Miracle-dz/UniFAR-FTUs huggingface dataset:
Stochastic Variance-Reduced Cubic Regularization for Nonconvex Optimization

Cubic regularization (CR) is an optimization method with emerging popularity due to its capability to escape saddle points and converge to second-order stationary solutions for nonconvex optimization. However, CR encounters a high sample complexity issue for finite-sum problems with a large data size. %Various inexact variants of CR have been proposed to improve the sample complexity. In this paper, we propose a stochastic variance-reduced cubic-regularization (SVRC) method under random sampling, and study its convergence guarantee as well as sample complexity. We show that the iteration complexity of SVRC for achieving a second-order stationary solution within $\epsilon$ accuracy is $O(\epsilon^{-3/2})$, which matches the state-of-art result on CR types of methods. Moreover, our proposed variance reduction scheme significantly reduces the per-iteration sample complexity. The resulting total Hessian sample complexity of our SVRC is ${\Oc}(N^{2/3} \epsilon^{-3/2})$, which outperforms the state-of-art result by a factor of $O(N^{2/15})$. We also study our SVRC under random sampling without replacement scheme, which yields a lower per-iteration sample complexity, and hence justifies its practical applicability.
The efficiency of elastography in the diagnostics of follicular lesions and nodules with an unequivocal FNA result.

INTRODUCTION The aim was to assess the usefulness of strain elastography (SEG) in the diagnostics of two groups of thyroid nodules (TNs): follicular lesions (FL) with low malignancy risk (< 20.0%) and low percentage of papillary carcinomas (PTCs) among cancers as well as TNs with unequivocal cytology (UC) and high percentage of PTCs among cancers. MATERIAL AND METHODS 168 TNs were analysed and eventually surgically treated: 100 UC (50 benign and 50 malignant - 90.0% PTCs) and 68 FL (60 benign, 8 malignant - 50.0% PTCs). Elasticity score (ES) and strain ratio (SR) were evaluated, and their effectiveness was compared with the evaluation of the number of ultrasound malignancy risk features (NoUMRFs). RESULTS In the UC group the evaluation of mean values of SR and ES in both sections (meanSR, meanES) was more efficient than NoUMRFs analysis (AUC: 0.903 and 0.869 vs. 0.754, p < 0.05). The following thresholds: meanSR ≥ 2.01, meanES ≥ 2.5, NoUMRFs ≥ 2, were related to the increased malignancy risk in nodules (OR: 45.0; 23.2; 5.4, respectively), but only meanSR ≥ 2.01 was an independent risk factor (OR: 20.3; SEN: 86.0%, SPC: 88.0%). In the FL group, only the evaluation of tSR (SR assessed in transverse section) had the value of AUC > 0.7, and only the set of features: tSR ≥ 1.7 and NoUMRFs ≥ 1 increased the malignancy risk in nodules (OR: 12.0; SEN: 75.0%, SPC: 75.0%). CONCLUSIONS SEG is more reliable than conventional US in the diagnostics of TNs. The efficacy of SEG decreases with lowering percentage of PTCs among cancers. But in FL nodules SEG may support the selection of nodules for surgical treatment.
Costs of the police service and mental healthcare pathways experienced by individuals with enduring mental health needs

Background Substantial policy, communication and operational gaps exist between mental health services and the police for individuals with enduring mental health needs. Aims To map and cost pathways through mental health and police services, and to model the cost impact of implementing key policy recommendations. Method Within a case-linkage study, we estimated 1-year individual-level healthcare and policing costs. Using decision modelling, we then estimated the potential impact on costs of three recommended service enhancements: street triage, Mental Health Act assessments for all Section 136 detainees and outreach custody link workers. Results Under current care, average 1-year mental health and police costs were £10 812 and £4552 per individual respectively (n = 55). The cost per police incident was £522. Models suggested that each service enhancement would alter per incident costs by between −8% and +6%. Conclusions Recommended enhancements to care pathways only marginally increase individual-level costs.
Policies in Relational Contracts

