Miracle-dz/UniFAR-FTUs huggingface dataset:
An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca)

Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern Black-eared Wheatear (O. melanoleuca). This species is part of the O. hispanica-complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50: 12.6 Mb; scaffold N50: 70 Mb), with 96% of the genome assembled at chromosome level and 96% BUSCO completeness. The nuclear genome was annotated with 18’160 protein-coding genes and 30’730 mRNAs, and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern Black-eared Wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.
On BLR Size Estimates in Reverberation Models

Following the approach of Melnikov & Shevchenko (2008), we explore how the nonlinearity in the emission-line luminosity Ll of a broad-line region cloud, in its dependence on the ionizing continuum flux Fi incident on the cloud, affects estimates of the size of the broad-line region by means of cross-correlation methods. We show that the estimates obtained by straightforward cross-correlation of emission-line and continuum light curves can significantly underestimate the BLR size. We demonstrate examples of direct reverberation modelling of AGN emission-line light curves taking into account the nonlinearity of the “Ll–Fi” relation. This nonlinearity allows one to explain the differences in the time lags for different lines. Cross-correlation estimates of the BLR size turn out to be small in comparison to the estimates obtained by the direct reverberation modelling.
Resistance mechanism to Notch inhibition and combination therapy in human T-cell acute lymphoblastic leukemia

Gain-of-function mutations in NOTCH1 are among the most frequent genetic alterations in T cell acute lymphoblastic leukemia (T-ALL), making the Notch signaling pathway a promising therapeutic target for personalized medicine. Yet, a major limitation for long-term success of targeted therapy is relapse due to tumor heterogeneity or acquired resistance. Thus, we performed a genome-wide CRISPR-Cas9 screen to identify prospective resistance mechanisms to pharmacological NOTCH inhibitors and novel targeted combination therapies to efficiently combat T-ALL. Mutational loss of Phosphoinositide-3-Kinase regulatory subunit 1 (PIK3R1) causes resistance to Notch inhibition. PIK3R1 deficiency leads to increased PIK3/Akt signaling which regulates the cell cycle and spliceosome machinery, both at the transcriptional and post-translational level. Moreover, several therapeutic combinations have been identified, where simultaneous targeting of the cyclin-dependent kinases 4 and 6 (CDK4/6) and NOTCH proved to be the most efficacious in T-ALL xenotransplantation models. Key points Mutational loss of PIK3R1 induces resistance to NOTCH1 inhibition in T-ALL Pharmacological Notch inhibition synergizes with CDK4/6 inhibitors in T-ALL
Application of a Long Short-Term Memory Recurrent Neural Network to Aviation Weather Forecasting

Weather forecast is vital to aviation safety. Inaccurate forecast not only causes problems to pilots and air traffic controllers, but also leads to aviation accidents and incidents. To enhance the forecast accuracy, a deep learning recurrent neural network by long short-term memory is proposed in this work. A dataset of 10 weather features of the whole year of 2020 in Taiwan was employed in the deep learning network, 90% of the data for training and 10% for testing. The data are first standardized in preprocessing and then trained by the long short-term memory network. The results show that the feature of sea pressure, dew point, relative humidity visible mean and cloud amount are most influential for predicting temperature, compared with the features of wind speed, wind direction, sunshine rate and global solar radiation. Deleting the less influential features can achieve the lowest root mean square error (RMSE) to 2.3872, while expediting the forecast calculation. The deep learning network is shown effective to forecast the aviation weather with the mean absolute percentage error (MAPE) 10.8682%.
The Use of Membrane Filters in Measurements of Ice Nucleus Concentration. I. Effect of Sampled Air Volume

Abstract The membrane filter technique for detecting ice nuclei in atmospheric air has the disadvantage that the measured concentration decreases with the volume of air sampled. Various possible causes are investigated. The effect is found to be due to the presence of small numbers of ice nuclei on the filters prior to use, which give a spurious “background count,” and to the presence of other particles, sampled simultaneously with the ice nuclei, which prevent the latter from being detected.
Landau fluid models of collisionless magnetohydrodynamics

