Miracle-dz/UniFAR-FTUs huggingface dataset:
CT perfusion imaging parameters and serum miR-106a-5p predict short- and long-term prognosis in acute cerebral infarction patients after intravenous thrombolysis

Background: Some microRNAs have been found to be abnormal in patients with acute cerebral infarction (ACI) after intravenous thrombolysis. This study aimed to measure the expression of miR-106a-5p in ACI patients before and after thrombolytic treatment, and to investigate the prognostic value of miR-106a-5p and computed tomography perfusion imaging (CTPI) parameters in ACI patients receiving thrombolysis. Methods: The levels of serum miR-106a-5p were detected by quantitative real-time PCR in 78 ACI patients before thrombolysis, 24 hours after thrombolysis, and 3 months (90 days) after onset. The correlation of miR-106a-5p with continuous variables were analyzed using Pearson correlation analysis. The association of miR-106a-5p and CTPI parameters with prognosis of patients receiving thrombolysis was evaluated by logistic regression analysis. The accuracy and thresholds of miR-106a-5p and CTPI parameters for discriminating patients with unfavorable prognosis after thrombolysis were assessed by receiver operating characteristic analysis. Results: Serum miR-106a-5p expression was decreased in ACI patient after thrombolysis. Then, significant correlations of miR-106a-5p with National Institutes of Health Stroke Scale and CTPI parameters were found. Moreover, miR-106a-5p, cerebral blood flow (CBF) and cerebral blood volume (CBV), which are 2 CTPI parameters, were independently correlated with short- and long-term prognosis after thrombolysis. Furthermore, miR-106a-5p, CBF and CBV revealed good accuracy in predicting the prognosis of patients after thrombolysis, and their combination showed the best accuracy. Conclusion: Thrombolysis downregulates miR-106a-5p in ACI patients, and miR-106a-5p, CBF and CBV have considerable potentials to predict short- and long-term prognosis in ACI patients receiving intravenous thrombolysis.
Application of Cuckoo Search Algorithms to South African Short-Term Electricity Load Forecasting

Cuckoo search is one of nature-inspired algorithms successfully used for solving different optimisation problems. Cuckoo search has proved to be very effective than other nature-inspired algorithms. In this paper, a back propagation neural networks configuration is used for South African short-term electricity load forecasting. Cuckoo search algorithm was used to overcome limitations of back propagation. Nine inputs were used to train the neural networks for each of various Cuckoo search algorithms. The first set of results confirmed that Cuckoo search algorithm whose random walk step sizes were derived from Gamma probability distribution out performed other probability based cuckoo search algorithm. It obtained mean average percentage error of 5.6% and Pareto based Cuckoo search obtained 5.8%, while the original Levy based Cuckoo search algorithm performed worse with mean average percentage error of 8.4%. The second set of results confirmed that Cuckoo search with linear decreasing switching parameter outperformed other dynamic changing switching parameter cuckoo search algorithm with mean average percentage error of 6.2% followed by cuckoo search with exponentially increasing switching parameter with mean average percentage error of 6.7%.
Brownfield land and health: A systematic review of the literature

Background Brownfield land is vacant or derelict land that was previously used for industrial or commercial purposes. Brownfield land is increasingly being targeted for housing development, however, depending on the previous use and remediation activity, it might pose potential risks to the health of residents on or in the vicinity of redeveloped sites. This systematic review of the literature synthesises the empirical evidence on the associations between brownfield land and health. Methods We systematically searched EMBASE, MEDLINE, Global Health, Web of Science, Scopus and GreenFile using a study protocol registered on PROSPERO (CRD42022286826). The search strategy combined the keywords “brownfield” and its interchangeable terms such as “previously developed land”, and any health outcomes such as “respiratory diseases” and “mortality”. Publications identified from the search were screened for eligibility by two authors, and data were extracted from the selected articles. Study quality was assessed based on the Newcastle-Ottawa Scale. Results Of the 1,987 records retrieved, 6 studies met the inclusion criteria; 3 ecological studies, 2 cross-sectional studies, and 1 longitudinal study. There was considerable heterogeneity in the exposure metrics and health outcomes assessed. All studies found significant positive associations between brownfield land proximity or density with at least one health relevant outcome, including poorer self-reported general health, increased mortality rates, increased birth defects, increased serum metal levels, and accelerated immune ageing. Conclusions Brownfield land may negatively affect the health of nearby residents. The epidemiological evidence on health effects associated with brownfield land in local communities, however, remains inconclusive and limited. Further studies are required to build the evidence base to inform future housing policies and urban planning.
Improved USER cloning for TALE assembly and its application to base editing

