Miracle-dz/UniFAR-FTUs huggingface dataset:
Generating weighted and thresholded gene coexpression networks using signed distance correlation

Even within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes or proteins, using a network of gene coexpression data that includes functional annotations. Signed distance correlation has proved useful for the construction of unweighted gene coexpression networks. However, transforming correlation values into unweighted networks may lead to a loss of important biological information related to the intensity of the correlation. Here introduce a principled method to construct weighted gene coexpression networks using signed distance correlation. These networks contain weighted edges only between those pairs of genes whose correlation value is higher than a given threshold. We analyse data from different organisms and find that networks generated with our method based on signed distance correlation are more stable and capture more biological information compared to networks obtained from Pearson correlation. Moreover, we show that signed distance correlation networks capture more biological information than unweighted networks based on the same metric. While we use biological data sets to illustrate the method, the approach is general and can be used to construct networks in other domains. Data and code availability https://github.com/javier-pardodiaz/sdcorGCN
Genetics of Carcass Composition in Irish Cattle Exploiting Carcass Video Image Analysis

In this thesis we investigated the feasibility of breeding for phenotypes predicted from video image analysis (VIA). In meat factories in Ireland, digital images are routinely taken after slaughter to derive EUROP conformation and fat grades. Two datasets (1,048 carcasses in total) on individual carcass dissections were made available for this study, one by a research center and the other by a commercial partner. Dissection data consisted of eight and six primal cuts taken in the hind- and fore-quarter, respectively, and analyses revealed significant genetic variations in these data. Heritabilities of primal cut weights ranged from 0.03 to 0.83 in the fore-quarter cuts, and from 0.14 to 0.86 in the hind-quarter cuts. Primal cut weights were subsequently grouped into four wholesale cut weights according to their retail values: lower value cuts, medium value cuts, high value cuts, and very high value cuts. Equations to predict wholesale cut weights were subsequently derived from VIA image parameters. Accuracy of prediction were >0.84 and >0.72 in the steer and heifer datasets, respectively. Genetic analysis of the wholesale cut weights predicted in a large national dataset of steers and heifers revealed heritabilities of 0.18, 0.27, 0.40, and 0.17 for lower value cuts, medium value cuts, high value cuts, and very high value cuts, respectively. Genetic correlations among predicted wholesale cut weights ranged from 0.45 to 0.89 across genders. Predicted wholesale cut weights were also strongly genetically correlated with animal price at weaning age (0.37 to 0.66), as well as price at postweaning age (0.50 to 0.67) suggesting a benefit of indirect selection especially where data on carcass cut weights were not yet available. Including predicted wholesale cut weights in a selection criteria increased genetic gain for carcass traits over and above the current selection practice of selection on EUROP conformation score. Expanding knowledge on wholesale cut weights and extending it to meat quality traits is an attractive option for Ireland.
Diagnostic Accuracy of Liquid Biopsy in Endometrial Cancer

Simple Summary The number of endometrial cancer (EC) cases is constantly growing. However, the current diagnostic approach is still rather imprecise, leaving 1/3 of patients temporarily undiagnosed. Moreover, final diagnosis is made after the surgery. That mean the histology of tumor, which influences scope of resection, is uncertain during procedure. This results in over- and undertreatment of EC patients. Those diagnostic problems might be solved by liquid biopsy—a new, minimally invasive method to obtain tumor biomarkers. Therefore, this study aimed to evaluate the usefulness of information obtained from liquid biopsy components (tumor educated platelets and circulating tumor DNA) coupled with random forest algorithm and deep neural networks to diagnose EC patients and evaluate tumor histology preoperatively. Abstract Background: Liquid biopsy is a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, the potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination. Methods: TEPs from 295 subjects (53 EC patients, 38 patients with benign gynecologic conditions, and 204 healthy women) were RNA-sequenced. DNA sequencing data were obtained for 519 primary tumor tissues and 16 plasma samples. Artificial intelligence was applied to sample classification. Results: Platelet-dedicated classifier yielded AUC of 97.5% in the test set when discriminating between healthy subjects and cancer patients. However, the discrimination between endometrial cancer and benign gynecologic conditions was more challenging, with AUC of 84.1%. ctDNA-dedicated classifier discriminated primary tumor tissue samples with AUC of 96% and ctDNA blood samples with AUC of 69.8%. Conclusions: Liquid biopsies show potential in EC diagnosis. Both TEPs and ctDNA profiles coupled with artificial intelligence constitute a source of useful information. Further work involving more cases is warranted.
Comparison of Parallel Implementation Strategies in GPU-Accelerated System-on-Chip Under Proton Irradiation

