Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and evaluation of a deep learning based artificial intelligence for automatic identification of gold fiducial markers in an MRI-only prostate radiotherapy workflow

Identification of prostate gold fiducial markers in magnetic resonance imaging (MRI) images is challenging when CT images are not available, due to misclassifications from intra-prostatic calcifications. It is also a time consuming task and automated identification methods have been suggested as an improvement for both objectives. Multi-echo gradient echo (MEGRE) images have been utilized for manual fiducial identification with 100% detection accuracy. The aim is therefore to develop an automatic deep learning based method for fiducial identification in MRI images intended for MRI-only prostate radiotherapy. MEGRE images from 326 prostate cancer patients with fiducials were acquired on a 3T MRI, post-processed with N4 bias correction, and the fiducial center of mass (CoM) was identified. A 9 mm radius sphere was created around the CoM as ground truth. A deep learning HighRes3DNet model for semantic segmentation was trained using image augmentation. The model was applied to 39 MRI-only patients and 3D probability maps for fiducial location and segmentation were produced and spatially smoothed. In each of the three largest probability peaks, a 9 mm radius sphere was defined. Detection sensitivity and geometric accuracy was assessed. To raise awareness of potential false findings a ‘BeAware’ score was developed, calculated from the total number and quality of the probability peaks. All datasets, annotations and source code used were made publicly available. The detection sensitivity for all fiducials were 97.4%. Thirty-six out of thirty-nine patients had all fiducial markers correctly identified. All three failed patients generated a user notification using the BeAware score. The mean absolute difference between the detected fiducial and ground truth CoM was 0.7 ± 0.9 [0 3.1] mm. A deep learning method for automatic fiducial identification in MRI images was developed and evaluated with state-of-the-art results. The BeAware score has the potential to notify the user regarding patients where the proposed method is uncertain.
The Prediction of Stiffness of Bamboo-Reinforced Concrete Beams Using Experiment Data and Artificial Neural Networks (ANNs)

Stiffness is the main parameter of the beam’s resistance to deformation. Based on advanced research, the stiffness of bamboo-reinforced concrete beams (BRC) tends to be lower than the stiffness of steel-reinforced concrete beams (SRC). However, the advantage of bamboo-reinforced concrete beams has enough good ductility according to the fundamental properties of bamboo, which have high tensile strength and high elastic properties. This study aims to predict and validate the stiffness of bamboo-reinforced concrete beams from the experimental results data using artificial neural networks (ANNs). The number of beam test specimens were 25 pieces with a size of 75 mm × 150 mm × 1100 mm. The testing method uses the four-point method with simple support. The results of the analysis showed the similarity between the stiffness of the beam’s experimental results with the artificial neural network (ANN) analysis results. The similarity rate of the two analyses is around 99% and the percentage of errors is not more than 1%, both for bamboo-reinforced concrete beams (BRC) and steel-reinforced concrete beams (SRC).
A Review on Purification and Characterization of Anti-proliferative Peptides Derived from Fish Protein Hydrolysate

ABSTRACT Bioactive peptide with anti-proliferative activity is a novel prospect to develop cancer drugs with fewer or no side effects, as well as cost benefits. The current review provides a development strategy for anti-proliferative peptides derived from fish and its discards through fish protein hydrolysate. The study indicates that enzymatic hydrolysates act as a superior anti-proliferative agent through superior enzyme selection. In general, ion-exchange chromatography, RP-HPLC, ultra, and gel filtration methods are used to purify bioactive peptides. Characterization of the purified peptide can be done with the help of cytotoxicity assay, molecular mass, amino acid composition, and sequence. Most studies on anti-proliferative bioactive peptides have been carried out via in vitro analysis. However, very few studies have provided confirmatory results through in vivo analysis. Graphical Abstract
Pathohistological diagnosis of adrenal tumors: experience of a single center

1 Faculty of Medicine Osijek, Josip Juraj Strossmayer University Osijek, Croatia 2 Department of Pathology and Forensic Medicine, University Hospital Center Osijek, Croatia 3 Surgery Clinic, Department of Abdominal Surgery, University Hospital Center Osijek, Croatia 4 Department of Internal Medicine, Našice General Hospital, Našice, Croatia 5 Clinic for Internal Medicine, Department of Endocrinology, University Hospital Center Osijek, Croatia
Assessment of Short Rectangular-Tab Actuation of Supersonic Jet Mixing

