depths in water or DAPR20,10, were studied to yield more information on its feasibility over the conventional quality specifier tissue-phantom ratio or TPR20,10. The DAPR20,10 may be measured with a large-area ionization chamber (LAC) instead of small volume chambers or semi-conductors where detector, beam and water phantom positioning and beam perturbations introduce uncertainties. The effects of beam shape, size and energy on the DAPR20,10 were studied and it was shown that the DAPR20,10 increases with increasing beam energy similarly to TPR20,10 but in contrast exhibits a small beam size and shape dependence. The beam profile outside the beam limiting devices has been shown to have a large contribution to the DAPR20,10. There is potential in large area chambers to be used in DAPR measurement and its use in dosimetry of small-beam RT for beam quality measurements.
Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting

Abstract The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
Short Chain Fatty Acid and Fecal Microbiota Profiles Are Linked to Fibrosis in Primary Biliary Cholangitis.

The gut microbiota and metabolome could play a role in primary biliary cholangitis (PBC) progression. We aimed to assess fecal microbiota and fecal short chain fatty acids (SCFA) in PBC according to fibrosis. In a cross-sectional study of 23 PBC patients, fecal microbiota and SCFAs were determined using 16S rRNA sequencing and nuclear magnetic resonance spectroscopy, respectively. Fecal acetate and SCFAs were higher in advanced fibrosis. Advanced fibrosis microbiota exhibited decreased alpha diversity, increased Weisella, and a distinct community composition. SCFAs correlated with individual taxa in non-advanced fibrosis. Fecal microbiota and SCFAs correspond with fibrosis in PBC.
A decade of improved glycemic control in young children with type 1 diabetes: A population‐based cohort study

Early‐onset type 1 diabetes (T1D) is associated with high risk of early cardiovascular complications and premature death. The strongest modifiable risk factor is HbA1c. Other modifiable factors, such as overweight, also increase the risk of complications. During the last decade, the introduction of continuous glucose monitoring (CGM) has offered new options in the treatment of T1D.
A novel decoding method for motor imagery tasks with 4D data representation and 3D convolutional neural networks

Objective. Motor imagery electroencephalography (MI-EEG) produces one of the most commonly used biosignals in intelligent rehabilitation systems. The newly developed 3D convolutional neural network (3DCNN) is gaining increasing attention for its ability to recognize MI tasks. The key to successful identification of movement intention is dependent on whether the data representation can faithfully reflect the cortical activity induced by MI. However, the present data representation, which is often generated from partial source signals with time-frequency analysis, contains incomplete information. Therefore, it would be beneficial to explore a new type of data representation using raw spatiotemporal dipole information as well as the possible development of a matching 3DCNN. Approach. Based on EEG source imaging and 3DCNN, a novel decoding method for identifying MI tasks is proposed, called ESICNND. MI-EEG is mapped to the cerebral cortex by the standardized low resolution electromagnetic tomography algorithm, and the optimal sampling points of the dipoles are selected as the time of interest to best reveal the difference between any two MI tasks. Then, the initial subject coordinate system is converted to a magnetic resonance imaging coordinate system, followed by dipole interpolation and volume down-sampling; the resulting 3D dipole amplitude matrices are merged at the selected sampling points to obtain 4D dipole feature matrices (4DDFMs). These matrices are augmented by sliding window technology and input into a 3DCNN with a cascading architecture of three modules (3M3DCNN) to perform the extraction and classification of comprehensive features. Main results. Experiments are carried out on two public datasets; the average ten-fold CV classification accuracies reach 88.73% and 96.25%, respectively, and the statistical analysis demonstrates outstanding consistency and stability. Significance. The 4DDFMs reveals the variation of cortical activation in a 3D spatial cube with a temporal dimension and matches the 3M3DCNN well, making full use of the high-resolution spatiotemporal information from all dipoles.
Trends in antipsychotic prescribing among long‐term care residents receiving hospice care

The Centers for Medicare & Medicaid Services' (CMS) National Partnership to Improve Dementia Care in Nursing Homes (“CMS National Partnership”) focuses on reducing antipsychotic prescribing to long‐term care residents. Hospice enrollment is not an exclusionary condition for the antipsychotic quality measure reported by CMS. It is unclear how prescribing in hospice may have been impacted by the initiative.
Updated Meta-analysis of Minimally Invasive Versus Open Surgery for Pancreatic Neuroendocrine Neoplasms