We consider how a firm’s policies constrain its relational contracts. A policy is a sequence of decisions made by a principal; each decision determines how agents’ efforts affect their outputs. We consider surplus-maximizing policies in a flexible dynamic moral hazard problem between a principal and several agents with unrestricted vertical transfers and no commitment. If agents cannot coordinate to punish the principal following a deviation, then the principal might optimally implement dynamically inefficient, history-dependent policies to credibly reward high-performing agents. We develop conditions under which such backward-looking policies are surplus-maximizing and illustrate how they influence promotions, hiring, and performance. (JEL D21, D82, D86, M51)
Phases in pure hafnium

Hafnium (Hf) is an important material for a wide range of applications including filaments, electrodes and control rods for nuclear reactors. Based on the equilibrium phase diagram, Hf exists in the form of a hexagonal closed-packed structure at temperature below 1743 °C or a body-centred cubic structure at temperature above 1743 °C. Here, we report the coexistence at ambient temperature of a hexagonal closed-packed structure, a body-centred cubic structure and a face-centred cubic structure with well-defined crystallographic orientation relationships in pure Hf produced by the iodide decomposition method.
Feature-Based Change Detection Reveals Inconsistent Individual Differences in Visual Working Memory Capacity

Visual working memory (VWM) is a key cognitive system that enables people to hold visual information in mind after a stimulus has been removed and compare past and present to detect changes that have occurred. VWM is severely capacity limited to around 3–4 items, although there are robust individual differences in this limit. Importantly, these individual differences are evident in neural measures of VWM capacity. Here, we capitalized on recent work showing that capacity is lower for more complex stimulus dimension. In particular, we asked whether individual differences in capacity remain consistent if capacity is shifted by a more demanding task, and, further, whether the correspondence between behavioral and neural measures holds across a shift in VWM capacity. Participants completed a change detection (CD) task with simple colors and complex shapes in an fMRI experiment. As expected, capacity was significantly lower for the shape dimension. Moreover, there were robust individual differences in behavioral estimates of VWM capacity across dimensions. Similarly, participants with a stronger BOLD response for color also showed a strong neural response for shape within the lateral occipital cortex, intraparietal sulcus (IPS), and superior IPS. Although there were robust individual differences in the behavioral and neural measures, we found little evidence of systematic brain-behavior correlations across feature dimensions. This suggests that behavioral and neural measures of capacity provide different views onto the processes that underlie VWM and CD. Recent theoretical approaches that attempt to bridge between behavioral and neural measures are well positioned to address these findings in future work.
Feasibility, acceptability and clinical utility of the Cultural Formulation Interview: Mixed-methods results from the DSM-5 international field trial

Background There is a need for clinical tools to identify cultural issues in diagnostic assessment. Aims To assess the feasibility, acceptability and clinical utility of the DSM-5 Cultural Formulation Interview (CFI) in routine clinical practice. Method Mixed-methods evaluation of field trial data from six countries. The CFI was administered to diagnostically diverse psychiatric out-patients during a diagnostic interview. In post-evaluation sessions, patients and clinicians completed debriefing qualitative interviews and Likert-scale questionnaires. The duration of CFI administration and the full diagnostic session were monitored. Results Mixed-methods data from 318 patients and 75 clinicians found the CFI feasible, acceptable and useful. Clinician feasibility ratings were significantly lower than patient ratings and other clinician-assessed outcomes. After administering one CFI, however, clinician feasibility ratings improved significantly and subsequent interviews required less time. Conclusions The CFI was included in DSM-5 as a feasible, acceptable and useful cultural assessment tool.
Correlations between Tumor to Background Ratio on Breast-Specific Gamma Imaging and Prognostic Factors in Breast Cancer