Transcription activator-like effectors (TALEs) have been widely used for genome editing, transcriptional regulation, and locus-specific DNA imaging. However, TALEs are difficult to handle in routine laboratories because of their complexity and the considerable time consumed in TALE construction. Here, we described a simple and rapid TALE assembly method based on uracil-specific excision reagent (USER) cloning. Polymerase chain reaction was amplified with TALE trimer templates and deoxyuridine-containing primers. The products were treated with USER at 37°C for 30 min, followed by the treatment of T4 DNA Ligase at 16°C for 30 min. The TALE trimer unit could be rejoined hierarchically to form complete TALE expression vectors with high efficiency. This method was adopted to construct TALE-deaminases, which were used in combination with Cas9 nickases to generate efficient C-to-T or A-to-G base editing while eliminating predictable DNA off-target effects. This improved USER assembly is a simple, rapid, and laboratory-friendly TALE construction technique that will be valuable for DNA targeting.
Generation and characterization of a zebrafish knockout model of abcb4, a homolog of the human multidrug efflux transporter P-glycoprotein

The ATP-binding cassette subfamily B member 1 (ABCB1), encoding a multidrug transporter referred to as P-glycoprotein (Pgp), plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy. Therefore, developing high throughput animal models to screen for Pgp function and bioavailability of substrates and inhibitors is paramount. Here, we generated and validated a zebrafish knockout line of abcb4, a human Pgp transporter homolog. CRISPR/Cas9 genome editing technology was deployed to generate a frameshift mutation in exon 4 of zebrafish abcb4. The zebrafish abcb4 homozygous mutant exhibited elevated accumulation of fluorescent rhodamine 123, a substrate of human Pgp, in the intestine and brain area of embryos. Moreover, abcb4 knockout embryos were sensitized toward toxic compounds such as doxorubicin and vinblastine compared to the WT zebrafish. Immuno-staining for zebrafish Abcb4 colocalized in the endothelial brain cells of adult zebrafish. Transcriptome profiling using Gene Set Enrichment Analysis (GSEA) uncovered that the ‘cell cycle process,’ ‘mitotic cell cycles,’ and ‘microtubule-based process’ were significantly downregulated in the abcb4 knockout brain with age. This study establishes and validates the abcb4 knockout zebrafish as an animal model to study Pgp function in vivo. Unexpectedly it reveals a potentially novel role for zebrafish abcb4 in age-related changes in the brain. The zebrafish lines generated here will provide a platform to aid in the discovery of modulators of Pgp function as well as the characterization of human mutants thereof.
Characterization of mechanical properties of battery electrode films from acoustic resonance measurements

Measurements of the mechanical properties of lithium-ion battery electrode films can be used to quantify and improve manufacturing processes and to predict the mechanical and electrochemical performance of the battery. This paper demonstrates the use of acoustic resonances to distinguish among commercial-grade battery films with different active electrode materials, thicknesses, and densities. Resonances are excited in a clamped circular area of the film using a pulsed infrared laser, and responses are measured using an electret condenser microphone. A numerical model is used to quantify the sensitivity of resonances to changes in mechanical properties. When the numerical model is compared to simple analytical models for thin plates and membranes, the battery films measured here trend more similarly to the membrane model. Resonance measurements are also used to monitor the drying process. Results from a scanning laser Doppler vibrometer verify the modes excited in the films, and a combination of experimental and simulated results is used to estimate the Young's modulus of the battery electrode coating layer.Measurements of the mechanical properties of lithium-ion battery electrode films can be used to quantify and improve manufacturing processes and to predict the mechanical and electrochemical performance of the battery. This paper demonstrates the use of acoustic resonances to distinguish among commercial-grade battery films with different active electrode materials, thicknesses, and densities. Resonances are excited in a clamped circular area of the film using a pulsed infrared laser, and responses are measured using an electret condenser microphone. A numerical model is used to quantify the sensitivity of resonances to changes in mechanical properties. When the numerical model is compared to simple analytical models for thin plates and membranes, the battery films measured here trend more similarly to the membrane model. Resonance measurements are also used to monitor the drying process. Results from a scanning laser Doppler vibrometer verify the modes excited in the films, and a combination of experimen.
Harmonic decomposition of three-particle azimuthal correlations at energies available at the BNL Relativistic Heavy Ion Collider