Supplemental digital content is available in the text. Objectives The aim of this study was to compare the short-term and long-term outcomes of minimally invasive surgery (MIS) with those of open pancreas surgery (OPS) for the treatment of pancreatic neuroendocrine neoplasms (pNENs). Methods Studies reporting the effects of MIS and OPS for pNENs, published on PubMed, Embase, and Cochrane Library before May 2020 were reviewed. Results Seventeen cohort studies with a total of 1853 patients were eligible for analysis, including 655 patients in the MIS group and 1198 patients in the OPS group. The estimated blood loss, postoperative hospitalization time, overall complications, severe complications, spleen preservation, mortality, and recurrence in the MIS group were lower than those in the OPS group. The R0 rate, 3-year overall survival (OS), and 5-year OS in the MIS group were higher than those in the OPS group. There were no significant differences in operative time, postoperative pancreatic fistula, clinical postoperative pancreatic fistula, postoperative bleeding, reoperation, readmission, and 1-year OS. Conclusions Minimally invasive surgery can reach lower recurrence rate, higher long-term survival rate, and better outcomes in terms of estimated blood loss, postoperative hospitalization time, R0 rate, mortality, overall complications, and severe complications for pNENs. More high quality studies need to be conducted for further verification.
COVID-19 and chronic kidney disease: a comprehensive review

Abstract Kidney impairment in hospitalized patients with SARS-CoV-2 infection is associated with increased in-hospital mortality and worse clinical evolution, raising concerns towards patients with chronic kidney disease (CKD). From a pathophysiological perspective, COVID-19 is characterized by an overproduction of inflammatory cytokines (IL-6, TNF-alpha), causing systemic inflammation and hypercoagulability, and multiple organ dysfunction syndrome. Emerging data postulate that CKD under conservative treatment or renal replacement therapy (RRT) is an important risk factor for disease severity and higher in-hospital mortality amongst patients with COVID-19. Regarding RAAS blockers therapy during the pandemic, the initial assumption of a potential increase and deleterious impact in infectivity, disease severity, and mortality was not evidenced in medical literature. Moreover, the challenge of implementing social distancing in patients requiring dialysis during the pandemic prompted national and international societies to publish recommendations regarding the adoption of safety measures to reduce transmission risk and optimize dialysis treatment during the COVID-19 pandemic. Current data convey that kidney transplant recipients are more vulnerable to more severe infection. Thus, we provide a comprehensive review of the clinical outcomes and prognosis of patients with CKD under conservative treatment and dialysis, and kidney transplant recipients and COVID-19 infection.
An ultra‐high affinity protein–protein interface displaying sequence‐robustness

Protein–protein interactions are crucial in biology and play roles in for example, the immune system, signaling pathways, and enzyme regulation. Ultra‐high affinity interactions (Kd <0.1 nM) occur in these systems, however, structures and energetics behind stability of ultra‐high affinity protein–protein complexes are not well understood. Regulation of the starch debranching barley limit dextrinase (LD) and its endogenous cereal type inhibitor (LDI) exemplifies an ultra‐high affinity complex (Kd of 42 pM). In this study the LD–LDI complex is investigated to unveil how robust the ultra‐high affinity is to LDI sequence variation at the protein–protein interface and whether alternative sequences can retain the ultra‐high binding affinity. The interface of LD–LDI was engineered using computational protein redesign aiming at identifying LDI variants predicted to retain ultra‐high binding affinity. These variants present a very diverse set of mutations going beyond conservative and alanine substitutions typically used to probe interfaces. Surface plasmon resonance analysis of the LDI variants revealed that high affinity of LD–LDI requires interactions of several residues at the rim of the protein interface, unlike the classical hotspot arrangement where key residues are found at the center of the interface. Notably, substitution of interface residues in LDI, including amino acids with functional groups different from the wild‐type, could occur without loss of affinity. This demonstrates that ultra‐high binding affinity can be conferred without hotspot residues, thus making complexes more robust to mutational drift in evolution. The present mutational analysis also demonstrates how energetic coupling can emerge between residues at large distances at the interface.
Genomic Risk Score for Melanoma in a Prospective Study of Older Individuals.