A closed set of fluid moment equations including models of kinetic Landau damping is developed which describes the evolution of collisionless plasmas in the magnetohydrodynamic parameter regime. The model is fully electromagnetic and describes the dynamics of both compressional and shear Alfven waves, as well as ion acoustic waves. The model allows for separate parallel and perpendicular pressures p∥ and p⊥, and, unlike previous models such as the Chew–Goldberger–Low theory, correctly predicts the instability threshold for the mirror instability. Both a simple 3+1 moment model and a more accurate 4+2 moment model are developed, and both could be useful for numerical simulations of astrophysical and fusion plasmas.
Numerical bifurcation analysis of a nonlinear stage structured cannibalism population model

We study the long-term dynamics of a two-dimensional stage structured population model for the Barents Sea cod stock with nonlinear cannibalism terms introduced by Wikan and Eide (2004). The model is represented by a two-dimensional system of difference equations for two stages of population. Following Wikan and Eide, we consider three special cases of the original model with different ranges of cannibalism pressures on the newborn, immature and the oldest part of immature. Using the map version of the software Cl_MatCont, we discuss mathematical features of the model that were not considered heretofore. This includes the continuation of curves of codimension 1 bifurcations of fixed points and normal form analysis of codim 1 and codim 2 bifurcations. In this way, we can compute the stability domains of the map and its iterates. We concentrate in particular on the third and fourth iterates of the map and their relation to the 1:3 and 1:4 resonant Neimark–Sacker (NS) points.
Comparison of total intravenous anesthesia and inhalation anesthesia on postoperative quality of recovery after laparoscopic hysterectomy: A protocol for systematic review and meta-analysis

Background: Postoperative recovery is a complex process and affected mainly by factors from patients, surgery and anesthesia. Although we have all kinds of sedatives and hypnotics now, the selection of an ideal medication for general anesthesia is still challenging. In this study, we perform a protocol for systematic review and meta-analysis to compare the effect of propofol-based total intravenous anesthesia and sevoflurane-based inhalation anesthesia on postoperative quality of recovery in patients undergoing laparoscopic hysterectomy. Methods: The protocol of this review was registered in PROSPERO (CRD42022379485). Meanwhile, it will be reported follow the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol. We will search 3 foreign electronic databases (Cochrane Library, Embase, Pubmed) and 4 Chinese electronic databases (China National Knowledge Infrastructure, WangFang Database, Chinese Biomedical Literature Database and Chinese Scientific Journal Database) to collect potential studies from their inceptions to December 2022. Only randomized controlled trials will be included. Two reviewers will independently perform study selection, data extraction and risk of bias assessment. Data synthesis and statistical analysis will be performed using the RevMan 5.4 (The Cochrane Collaboration, Copenhagen, Denmark) software. Results: The results of this systematic review and meta-analysis will be publicly available and published in a peer-reviewed journal. Conclusion: This study may provide the evidence regarding the efficacy and safety of total intravenous anesthesia and inhalation anesthesia on postoperative quality of recovery after laparoscopic hysterectomy.
Effects of preoperative nasal spray esketamine on separation anxiety and emergence agitation in pediatric strabismus surgery: A randomized clinical trial