Commercial off-the-shelf (COTS) system-on-chip (SoC) are becoming widespread in embedded systems. Many of them include a multicore central processing unit (CPU) and a high-end graphics processing unit (GPU). They combine high computational performance with low power consumption and flexible multilevel parallelism. This kind of device is also being considered for radiation environments where large amounts of data must be processed or compute-intensive applications must be executed. In this article, we compare three different strategies to perform matrix multiplication in the GPU of a Tegra TK1 SoC. Our aim is to analyze how the different use of the resources of the GPU influences not only the computational performance of the algorithm, but also its radiation sensitivity. Radiation experiments with protons were performed to compare the behavior of the three strategies. Experimental results show that most of the errors force a reboot of the platform. The number of errors is directly related with how the algorithms use the internal memories of the GPU and increases with the matrix size. It is also related with the number of transactions with the global memory, which in our experiments is not affected by the radiation. Results show that the smallest cross section is obtained with the fastest algorithm, even if it uses the cores of the GPU more intensively.
The Role of Peer Victimization in Predicting Aggression and Internalizing Problems in Early Childhood: The Moderating Effect of Emotion Regulation and Gender

ABSTRACT Research Findings: This study (N = 300; M age = 44.72 months, SD = 4.39) aimed to elucidate the distinct pathways leading to maladjustment in early childhood by examining whether or not peer victimization differentially predicts aggression and internalizing problems. Hypotheses were guided by the relational vulnerability model, which suggests peer victimization and relational aggression have deleterious effects on socioemotional adjustment. This study was novel in its hypotheses that these effects will depend on form of victimization (physical/relational) and that emotion regulation and gender moderate the association. Information was collected through naturalistic observations and teacher-report, and analyzed using structural equation modeling. Results demonstrated that, across 12 months, relational victimization predicted increased anxiety symptoms, whereas relational aggression predicted decreased overall internalizing symptoms. Emotion regulation, but not gender, was concluded to be a significant moderator, where the effect of relational victimization on anxiety symptoms was significant for those with average to high emotion regulation skills. Practice & Policy: Examination of differential pathways leading to maladjustment in early childhood is critical, as early identification of risk factors, such as relational victimization, may improve developmental outcomes. Thus, this knowledge can be used by early childhood educators and providers in maximizing socioemotional adjustment across development.
Smiling By Way of Zygomatic Electrical Stimulation: Investigating the Facial Feedback Hypothesis

While it is widely accepted that affective states precede facial expressions, the facial feedback hypothesis (FFH) proposes the inverse. The FFH postulates that facial muscle region activity (e.g., smiling or frowning) directly influences the experience of emotion. The purpose of the present study was to evaluate the validity of the FFH - specifically whether smiling independently enhances positive mood.
Photoacoustic imaging of periorbital skin cancer ex vivo: unique spectral signatures of malignant melanoma, basal, and squamous cell carcinoma.