BACKGROUND Recent genome-wide association meta-analysis for melanoma doubled the number of previously identified variants. We assessed the performance of an updated polygenic risk score (PRS) in a population of older individuals, where melanoma incidence and cumulative ultraviolet radiation exposure is greatest. METHODS We assessed a PRS for cutaneous melanoma comprising 55 variants in a prospective study of 12,712 individuals in the ASPirin in Reducing Events in the Elderly trial. We evaluated incident melanomas diagnosed during the trial and prevalent melanomas diagnosed pre-enrolment (self-reported). Multivariable models examined associations between PRS as a continuous variable (per standard deviation [SD]), and categorical (low-risk [0-20%], medium-risk [21-80%], high-risk [81-100%] groups) with incident melanoma. Logistic regression examined the association between PRS and prevalent melanoma. RESULTS At baseline, mean participant age was 75 years; 55.0% were female, and 528 (4.2%) had prevalent melanomas. During follow-up (median = 4.7 years), 120 (1.0%) incident cutaneous melanomas occurred, 98 of which were in participants with no history. PRS was associated with incident melanoma (hazard ratio = 1.46 per SD, 95% confidence interval [CI] = 1.20-1.77) and prevalent melanoma (odds ratio [OR]=1.55 per SD, 95% CI = 1.42-1.69). Participants in the highest-risk PRS group had increased risk compared to the low-risk group for incident (OR = 2.51, 95% CI = 1.28-4.92) and prevalent (OR = 3.66, 95% CI = 2.69-5.05). When stratifying by sex, only males had an association between the PRS and incident melanoma, whereas both sexes had an association between the PRS and prevalent melanoma. CONCLUSION A genomic risk score is associated with melanoma risk in older individuals, and may contribute to targeted surveillance.
The Diagnostic Value of an X‐ray‐based Scoring System for Degeneration of the Cervical Spine: A Reproducibility and Validation Study

In interventional pain medicine, cervical facet joint (CFJ) pain is commonly treated with CFJ denervation techniques, almost automatically assuming degeneration of the CFJs as an important cause of CFJ pain. A standard cervical X‐ray is still commonly used in the clinical evaluation of patients suspected for CFJ degeneration. Although degenerative features can be visualized by different radiological imaging techniques, the relation between radiological degenerative features of the cervical spine and pain remains controversial. Paramount in order to estimate the clinical usefulness of a radiological imaging is to establish the reproducibility of the radiological scoring system. A reproducible and clinically feasible diagnostic scoring system was developed to estimate cervical degeneration on standard cervical X‐rays.
A Blood Glucose Detecting System Based on Three Wavelengths

A system based on three-wavelength in near-infrared range was designed to detect the blood glucose concentration.The system is composed of a light source,a chopper,a detector and a lock-in amplifier.1 200 nm,1 350 nm,1 610 nm were chosen in this system.The detector contained ring source and round photodiode.And the distance of source-detector was 3～5 mm which is derived by theoretic analysis.The result indicated that the ratio of absorption difference D depended on the glucose level linearly,and the relative coefficient was 0.972. When using partial least square(PLS) to predict,the root mean square error of prediction (RMSEP) was 17.08 mg/dL and the relative coefficient was 0.997.
The first-principles study of electronic structures, magnetic and optical properties for Ce-doped ZnO

ABSTRACT Electronic structures, magnetic and optical properties of Ce-doped zinc-blende ZnO are studied by the first-principles of local spin density approximation based on the density function theory (DFT). Band structures, total density of states (TDOS), partial density of states (PDOS), ferromagnetic (FM), antiferromagnetic (AFM) and optical properties of Ce-doped ZnO are examined. The results show that the Fermi level move up to the conduction band and Ce-doped zinc-blende ZnO exhibits metallic, the band-gap become wider, and their conductivity are significantly improved in comparison to undoped system. All of these materials are direct transition semiconductor and shown metallic property. The conduction band and density of states have an obvious change. The Ce 4f orbital move into the conduction band, thus the bottom of conduction bands move to the low energy and show magnetism. The magnetic moments mainly arise from the Ce 4f orbitals. The absorption edge shift to the blue orientation and its intensity descend, which suggest the Ce-doped ZnO can be applied in magnetic system and photo-electronic sensor.
Phylogeography and systematics of Algyroides (Sauria: Lacertidae) of the Balkan Peninsula