Objective: To investigate the effects of preoperative nasal spray esketamine on separation anxiety and postoperative emergence agitation in pediatric strabismus surgery. Method: Ninety children aged 3 to 6 years who underwent elective strabismus surgery were randomly divided into 3 groups that received 0.5 mg/kg (group S1), 1 mg/kg of esketamine (group S2), and the same volume of normal saline (group C) by nasal spray 10 minutes before surgery. The observation indicators of this test include the Ramsay sedation score, separation anxiety score, mask induction score, and the incidences of postoperative emergence agitation. Patient’s heart rate, blood oxygen, post anesthesia care unit stay time, and any adverse events were recorded. Results: The Ramsay sedation score was significantly lower in group C than those in groups S1 and S2 (P < .001). The separation anxiety scores and the mask induction scores were significantly higher in group C than those in groups S1 and S2 (P < .001). The incidences of emergence agitation in groups S1 and S2 were significantly lower than that in C group (P < .001). No obvious clinical complication was observed. Conclusion: Preoperative nasal spray esketamine reduced the preoperative separation anxiety and decrease emergence agitation in pediatric strabismus surgery.
Percutaneous transforaminal endoscopic discectomy combined with acupuncture for lumbar disc herniation: A protocol for systematic review and meta-analysis

Background: Lumbar disc herniation (LDH) is a common orthopedic disease, which is one of the main causes of global chronic pain and motor function defect. For intractable LDH, the surgical treatment of percutaneous transforaminal endoscopic discectomy (PTED) is often used in clinical practice. Although the operation is relatively mature, there may still be some limitations and surgical risks delaying the recovery process of patients. Some studies have found that the combination of acupuncture therapy and PTED can bring more benefits to patients, but these conclusions are still lack of evidence support. Therefore, this study will adopt the method of meta-analysis to estimate the effectiveness and safety of acupuncture combined with PTED in patients with LDH, in order to provide a basis for clinical decision-making. Methods: This study will conduct a systematic search of the following databases: the Chinese databases China National Knowledge Infrastructure, formerly Chinese Biomedical Database, Wanfang Data, Chongqing VIP Database for Chinese Technical Periodicals, the PubMed, Medline, Embase, Web of Science and The Cochrane library, from their inception to December 1, 2022. In addition, we will search their references to avoid missing other eligible studies. The language will be limited to English and Chinese. RevMan 5.4 will be used to perform the meta-analysis. And GRADE Profiler software will be used to rate the quality of evidence. Results: The results will be submitted to a peer-reviewed journal. Conclusion: This study can provide evidence support for acupuncture combined with PTED in the treatment of LDH.
A Product Quality — Supply Chain Integration Framework

Product quality is one of the key competitive factors that will enable firms to survive and succeed in the global market place. Product quality is an important dimension of operational performance in supply chain management that has not received sufficient attention from the research community. Previous researches in this field have neglected to consider the relationship between supply chain integration and dimensions of product quality. Hence, the effect of supply chain integration on quality performance has received less attention. Therefore consideration must be given to the development of collaborative activities between manufacturer, supplier and costumer which enables firms to work together and improve product quality. Accordingly, the primary focus of this study is to investigate the relationship between dimensions of product quality and supply chain integration. The dimensions considered for product quality are design quality and conformance quality, whereas the dimensions for supply chain integration are customer integration, supplier integration, and internal integration. The relationships between these dimensions are then embodied in a framework which will be validated. This research adopts both a qualitative conceptual approach and a quantitative approach in the development of the framework. The literature is consulted in identifying the dimensions of supply chain integration and product quality. These dimensions are then modeled into a questionnaire survey, and are administered to identify manufacturing companies. Validity and reliability of the scales for the construct of interest were assessed through a factor analysis and Cronbach-alpha test. The results provide considerable support for our product quality-supply chain integration framework that can be used in the manufacturing sector.
Limb salvage surgery for calcaneal chondrosarcoma: A case report