The purpose of this study was to investigate the correlations between tumor-to-background ratio (TBR) obtained from breast-specific gamma imaging (BSGI) and the prognostic factors of breast cancer. Sixty-seven patients with invasive ductal carcinoma who underwent preoperative BSGI were enrolled. The BSGI images were visually scored from 1 to 5 according to a breast imaging reporting and data system (BIRADS). The TBR results obtained from positive BSGI images were compared according to the following prognostic factors: tumor size; axillary lymph node metastasis; nuclear grade (NG); histologic grade (HG); subtype; Ki-67; and the expression profile of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Among 67 images, 60 were classified as a positive finding (sensitivity 89.6%). A higher TBR value was significantly correlated with tumor size ≥ 2 cm (P = 0.001), axillary lymph node metastasis (P = 0.007), high HG (P = 0.029), negative PR status (P = 0.036), and Ki-67 ≥ 14% (P = 0.007). The TBR showed a significant difference between the luminal A and non-luminal A subtypes (P = 0.007). On multivariate analysis, TBR had a high correlation with tumor size ≥ 2 cm, axillary lymph node metastasis, and negative PR status (P = 0.003, 0.048, and 0.030, respectively). A high TBR on BSGI was significantly correlated with poor prognostic factors of breast cancer. Luminal A subtype, a breast cancer subtype with more favorable prognosis, was associated with a low TBR on BSGI.
Spontaneous and posed smile recognition based on spatial and temporal patterns of facial EMG

Facial expressions are one of the most salient cues of affect. However, they are also a communication tool that can be expressed voluntarily. Spontaneous and posed facial expressions have different characteristics. In this study, we show the potential of using Electromyography (EMG) in a wearable device to automatically differentiate between posed and spontaneous smiles. This classification is moderately successful when using spatial and magnitude features, and increases significantly if temporal features are included. Hence, the high temporal resolution of EMG-based detection is advantageous in this task.
Partial deletion of the ALK gene in ALK‐positive anaplastic large cell lymphoma

Anaplastic lymphoma kinase (ALK) protein is an orphan receptor tyrosine kinase that is constitutively activated by aberrant translocations of the ALK gene in anaplastic large cell lymphoma, ALK‐positive and several other cancers. Additionally, aberrant mutation and amplification of the ALK gene, resulting in ALK kinase activation, were detected mainly in neuroblastoma. Recently, truncated ALK protein was also reported in neuroblastoma. Here, we describe a novel truncated form of the ALK transcript with in‐frame skipping through exons 2 to 17 (ALKΔ2‐17) in anaplastic large cell lymphoma, ALK‐positive. The ALKΔ2‐17 showed ligand‐independent deregulated phosphorylation that initiated strong STAT3 signalling in NIH3T3 cells. The ALKΔ2‐17–transduced NIH3T3 cells showed oncogenic potential in a colony formation assay. Our data indicate that the aberrant deletion of the ALK gene might be oncogenic, providing a novel insight into the oncogenic role of the ALK pathway.
Variance Stabilizing Transformations for Electricity Spot Price Forecasting

Most electricity spot price series exhibit price spikes. These extreme observations may significantly impact the obtained model estimates and hence reduce efficiency of the employed predictive algorithms. For markets with only positive prices, the logarithmic transform is the single most commonly used technique to reduce spike severity and consequently stabilize the variance. However, for datasets with very close to zero (like the Spanish) or negative (like the German) prices the log-transform is not feasible. What reasonable choices do we have then? To address this issue, we evaluate 16 variance stabilizing transformations within a comprehensive forecasting study involving two model classes (regression models, neural networks) and 12 datasets from diverse power markets. We show that the probability integral transform combined with the standard Gaussian distribution yields the best approach, significantly better than many of the considered alternatives.
Translation system engineering in Escherichia coli enhances non‐canonical amino acid incorporation into proteins

The ability to site‐specifically incorporate non‐canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site‐specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p‐azido‐phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p‐azido‐phenylalanyl‐tRNA synthetase anti‐codon binding domain, (ii) evolving the elongation factor Tu amino acid‐binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi‐site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site‐specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074–1086. © 2016 Wiley Periodicals, Inc.
Endothelin‐1 modulates methacholine‐induced cutaneous vasodilatation but not sweating in young human skin