Author(s): Adamczyk, L; Adkins, JK; Agakishiev, G; Aggarwal, MM; Ahammed, Z; Ajitanand, NN; Alekseev, I; Anderson, DM; Aoyama, R; Aparin, A; Arkhipkin, D; Aschenauer, EC; Ashraf, MU; Attri, A; Averichev, GS; Bai, X; Bairathi, V; Behera, A; Bellwied, R; Bhasin, A; Bhati, AK; Bhattarai, P; Bielcik, J; Bielcikova, J; Bland, LC; Bordyuzhin, IG; Bouchet, J; Brandenburg, JD; Brandin, AV; Brown, D; Bunzarov, I; Butterworth, J; Caines, H; Sanchez, M Calderon de la Barca; Campbell, JM; Cebra, D; Chakaberia, I; Chaloupka, P; Chang, Z; Chankova-Bunzarova, N; Chatterjee, A; Chattopadhyay, S; Chen, X; Chen, JH; Cheng, J; Cherney, M; Christie, W; Contin, G; Crawford, HJ; Das, S; De Silva, LC; Debbe, RR; Dedovich, TG; Deng, J; Derevschikov, AA; Didenko, L; Dilks, C; Dong, X; Drachenberg, JL; Draper, JE; Dunkelberger, LE; Dunlop, JC; Efimov, LG; Elsey, N; Engelage, J; Eppley, G; Esha, R; Esumi, S; Evdokimov, O; Ewigleben, J; Eyser, O; Fatemi, R; Fazio, S; Federic, P; Federicova, P; Fedorisin, J; Feng, Z; Filip, P; Finch, E; Fisyak, Y; Flores, CE; Fulek, L; Gagliardi, CA; Garand, D; Geurts, F | Abstract: We present measurements of three-particle correlations for various harmonics in Au+Au collisions at energies ranging from $\sqrt{s_{{\rm NN}}}=7.7$ to 200 GeV using the STAR detector. The quantity $\langle\cos(m\phi_1+n\phi_2-(m+n)\phi_3)\rangle$ is evaluated as a function of $\sqrt{s_{{\rm NN}}}$, collision centrality, transverse momentum, $p_T$, pseudo-rapidity difference, $\Delta\eta$, and harmonics ($m$ and $n$). These data provide detailed information on global event properties like the three-dimensional structure of the initial overlap region, the expansion dynamics of the matter produced in the collisions, and the transport properties of the medium. A strong dependence on $\Delta\eta$ is observed for most harmonic combinations consistent with breaking of longitudinal boost invariance. Data reveal changes with energy in the two-particle correlation functions relative to the second-harmonic event-plane and provide ways to constrain models of heavy-ion collisions over a wide range of collision energies.
Pest categorisation of Setoptus parviflorae