Background: Limb salvage surgery for calcaneal sarcomas remains challenging due to its poor compartmentalization. While below-knee amputation is still the standard choice of operative treatment, total calcanectomy with or without reconstruction was advocated. This report aims to analyze the clinical outcome of calcaneal reconstruction with cement and replantation in situ after the inactivation of tumor. Methods: We describe a 73-year-old male patient who suffered chronic pain and increasingly larger neoplasm in the left foot for about 3 years. Based on the results of percutaneous biopsy, a diagnosis of chondrosarcoma was made. Results: The patient underwent total calcanectomy, inactivation of calcaneus tumor, and reconstruction with cement. The Achilles tendon was detached through a Cincinnati incision. No adverse events occurred both during and after the surgery. At the last follow-up of 29 months, the patient claimed no pain, no evident limp, or any limitation of daily activities. Image examination, weight-bearing test, and MSTS score revealed a satisfactory result. Conclusion: Calcaneal reconstruction with bone cement after total calcanectomy, inactivation of calcaneus tumor, and replantation in situ is likely to provide a feasible surgical choice and a satisfactory clinical outcome.
Modeling of structural uncertainties in Reynolds-averaged Navier-Stokes closures

Estimation of the uncertainty in numerical predictions by Reynolds-averaged Navier-Stokes closures is a vital step in building confidence in such predictions. An approach to model-form uncertainty quantification that does not assume the eddy-viscosity hypothesis to be exact is proposed. The methodology for estimation of uncertainty is demonstrated for plane channel flow, for a duct with secondary flows, and for the shock/boundary-layer interaction over a transonic bump.
Classical/quantum integrability in AdS/CFT

We discuss the AdS/CFT duality from the perspective of integrable systems and establish a direct relationship between the dimension of single trace local operators composed of two types of scalar fields in = 4 super Yang-Mills and the energy of their dual semiclassical string states in AdS5 × S5. The anomalous dimensions can be computed using a set of Bethe equations, which for ``long'' operators reduces to a Riemann-Hilbert problem. We develop a unified approach to the long wavelength Bethe equations, the classical ferromagnet and the classical string solutions in the SU(2) sector and present a general solution, governed by complex curves endowed with meromorphic differentials with integer periods. Using this solution we compute the anomalous dimensions of these long operators up to two loops and demonstrate that they agree with string-theory predictions.
High Level Information Fusion (HLIF) with nested fusion loops

Situation modeling and threat prediction require higher levels of data fusion in order to provide actionable information. Beyond the sensor data and sources the analyst has access to, the use of out-sourced and re-sourced data is becoming common. Through the years, some common frameworks have emerged for dealing with information fusion—perhaps the most ubiquitous being the JDL Data Fusion Group and their initial 4-level data fusion model. Since these initial developments, numerous models of information fusion have emerged, hoping to better capture the human-centric process of data analyses within a machine-centric framework. 21st Century Systems, Inc. has developed Fusion with Uncertainty Reasoning using Nested Assessment Characterizer Elements (FURNACE) to address challenges of high level information fusion and handle bias, ambiguity, and uncertainty (BAU) for Situation Modeling, Threat Modeling, and Threat Prediction. It combines JDL fusion levels with nested fusion loops and state-of-the-art data reasoning. Initial research has shown that FURNACE is able to reduce BAU and improve the fusion process by allowing high level information fusion (HLIF) to affect lower levels without the double counting of information or other biasing issues. The initial FURNACE project was focused on the underlying algorithms to produce a fusion system able to handle BAU and repurposed data in a cohesive manner. FURNACE supports analyst’s efforts to develop situation models, threat models, and threat predictions to increase situational awareness of the battlespace. FURNACE will not only revolutionize the military intelligence realm, but also benefit the larger homeland defense, law enforcement, and business intelligence markets.
Pitch tournament designs and other BIBDs—existence results for the case ν = 8n

A pitch tournament is a resolvable or near resolvable(ν,8,7) BIBD that satisfies certain criteria in addition to theusual condition that ν ≡ 0 or 1 (mod 8). Here we establish that for the case ν = 8n the necessary condition forpitch tournaments is sufficient for all n > 1615, with at most 187 smaller exceptions. This complements our earlier study of the ν = 8n + 1 case, where we established sufficiency for all n > 224, with at most 28 smaller exceptions. The four missing cases for (ν,8,7) BIBDs are provided, namely ν∈{48,56,96,448}, thereby establishing that the necessary existence conditions are sufficient without exception. Some constructions for resolvable designs are also provided, reducing the existence question for (ν,8,7) RBIBDs to 21 possible exceptions. © 2001 John Wiley & Sons, Inc. J Combin Designs 9: 334–356, 2001
Comparative study of internal fixation and external fixation after osteotomy of hallux valgus: A protocol for meta-analysis of comparative studies