This work explores the extent of jet mixing for a supersonic jet coming out of a Mach 1.8 convergent-divergent nozzle, controlled with two short rectangular vortex-generating actuators located diametrically opposite to each other with an emphasis on numerical methodology. The blockage ratio offered by the tabs is around 0.05. The numerical investigations were carried out by using a commercial computational fluid dynamics (CFD) package and all the simulations were performed by employing steady Reynolds-averaged Navier–Stokes equations and shear-stress transport k−ω turbulence model on a three-dimensional computational space for more accuracy. The numerical calculations are administered at nozzle pressure ratios (NPRs) of 4, 5, 6, 7 and 8, covering the overexpanded, the correctly expanded and the underexpanded conditions. The centerline pressure decay and the pressure profiles are plotted for both uncontrolled and the controlled jets. Numerical schlieren images are used to capture the barrel shock, the expansion fans and the Mach waves present in the flow field. Mach contours are also delineated at varying NPRs indicating the number of shock cells, their length and the variation of the shock cell structure and strength, to substantiate the prominent findings. The outcomes of this research are observed to be in sensible concurrence with the demonstrated exploratory findings. A reduction in the jet core length of 75% is attained with small vortex-generating actuators, compared to an uncontrolled jet, corresponding to nozzle pressure ratio 5. It was also seen that the controlled jet gets bifurcated downstream of the nozzle exit at a distance of about 5 D, where D is the nozzle exit diameter. Furthermore, it was fascinating to observe that the jet spread increases downstream of the nozzle exit for the controlled jet, as compared to the uncontrolled jet at any given NPR.
Activation of pro-apoptotic cells, reactive astrogliosis and hyperphosphorylation of tau protein in trimethyltin-induced hippocampal injury in rats

Neurodegenerative diseases cause neural cells to lose both the functional and sensory abilities as a result of genetic factors, proteopathies and mitochondrial dysfunction. Neurodegeneration forms the basis of most neurodegenerative disorders for example Alzheimer’s disease, Huntington’s diseases, and Parkinson’s diseases. The mechanism that underlines the process of neurodegeneration is not well understood. Understanding the process and mechanism involved in neurodegeneration might offer a better therapeutic approach to positively manage cases of neurodegenerative diseases. Therefore, this study’s target was to create an animal model to study neurodegeneration. Sixteen adult male Wistar rats were used in the study and divided into two groups. Control (0.2 mL of normal saline (NS)), and trimethyltin-treated (TMT, 8 mg/kg stat dose only). These animals underwent perfusion with 4% paraformaldehyde, brain excision and analysis of p53 antigen, GFAP and Bielshowsky on these tissues. The results showed that animals in the control group showed presence of activated p53 antigen, reactive astrogliosis, neurofibrillary tangles, and amyloid plaques within the cytoplasm of the hippocampal cells. Cornus Ammonis (CA2) and (CA3) showed more of the trimethylrtin injury than CA1 and CA4. This study thus revealed that, intra-peritoneal administration of single dose of 8mg/kg of trimethyltin can offer an attractive disease model to study some neurodegenerative diseases. Keywords: p53 antigen, Bielshowsky, Glia fibrillary acidic protein, Trimethyltin, Hippocampus,
Synthesis and crystal structure of methyl 2-(2-((tert-butoxycarbonyl)amino)phenyl)-2-(4-oxo-4H-chromen-3-yl)acetate, C23H23NO6

Abstract C23H23NO6, monoclinic, P21/n (no. 14), a = 7.5845(4) Å, b = 14.7024(5) Å, c = 18.1433(6) Å, β = 98.753(4)°, V = 1999.62(14) Å3, Z = 4, Rgt(F) = 0.0389, wRref(F2) = 0.0965, T = 293 K.
Interpretation of deep learning in genomics and epigenomics