Endothelin‐1 (ET‐1) is a potent endothelial‐derived vasoconstrictor that may modulate cholinergic cutaneous vascular regulation. Endothelin receptors are also expressed on the human eccrine sweat gland, although it remains unclear whether ET‐1 modulates cholinergic sweating. We investigated whether ET‐1 attenuates cholinergic cutaneous vasodilatation and sweating through a nitric oxide synthase (NOS)‐dependent mechanism. Our findings show that ET‐1 attenuates methacholine‐induced cutaneous vasodilatation through a NOS‐independent mechanism. We also demonstrate that ET‐1 attenuates cutaneous vasodilatation in response to sodium nitroprusside, suggesting that ET‐1 diminishes the dilatation capacity of vascular smooth muscle cells. We show that ET‐1 does not modulate methacholine‐induced sweating at any of the administered concentrations. Our findings advance our knowledge pertaining to the peripheral control underpinning the regulation of cutaneous blood flow and sweating and infer that ET‐1 may attenuate the heat loss responses of cutaneous blood flow, but not sweating.
Sensor-enabled Activity Class Recognition in Preschoolers: Hip versus Wrist Data

PurposePattern recognition approaches to accelerometer data processing have emerged as viable alternatives to cut-point methods. However, few studies have explored the validity of pattern recognition approaches in preschoolers, and none have compared supervised learning algorithms trained on hip and wrist data. Purpose of this study was to develop, test, and compare activity class recognition algorithms trained on hip, wrist, and combined hip and wrist accelerometer data in preschoolers. MethodsEleven children 3–6 yr of age (mean age, 4.8 ± 0.9 yr) completed 12 developmentally appropriate physical activity (PA) trials while wearing an ActiGraph GT3X+ accelerometer on the right hip and nondominant wrist. PA trials were categorized as sedentary, light activity games, moderate-to-vigorous games, walking, and running. Random forest (RF) and support vector machine (SVM) classifiers were trained using time and frequency domain features from the vector magnitude of the raw signal. Features were extracted from 15-s nonoverlapping windows. Classifier performance was evaluated using leave-one-out cross-validation. ResultsCross-validation accuracy for the hip, wrist, and combined hip and wrist RF models was 0.80 (95% confidence interval (CI), 0.79–0.82), 0.78 (95% CI, 0.77–0.80), and 0.82 (95% CI, 0.80–0.83), respectively. Accuracy for hip, wrist, and combined hip and wrist SVM models was 0.81 (95% CI, 0.80–0.83), 0.80 (95% CI, 0.79–0.80), and 0.85 (95% CI, 0.84–0.86), respectively. Recognition accuracy was consistently excellent for sedentary (>90%); moderate for light activity games, moderate-to-vigorous games, and running (69%–79%); and modest for walking (61%–71%). ConclusionsMachine learning algorithms such as RF and SVM are useful for predicting PA class from accelerometer data collected in preschool children. Although classifiers trained on hip or wrist data provided acceptable recognition accuracy, the combination of hip and wrist accelerometer delivered better performance.
PseDNA‐Pro: DNA‐Binding Protein Identification by Combining Chou’s PseAAC and Physicochemical Distance Transformation