Radical excision of periorbital skin tumors is difficult without sacrificing excessive healthy tissue. Photoacoustic (PA) imaging is an emerging non-invasive biomedical imagi--ng modality that has potential for intraoperative micrographic control of surgical margins. This is the first study to assess the feasibility of PA imaging for the detection of periocular skin cancer. Eleven patients underwent surgical excision of periocular skin cancer, one of which was a malignant melanoma (MM), eight were basal cell carcinomas (BCCs), and two squamous cell carcinomas (SCCs). Six tumors were located in the eyelid, and five in periocular skin. The excised samples, as well as healthy eyelid samples, were scanned with PA imaging postoperatively, using 59 wavelengths in the range 680-970 nm, to generate 3D multispectral images. Spectral unmixing was performed using endmember spectra for oxygenated and deoxygenated Hb, melanin, and collagen, to iden--tify the chromophore composition of tumors and healthy eyelid tissue. After PA scanning, the tumor samples were examined histopathologically using standard hematoxylin and eosin staining. The PA spectra of healthy eyelid tissue were dominated by melanin in the skin, oxygenated and deoxygenated hemoglobin in the orbicularis oculi muscle, and collagen in the tarsal plate. Multiwavelength 3D scanning provided spectral information on the three tumor types. The spectrum from the MM was primarily reconstructed by the endmember melanin, while the SCCs showed contributions primarily from melanin, but also HbR and collagen. BCCs showed contributions from all four endmembers with a predominance of HbO2 and HbR. PA imaging may be used to distinguish different kinds of periocular skin tumors, paving the way for future intraoperative micrographic control.
Virtual design of medical transducers

Computer simulation has been used widely in medical ultrasonic transducer designs. One could now construct and test an transducer entirely ion a virtual basis. Such a virtual design and testing procedure not only can save us time and money, but also provide better understanding on design failures and allow us to modify designs more efficiently and economically. This paper is intended to give a brief review on virtual transducer design procedure using a few examples and also list the necessary precautions while using such advanced design tools.
Perception of genital self-image, sexual quality of life and marital adjustment in infertile women

Abstract This study was conducted to determine the perception of genital self-image, sexual quality of life and marital adjustment in infertile women. The sample of this descriptive study consisted of 135 infertile women who applied to a university hospital in a provincial center in the east of Turkey between November 2020-January 2021. Data were collected using Personal Information Form, Female Genital Self-Image Scale (FGSIS),Marital Adjustment Test (MAT) and Sexual Quality of Life Questionnaire-Female (SQoL-F). Data analysis was performed using descriptive statistics, independent-samples t-test, one-way analysis of variance(ANOVA), Kruskal-Wallis test, Tamhane’s T2 test, and Pearson’s correlation analysis. FGSIS, SQoL-F, and MAT were found at moderate levels in the women who participated in the study (17.99 ± 4.87, 65.58 ± 26.77, 37.77 ± 14.16, respectively). There was a moderate positive correlation between the total scores of FGSIS and SQoL-F, and a moderate and weak positive correlation between FGSIS and MAT and its sub-dimensions (p < 0.01). A moderate and weak positive correlation was found between SQoL-F and MAT and its sub-dimensions(p < 0.01). An increase in a positive genital self-image was associated with an increase in sexual life quality, marital adjustment, and agreement and positive relationship with the spouse. In addition, an increase in sexual quality of life was also associated with an increase in marital adjustment and agreement and positive relationship with the spouse. The vice versa could also be valid. LAY SUMMARY In this study, which was conducted to determine genital self-image, sexual quality of life and marital adjustment in infertile women, it was determined that low genital self-image negatively affected sexual life quality of life and marital adjustment. As the sexual life quality of women decreases, marital adjustment, agreement with their spouse and positive relationship style decrease.
Traffic Congestion in Rural Tourist Areas and Sustainable Mobility Services. The Case of Ticino (Switzerland) Valleys