The area of the south‐western Balkans hosts a remarkably high species richness and has been considered a biodiversity hotspot. The significance of the Balkan Peninsula as a biodiversity refugium during the Quaternary climatic fluctuations has been repeatedly pointed out in literature, yet the area remains quite understudied in terms of phylogeography. Contributing to the biogeography and phylogeography of the Balkan area, we herein present the phylogeographic relationships within the lizards of the genus Algyroides, focusing on the two species that occur in the Balkans (namely, A. nigropunctatus and A. moreoticus), including representatives of Dinarolacerta and Lacerta lizards as outgroups. We combined phylogenetic, phylogeographic and species distribution modelling analyses, using both mitochondrial and nuclear DNA data, in order to uncover the phylogeographic history of the genus and evaluate the validity of the extant taxonomy. Our results reveal three major clades within Algyroides in southern Balkans; one corresponds to A. moreoticus, having sister group relationships with the genus Dinarolacerta, and the other two to A. nigropunctatus, each corresponding to one of the morphological subspecies, which seem to be monophyletic, allopatric and reproductively isolated. These results expose an unprecedented phylogeographic pattern in the area of western Greece where the two major clades of A. nigropunctatus meet, and can contribute to a taxonomic re‐evaluation of the species. Moreover, questions are raised on the validity of Dinarolacerta as a genus due to it clustering within the genus Algyroides.
An improved primary culture and freezing and recovery method of human retina pigment epithelium

Objective To establish the method of a simple,effective and optimized primary culture,freezing and recovery to human retina pigment epithelium(RPE) was established.By using this method,RPE was identified.This study yielded a large amount of RPE to investigate RPE function and treat related with ocular diseases.Methods RPE was isolated by twice digestions of 0.25% pancreatin and 0.02% EDTA,respectively.Following digestion,the obtained cells were passaged by 0.125% pancreatin.Finally,RPE was identified by detecting the expressions of keratin and S100 using immunohistoc-hemical method.The harvested RPE was freezed in-80 ℃ freezer.The cellular activity was assessed following recovery.Results RPE showed vigorous growth when cultured in vitro,and cell attachment appeared 1 h later.During early culture stage,the cells were round and the cellular walls were filled with black pigment.After passage,the cells became transparent with round or irregular shapes.The strong positive expressions of keratin and S100 protein were detected.Together with these findings,the results verified that the harvested cells were RPE with a purity of 100%. Even though RPE were pre-freezed,these cells still grew vigorously following recovery.No significant difference was noted regarding cellular morphology before and after recovery.Conclusion After twice digestions of trypsin,a large amount of RPE can be isolated,ensuring the successful establishment of RPE culture in vitro.The freezing method of RPE in-80 ℃ freezer is a simple and low-cost option.Moreover,there is no significant difference in cellular morphology before and after recovery.Therefore,it is a preferred storage way for RPE.
Emerging patterns in phylogenetic studies of trichomycterid catfishes (Teleostei, Siluriformes) and the contribution of Andean diversity

Consensus is emerging among studies using DNA sequence data addressing problems in the taxonomy and relationships of trichomycterid catfishes, a dominant component of the Neotropical freshwater ichthyofauna, that have heretofore eluded efforts based on morphological data alone. No previous studies using molecular data have included representatives of Hatcheria and Silvinichthys, and none have included dense representation of the diverse Andean species of Trichomycterus. This study assembled both available and novel comparative DNA sequence data inclusive of Hatcheria, Silvinichthys, and additional Trichomycterus species not represented in previous studies to form the most taxonomically comprehensive molecular dataset of the Trichomycterinae at the genus level to date. Our results confirm previous findings of strong support for a monophyletic subfamily Trichomycterinae while rejecting the monophyly of its most diverse genus, Trichomycterus. Our results do not corroborate Trichomycterinae split into two reciprocally monophyletic groups, and we show strong support for a sister‐group relationship between Eremophilus mutisii and Trichomycterus bogotensis that suggests some degree of evolutionary distinctiveness for this clade of Colombian‐endemic species. Within Trichomycterus, we uncovered a novel clade of central Andean species and reveal a close relationship among southern Andean taxa that included a non‐monophyletic Silvinichthys, Bullockia, Hatcheria, plus a number of Trichomycterus species. Our results are broadly congruent with recent studies that have uncovered rampant polyphyly within the genus Trichomycterus and provide emerging evidence, as a result of increased taxonomic representation, for geographically circumscribed subclades of Trichomycterus species. Nevertheless, the widespread low support and resolution at most basal nodes pose a considerable challenge in understanding major patterns of intergeneric relationships, which in turn hinders our efforts to shed critical light on the biogeographic history of the group.