Abstract The EFSA Plant Health Panel performed a pest categorisation of Setoptus parviflorae (Acari: Eriophyoidea: Phytoptidae) for the European Union (EU). This mite is not listed in Annex II of Commission Implementing Regulation (EU) 2019/2072. It is known to occur in the Nanjing Botanical Garden (China) on Pinus parviflora. This is its only known host plant and location. The mite occurs on the needles and in the needle sheaths. Details about its life cycle are mostly unknown. Plants for planting, including dwarfed plants, of P. parviflora are the main potential pathway for entry into the EU. However, plants of the genus Pinus other than fruit and seeds are mostly prohibited from entering the EU (Commission Implementing Regulation (EU) 2019/2072). The host, P. parviflora, can be found in temperate‐zone gardens and arboreta, and is a popular tree for bonsai in the EU. Although the Köppen–Geiger climate type Cfa (humid subtropical), which occurs in Nanjing, can be found in the EU, the growing conditions of P. parviflora at the Nanjing Botanical Garden were not reported. This adds uncertainty about where in the EU this mite could establish, most probably on ornamental P. parviflora. There is no evidence of impact of S. parviflorae. Measures to prevent entry and spread are available. S. parviflorae does not satisfy all the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest, as there is no evidence of impact.
Single-dose mucosal replicon-particle vaccine protects against lethal Nipah virus infection up to 3 days after vaccination

Nipah virus (NiV) causes a highly lethal disease in humans who present with acute respiratory or neurological signs. No vaccines against NiV have been approved to date. Here, we report on the clinical impact of a novel NiV-derived nonspreading replicon particle lacking the fusion (F) protein gene (NiVΔF) as a vaccine in three small animal models of disease. A broad antibody response was detected that included immunoglobulin G (IgG) and IgA subtypes with demonstrable Fc-mediated effector function targeting multiple viral antigens. Single-dose intranasal vaccination up to 3 days before challenge prevented clinical signs and reduced virus levels in hamsters and immunocompromised mice; decreases were seen in tissues and mucosal secretions, critically decreasing potential for virus transmission. This virus replicon particle system provides a vital tool to the field and demonstrates utility as a highly efficacious and safe vaccine candidate that can be administered parenterally or mucosally to protect against lethal Nipah disease.
Bioinformatic analysis the expression and clinical significance of CDRT15 in cholangiocarcinoma using TCGA database

Cholangiocarcinoma (CCA) is a common and lethal malignant tumor originating from bile duct epithelial cells. Various tumor biomarkers have been used for its clinical screening, such as carbohydrate antigen 19-9 and carcinoembryonic antigen. This study aimed to demonstrate the value of associated genes—CMT1A duplicated region transcript 15 (CDRT15) for prognosis of CCA by integrated bioinformatics analysis. We obtained CDRT15 expression data and clinical information on patients with CCA from The Cancer Genome Atlas database. Then, we processed the data by differentially expressed gene analysis, gene set enrichment analysis, statistical analysis, etc. Gene Ontology enrichment analysis was aimed to explore the function of gene-related proteins. Single-sample gene set enrichment analysis was used to analyze the correlation between CDRT15 and immune cells. Finally, we constructed the nomogram to predict the prognosis of patients with CCA. The analysis of data in The Cancer Genome Atlas database revealed that CDRT15 was overexpressed in CCA tissues. We performed the interrelation analysis of immune infiltration, showing that CDRT15 are mainly associated with the immune/inflammatory response. ROC curve showed that CDRT15 can be a diagnostic marker of CCA. Subsequently, the prognostic analysis showed that the high expression of CDRT15 was correlated with the poor OS, and patients with high CDRT15 expression may have a poor prognosis. CDRT15 is more highly expressed in CCA, thus we identified that CDRT15 could be an efficient biomarker for patients. CDRT15 expression was negatively correlated with prognosis of CCA. CDRT15 may be involved in the immune infiltration process of CCA.
Assessing spatiotemporal trends of total and extreme precipitation in a subtropical highland region: A climate perspective

This study used a dataset of 30 years (1990–2020) of daily observations from 24 meteorological stations in the northern highlands of Pakistan to assess trends in extreme precipitation indices. The RClimDex model was used to analyze the indices, and the Modified Mann-Kendal test and the Theil-Sen slope estimator were applied to determine trends and slopes, respectively. The results showed a significant decrease in total annual precipitation amount (PRCPTOT) with varying rates of negative trend from -4.44 mm/year to -19.63 mm/year. The total winter and monsoon precipitation amounts were also decreased during the past three decades. The intensity-based precipitation indices (RX1Day, RX5Day, R95p, R99p, and SDII) showed a significant decrease in extreme intensity events over time, while the count of consecutive dry days (CDD) and consecutive wet days (CWD) indicated a significant decrease in duration at multiple stations. The annual counts of days with precipitation more than or equal to 10 mm (R10), 20 mm (R20), and 25 mm (R25) exhibited a significant decrease in frequency of extreme precipitation events, with the decrease more pronounced in the northern parts of the study domain. The findings of this study indicate a significant decline in the intensity, frequency, and extent of precipitation extremes across the northern highlands of Pakistan over the past 30 years.
Solution and fuzzy stability of a mixed type functional equation