Abstract Machine learning methods have been widely applied to big data analysis in genomics and epigenomics research. Although accuracy and efficiency are common goals in many modeling tasks, model interpretability is especially important to these studies towards understanding the underlying molecular and cellular mechanisms. Deep neural networks (DNNs) have recently gained popularity in various types of genomic and epigenomic studies due to their capabilities in utilizing large-scale high-throughput bioinformatics data and achieving high accuracy in predictions and classifications. However, DNNs are often challenged by their potential to explain the predictions due to their black-box nature. In this review, we present current development in the model interpretation of DNNs, focusing on their applications in genomics and epigenomics. We first describe state-of-the-art DNN interpretation methods in representative machine learning fields. We then summarize the DNN interpretation methods in recent studies on genomics and epigenomics, focusing on current data- and computing-intensive topics such as sequence motif identification, genetic variations, gene expression, chromatin interactions and non-coding RNAs. We also present the biological discoveries that resulted from these interpretation methods. We finally discuss the advantages and limitations of current interpretation approaches in the context of genomic and epigenomic studies. Contact:xiaoman@mail.ucf. edu, haihu@cs.ucf. edu
Modulation instability-enhanced frequency comb generation in graphene-based electro-optical modulator at terahertz frequency range

In this study, a modulation instability (MI)-enhanced optical frequency comb generation (FCG) method is proposed on the platform of graphene-dielectric heterostructure included in a Fabry–Perot microresonator. The latter can provide the enhanced nonlinearity required for initiating and proceeding the MI procedure and leads to the generation of extra sidebands within the comb spectrum. In the first step, the influence of Fermi energy/feedback depth on the FCG process is investigated, considering that the MI mechanism merely interferes in the FCG process. Then, the combination of MI mechanism and electro-optical modulation is assumed as a hybrid method to explore the effects of modulation depth and modulation frequency. It is shown that a tooth spacing of about 0.49 GHz can be obtained while the linewidth is almost 0.8 MHz as the best result. Other important features are the adjustable tooth spacing due to the tuneable Fermi energy of graphene with a very low bias voltage (less than 1 V), low turn-on power of 11 µW and the amplification of optical power more than 95 dB which is in consequence of the MI-induced amplifying scheme. On this basis, the graphene-based electro-optical modulator working in the MI regime can be suggested for applications in atomic clocks and molecular fingerprinting for which precise measurements are needed using a terahertz frequency comb.
Operating leverage and the cost of debt in European agri-food firms

Aim of study: To analyse the effect that operating leverage exerts on the cost of debt of agri-food firms in Europe, both in isolation and indirectly through its other risk factors.Area of study: We used panel data made up of 18,360 European firms from 2009 to 2016 (146,880 observations). Material and methods: The data were extracted from the ORBIS database and EUROSTAT. The econometric approach was estimated by the Generalized Method of Moments.Main results: The results obtained confirm that operating leverage or cost structure, in addition to affecting the cost of debt, also affects the relationship between that cost and other sources of risk. More specifically, indebtedness, size, specificity and age all affect the cost of debt to a greater or lesser extent, depending on the level of operating leverage of the company.Research highlights: The main contribution was the study of the cost of external financing as a function of the cost structure, because this directly influences the competitiveness of companies in a key sector of the European economy. We also demonstrated the country effect, taking into account the different policies and practices regarding the assumption of risk by firms. The agri-food sector has been subject to special aid programs of research & development distributed unevenly across countries. If we add to this the national subsidy programs, the level of indebtedness is not a clear determinant of the cost of debt. The main determinant of that cost is the operating leverage.
Assessing the impact of extreme flooding on survival in a southern European population of White-throated Dippers Cinclus cinclus

ABSTRACT Capsule: There were only weak effects of winter flooding episodes on apparent annual survival of a White-throated Dipper breeding population in northern Iberia. Aims: To test whether extreme winter flooding episodes affected survival in a breeding population of White-throated Dippers Cinclus cinclus. Methods: Dippers were ringed during the breeding seasons of seven consecutive years on rivers in northern Iberia. Cormack–Jolly–Seber models were used to estimate apparent annual survival in relation to flooding during the winter periods. Results: We obtained weak evidence for an effect of flooding during the winter on the surveyed population. Two of the six winters were characterized by having an exceptionally high discharge. Our models showed that survival in the subsequent breeding period tended to be lower, although models assuming constant survival were equally well supported. Conclusion: Extreme flooding in winter may affect survival of some White-throated Dippers in northern Iberia, but its impact at the population level seems to be weak.
Understanding the impact of intellectual capital on entrepreneurship: a literature review