Background: Hallux valgus (HV) is a common clinical deformity of the forefoot, primarily a deformity of the 1st metatarsophalangeal joint in which the bunion is deflected laterally relative to the 1st metatarsal, often in combination with a medial bunion or pain at the head of the 1st metatarsal. For HV bunions that do not respond to conservative treatment, surgical intervention is required, which generally involves osteotomy of the first metatarsal or the first phalanx. However, the choice of fixation method after osteotomy is controversial. Most scholars choose screws or plates for internal fixation (IF) to achieve strong and reliable fixation, while some experts do not perform IF after osteotomy, but reposition the osteotomized end and perform external fixation (EF) with a figure-of-eight bandage between the 1st and 2nd toes, which has been advocated by some scholars because it requires only local anesthesia and has the characteristics of minimally invasive and no additional material for IF, and has achieved good clinical results. Therefore, it is necessary to compare the choice of IF or EF after HV osteotomy to evaluate whether there is a difference between the 2 and to conduct a meta-analysis to provide a reliable basis for clinical guidance. Methods: We will search articles in 7 electronic databases including Chinese National Knowledge Infrastructure, Wanfang Data, Chinese Scientific Journals Database, Chinese databases SinoMed, PubMed, Embase, and Cochrane Library databases. All the publications, with no time restrictions, will be searched without any restriction of language and status, the time from the establishment of the database to October 2022. We will apply the risk-of-bias tool of the Cochrane Collaboration for randomized controlled trials to assess the methodological quality. Risk-of-Bias Assessment Tool for Non-randomized Studies was used to evaluate the quality of comparative studies. Statistical analysis will be conducted using RevMan 5.4 software. Results: This systematic review will evaluate the functional outcomes and radiographic results of internal versus EF after HV osteotomy. Conclusion: The findings of this study will provide evidence to determine whether IF or external fixation is more effective after HV osteotomy.
Missing data imputation using K-NN and LWD for software project effort prediction

The accurate of software development effort prediction plays an important role to estimate how much effort should be prepared during the works of a software project so that it can be completed on time and budget. Achieving good prediction accuracy is rely on the quality of data set. Unfortunately, missing data is one of big problem regards to the software effort data set, beside imbalance, noisy and irrelevant problem. Low quality of data set would decrease the performance of prediction model. This study aims to investigating the accuracy of software effort prediction with missing data set by using KNN missing data imputation and List Wise Deletion (LWD) techniques. It was continued by applying stepwise regression with backward elimination for feature selection and implementing two effort prediction methods of Multiple Linear Regression (MLR) and Analogy. The result shows that missing data imputation using KNN and listwise deletion with multiple linear regression approach outperforms the Analogy approach significantly (p>0.05).
Topics in Natural Language Processing Japanese Morphological Analysis

This paper discusses how traditional mainstream methods and neural-network-based methods have been applied to the task of Japanese morphological analysis in Natural Language Processing (NLP). The traditional methods, including rules, Hidden Markov Model (HMM), Conditional Random Fields (CRF), and Support Vector Machine (SVM), are mostly proposed more than 10 years ago. Based on these methods, a couple of morphological analysers are built, such as JUMAN, ChaSen, MeCab, and KyTea. Until recently, applying neural methods to Japanese morphological analysis is rarely seen. This paper introduces the various methods that have been proposed, collects information of Japanese corpora and dictionaries for NLP research, evaluates several morphological analysers on Japanese lem-matisation task, and proposes future directions based on recurrent neural networks language modelling.