Abstract In this paper, we obtain the general solution and we study the generalized Hyers–Ulam stability of the mixed type additive-quadratic functional equation f(-x) + f(2x - y) + f(2y) + f(x + y) - f(-x + y) - f(x - y) - f(-x - y) = 3f(x) + 3f(y) in a fuzzy normed space.
The Role of Interface Geometry and Appendages on the Mesoscale Mechanics of the Skin

The skin is the largest organ in the human body and serves various functions, including mechanical protection and mechanosensation. Yet, even though skin’s biomechanics are attributed to two main layers - epidermis and dermis-computational models have often treated this tissue as a thin homogeneous material or, when considering multiple layers, have ignored the most prominent heterogeneities of skin seen at the mesoscale. Here we create finite element models of representative volume elements (RVEs) of skin, including the three-dimensional variation of the interface between the epidermis and dermis as well as considering the presence of hair follicles. The sinusoidal interface, which approximates the anatomical features known as Rete ridges, does not affect the homogenized mechanical response of the RVE but contributes to stress concentration, particularly at the valleys of the Rete ridges. The stress profile is three-dimensional due to the skin’s anisotropy, leading to high-stress bands connecting the valleys of the Rete ridges through one type of saddle point. The peaks of the Rete ridges and the other class of saddle points of the sinusoidal surface form a second set of low-stress bands under equi-biaxial loading. Another prominent feature of the heterogeneous stress pattern is a switch in the stress jump across the interface, which becomes lower with respect to the flat interface at increasing deformations. These features are seen in both tension and shear loading. The RVE with the hair follicle showed strains concentrating at the epidermis adjacent to the hair follicle, the epithelial tissue surrounding the hair right below the epidermis, and the bulb or base region of the hair follicle. The regions of strain concentration near the hair follicle in equi-biaxial and shear loading align with the presence of distinct mechanoreceptors in the skin, except for the bulb or base region. This study highlights the importance of skin heterogeneities, particularly its potential mechanophysiological role in the sense of touch and the prevention of skin delamination.
Characterization of the complete chloroplast genome of a chinese endangered species Cymbidium wenshanense Y. S. Wu et F. Y. Liu

Abstract Cymbidium wenshanense Y. S. Wu et F. Y. Liu is of significant ornamental and breeding value. In this study, Illumina high-throughput sequencing was used to sequence and analyze the complete chloroplast genome of C. wenshanense, and the phylogenetic relationships between this and other Orchidaceae species were established. The whole chloroplast genome was 156,292 bp in length and contained 84 mRNA genes, 45 tRNA genes, and 4 rRNA genes. The phylogenetic tree of 11 Orchidaceae species revealed C. wenshanense to be most closely related to Cymbidium mastersii.
Trend-Filtered Projection for Principal Component Analysis

Principal component analysis is one of the most widely used dimension reduction techniques. We propose an approach for performing smoothed PCA of data that is observed over a dense and equally spaced grid. The proposed approach combines ideas from recent developments in convex relaxation of PCA and l1 Trend Filtering of time series. Our method produces smooth estimates of the projection matrix of the principal subspace that are locally adaptive, and is based on a convex optimization problem that is solved by an augmented alternating direction method of multipliers (augADMM) algorithm. We describe the method and the algorithm in detail and compare the proposed method with existing methods by a numerical study. The effect of the choice of a penalty on the estimates given by the proposed method is also illustrated in a numerical study. Moreover, we present applications of the proposed method to real data and demonstrate its effectiveness.