ABSTRACT Increased traffic congestion, lower air-quality, and worsening of destination’s image perception are just some of the negative externalities affecting destinations relying on natural amenities and supplying nature-based activities. Adopting a Stated Preference experiment, this research investigates southern Switzerland natural areas’ visitors’ reaction to the hypothetical introduction of sustainable means of transport, and puts forward possible interventions to reduce the share of car users. Results show that the introduction of innovative means of transport, such as a park-and-ride integrated with a shuttle service or a bike-sharing system, might have a strong impact in reducing traffic congestion. From a sample composed by 65% of car users, results show that if innovative sustainable mobility services were introduced, market share of cars would reduce to less than 20%. Furthermore, an increase in parking cost would further decrease the use of private vehicles, in favour to alternative solutions.
Study of an ultrafine w-EDM technique

A precision ultrafine w-EDM (wire electrical discharge machining) technique specifically for machining intricate parts and structures is developed in this paper. A thumb-sized and versatile w-EDM device equipped with a complete control system for wire tension (ultrafine tungsten wire of 13 µm diameter) is designed and employed for the study of ultrafine w-EDM. The tension of the wire electrode is controlled by magnetic repulsive force to steady the wire during machining. Ultrafine wire cutting can be conducted in vertical-, horizontal- or slantwise-wire arrangements. Via some experiments, optimal machining conditions including discharge capacitance, feed rate, wire tension and the appropriate design for the w-EDM device are obtained. Two miniature samples including a micro of Taipei's landmark 101 building and a micro relay are fabricated and the feasibility of the proposed approach is verified. It is confirmed that the ultrafine w-EDM technique using an ultrafine tungsten wire of 13 µm was realized successfully.
Financial experts on the top management team: Do they reduce investment inefficiency?

We examine the effect of Top Management Team (TMT) professional finance experience on firm investment efficiency. Top managers with a career background in finance help reduce deviations of investment from the level warranted by firm fundamentals. Reductions in investment inefficiencies are achieved by financial expert managers using project-specific, rather than company-wide, discount rates for project evaluation and facilitating debt and equity issuance at lower costs. Greater investment efficiency due to financial expertise of TMT improves firm performance. We demonstrate that these improvements are driven by the collective expertise of the TMT, rather than solely by chief executive officers.
Array signal processing

Array signal processing (ASP) represents a class of antenna system where the output from an array is subjected to various forms of signal processing (e.g. phase and amplitude control, time delay or frequency translation) in order to produce outputs which can simultaneously provide angular information relating to several different directions. A different aspect of ASP which has received considerable attention over the last few years is adaptive arrays and null steering antennas. Here, instead of defining a number of wanted directions for receiving signals we can specify some wanted and some unwanted directions; the latter may contain high-level interfering signals which must be minimised by means of directional nulls in the patterns. In some cases the directions of these nulls may be fixed or pre-programmed, but in many cases the antenna response must be adaptive. This means that the shape of the directional pattern is determined in response to the angular distribution of received signals in order to try to meet some desirable criterion. The simplest form of adaptive and null steering antenna is probably the sidelobe canceller. This can steer a single directional null within the sidelobe region of a normal directional pattern. Multiple null adaptive arrays in general define a 'wanted direction' and then introduce one or more feedback controls to minimise the signals from all other directions. Null steering systems have applications in radar, sonar and communication systems. In the latter case, there may be additional complications if it is not possible to specify the direction of the wanted signals.
A portable X-pinch design for x-ray diagnostics of warm dense matter