Identification of DNA‐binding proteins is an important problem in biomedical research as DNA‐binding proteins are crucial for various cellular processes. Currently, the machine learning methods achieve the‐state‐of‐the‐art performance with different features. A key step to improve the performance of these methods is to find a suitable representation of proteins. In this study, we proposed a feature vector composed of three kinds of sequence‐based features, including overall amino acid composition, pseudo amino acid composition (PseAAC) proposed by Chou and physicochemical distance transformation. These features not only consider the sequence composition of proteins, but also incorporate the sequence‐order information of amino acids in proteins. The feature vectors were fed into Support Vector Machine (SVM) for DNA‐binding protein identification. The proposed method is called PseDNA‐Pro. Experiments on stringent benchmark datasets and independent test datasets by using the Jackknife test showed that PseDNA‐Pro can achieve an accuracy of higher than 80 %, outperforming several state‐of‐the‐art methods, including DNAbinder, DNA‐Prot, and iDNA‐Prot. These results indicate that the combination of various features for DNA‐binding protein prediction is a suitable approach, and the sequence‐order information among residues in proteins is relative for discrimination. For practical applications, a web‐server of PseDNA‐Pro was established, which is available from http://bioinformatics.hitsz. edu.cn/PseDNA‐Pro/.
Three-Dimensional Measurement of Femoral Neck Anteversion and Neck Shaft Angle

Abstract We present a three-dimensional measurement technique for femoral neck anteversion and neck shaft angles which do not require alignment of the femoral and scanner axes. Two assessors performed the measurements on 11 patients (22 femurs). Repeatability between assessors was 2.7 degrees for femoral neck anteversion and 4.8 degrees for neck shaft angle. Measurements compared with an alternative single slice method were different by 2 degrees (3 degrees) in average. The method was repeatable and appropriate for clinical practice.
Machine-learning method for quality of transmission prediction of unestablished lightpaths

Predicting the quality of transmission (QoT) of a lightpath prior to its deployment is a step of capital importance for an optimized design of optical networks. Due to the continuous advances in optical transmission, the number of design parameters available to system engineers (e.g., modulation formats, baud rate, code rate, etc.) is growing dramatically, thus significantly increasing the alternative scenarios for lightpath deployment. As of today, existing (pre-deployment) estimation techniques for light-path QoT belong to two categories: “exact” analytical models estimating physical-layer impairments, which provide accurate results but incur heavy computational requirements, and margined formulas, which are computationally faster but typically introduce high link margins that lead to underutilization of network resources. In this paper, we explore a third option, i.e., machine learning (ML), as ML techniques have already been successfully applied for optimization and performance prediction of complex systems where analytical models are hard to derive and/ or numerical procedures impose high computational burden. We investigate a ML classifier that predicts whether the bit error rate of unestablished lightpaths meets the required system threshold based on traffic volume, desired route, and modulation format. The classifier is trained and tested on synthetic data and its performance is assessed over different network topologies and for various combinations of classification features. Results in terms of classifier accuracy are promising and motivate further investigation over real field data.
Comparison of mechanical and electrical activity and interstitial cells of Cajal in urinary bladders from wild‐type and W/Wv mice

Background and purpose: W/Wv and wild‐type murine bladders were studied to determine whether the W/Wv phenotype, which causes a reduction in, but not abolition of, tyrosine kinase activity, is a useful tool to study the function of bladder interstitial cells of Cajal (ICC).
A Multi‐Omics Analysis of Glycine max Leaves Reveals Alteration in Flavonoid and Isoflavonoid Metabolism Upon Ethylene and Abscisic Acid Treatment

Phytohormones are central to plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets, and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves. Targeting low‐abundance proteins, our previously established protamine sulfate precipitation method was applied, followed by label‐free quantification of identified proteins. A total of 4129 unique protein groups including 1083 differentially modulated in one (individual) or other (combined) treatments were discerned. Functional annotation of the identified proteins showed an increased abundance of proteins related to the flavonoid and isoflavonoid biosynthesis and MAPK signaling pathway in response to ET treatment. HPLC analysis showed an accumulation of isoflavones (genistin, daidzein, and genistein) upon ET treatment, in agreement with the proteomics results. A metabolome analysis assigned 79 metabolites and further confirmed the accumulation of flavonoids and isoflavonoids in response to ET. A potential cross‐talk between ET and MAPK signaling, leading to the accumulation of flavonoids and isoflavonoids in soybean leaves is suggested.