We describe the design and x-ray emission properties (temporal, spatial, and spectral) of Dry Pinch I, a portable X-pinch driver developed at Imperial College London. Dry Pinch I is a direct capacitor discharge device, 300 3 300 3 700 mm 3 in size and ∼ 50 kg in mass, that can be used as an external driver for x-ray diagnostics in high-energy-density physics experiments. Among key ﬁ ndings, the device is shown to reliably produce 1.1 ± 0.3 ns long x-ray bursts that couple ∼ 50 mJ of energy into photon energies from 1 to 10 keV. The average shot-to-shot jitter of these bursts is found to be 10 ± 4.6 ns using a combination of x-ray and current diagnostics. The spatial extent of the x-ray hot spot from which the radiation emanates agrees with previously published results for X-pinches — suggesting a spot size of 10 ± 6 μ m in the soft energy region (1 – 10 keV) and 190 ± 100 μ m in the hard energy region ( > 10 keV). These characteristics mean that Dry Pinch I is ideally suited for use as a probe in experiments driven in the laboratory or at external facilities when more conventional sources of probing radiation are not available. At the same time, this is also the ﬁ rst detailed investigation of an X-pinch operating reliably at current rise rates of less than 1 kA/ns.
Regional and sectorial impacts of the Covid‐19 crisis: Evidence from electronic payments

Abstract We use novel and comprehensive monthly data on electronic payments, by municipality and sector, together with cash withdrawals, to study the impact of Covid‐19 in Portugal. Our difference‐in‐differences event study identifies a causal decrease of 17 and 40 percentage points on the year‐on‐year growth rate of overall purchases in March and April 2020. We document a stronger impact of the crisis in more central and more urban municipalities, due to a combination of the sectorial composition effect of the local economy and the sharper confinement behavioral effect in these locations. We discuss the importance of tourism for the results.
Experience and lessons learnt from running high availability databases on network attached storage

The Database and Engineering Services Group of CERN's Information Technology Department supplies the Oracle Central Database services used in many activities at CERN. In order to provide High Availability and ease management for those services, a NAS (Network Attached Storage) based infrastructure has been setup. It runs several instances of the Oracle RAC (Real Application Cluster) using NFS (Network File System) as shared disk space for RAC purposes and Data hosting. It is composed of two private LANs (Local Area Network), one to provide access to the NAS filers and a second to implement the Oracle RAC private interconnect, both using Network Bonding. NAS filers are configured in partnership to prevent having single points of failure and to provide automatic NAS filer fail-over.
Aspects of Melisma Synthesis

The problem of restoration of the comparatively long fragments of songs called melisma was proposed to be cast in a framework of a signal synthesis. The paper investigates several possibilities to synthesize melisma employing original, approximated and modeled parameters of melisma. Several synthesis ways are explored: employing linear prediction coding (LPC) coefficients and original glottal signal, and LPC coefficients, modeled glottal signal, gain and pitch. New method for synthesis of melisma employing fragment of original glottal signal and original LPC coefficients, gain and pitch is proposed. In order to cope with the variability of speech signals simple but effective procedure based on the cross-correlation test is proposed. Ill. 4, bibl. 12 (in English; summaries in Lithuanian, English, Russian).
LRSDSFD: low-rank sparse decomposition and symmetrical frame difference method for moving video foreground-background separation

In scenes with dynamic background or measurement noise, the low-rank sparse decomposition background modeling algorithm based on kernel norm constraint is easy to separate the moving background or noise as part of the foreground and the foreground at the same time, and it has poor modeling performance for complex background. In order to solve this problem, this paper proposes a low-rank sparse decomposition and symmetrical frame difference method for moving video foreground-background separation. Firstly, low-rank sparse decomposition is used to constrain the background matrix. Secondly, the moving objects in the region of interest (ROI) are extracted by symmetrical frame difference method, and the background image is obtained by block background modeling. Numerical experiments show that compared with other five main algorithms, the proposed algorithm can separate moving objects more accurately in the scene with dynamic background.
Motion planning of the trident snake robot equipped with passive or active wheels

Abstract. We study the kinematics of the trident snake robot equipped with either active joints and passive wheels or passive joints and active wheels. A control system representation of the kinematics is derived, and control singularities examined. Two motion planning problems are addressed, corresponding to diverse ways of controlling the robot, and solved by means of the endogenous configuration space approach. The constraints imposed by the presence of control singularities are handled using the imbalanced Jacobian algorithm assisted by an auxiliary feedback. Performance of the motion planning algorithms is demonstrated by computer simulations.