PurposeThe present paper aims to explore and map the development of the intellectual capital (IC)-related studies by answering the following research questions: (1) what are the theoretical pillars on which prior literature focusing on the IC–entrepreneurship relationship has grown and expanded? ; (2) what are the main research areas covered by past literature focused on the IC–entrepreneurship relationship? ; (3) which areas of research should be explored in the future? Design/methodology/approachThe study relied on the co-citation analysis and bibliographic coupling techniques to investigate a complete data set of IC–entrepreneurship publications.FindingsFindings indicated that scholars' attention had increased, starting from the beginning of the 2000s due to the widespread recognition of the importance of knowledge for firms' competitive advantage. Results of the co-citation clustering analysis have identified five main theoretical building blocks of the IC–entrepreneurship literature, which addressed both the basics of IC foundations and more specific aspects related to IC (family firms and the measurement of IC). Results of the bibliographic coupling analysis indicated that future studies should consider the existence of interactions and synergies among the different components of IC. Furthermore, attention should be devoted to the management practices of IC.Originality/valueThe present study represents the contributions offered by IC to studies about entrepreneurship strategies. Building on findings emerging from a qualitative content analysis on clustered prior publications, the authors discuss a research agenda that is expected to inspire future studies to continue the exploration of the crucial characteristics of IC in contributing to entrepreneurial and managerial studies.
A Lithosphere‐Asthenosphere Boundary and Partial Melt Estimated Using Marine Magnetotelluric Data at the Central Middle Atlantic Ridge

The differential motion between the lithosphere and the asthenosphere is aseismic, so the magnetotelluric (MT) method plays an important role in studying the depth and nature of the lithosphere‐asthenosphere boundary (LAB). In March 2016, we deployed 39 marine MT instruments across the Middle Atlantic Ridge (MAR), 2,000 km away from the African coast, to study the evolution of the LAB with ages out to 45 million years (My). The MT acquisition time was limited to about 60 days by battery life. After analyzing dimensionality and coast effects for the MT data, determinant data were inverted for two‐dimensional resistivity models along two profiles north and south of the Chain Fracture Zone (CFZ). The imaged thickness of the lithospheric lid (>100 Ωm) ranges from 20 to 80 km, generally thickening with age. In the north of CFZ, punctuated low‐resistivity anomalies (<1 Ωm), likely associated with potential partial melts, occur along its base. In the south of CFZ, the base of the resistive lid is demarcated by a low‐resistivity channel (<1 Ωm) most likely fed by deeper melts. Sensitivity analyses and structural recovery tests indicate the robustness of these features. Resistivity models are in good agreement with results of seismic data. These results imply that partial melt is persistent over geologic timescales and that the LAB is dynamic features fed by upward percolation of mantle melt. The melt fraction is about 1–7% based on the resistivity, temperature, pressure, and hydrous basalt models, which is consistent with petrophysical observations.
What Feedback Matters? The Role of Experience in Motivating Crowdsourcing Innovation

Recent open innovation literature indicates increasing concern about the quality of crowdsourced ideas. Building on a framework of creativity capability, rooted in behavioral literature, and intrinsic (vs. extrinsic) motivation, derived from personnel economics and social psychology literature, this study predicts the influence of feedback on ideation performance. Specifically, the effectiveness of feedback on ideation performance in firm‐sponsored, non–financially incentivized, idea‐crowdsourcing communities may depend on its valence (positive vs. negative), source (peers vs. firm), and ideators’ ideation experience. Field data, obtained using text‐mining techniques from an idea‐crowdsourcing community, reveal that the effects of positive (negative) peer feedback for increasing (decreasing) subsequent idea quality strengthen (weaken) as ideators gain experience. However, the effects of positive (negative) firm feedback for increasing (decreasing) subsequent idea quality weaken with ideation experience. Experienced ideators are more motivated (less demotivated) to improve subsequent ideation performance when they receive positive peer (negative firm) feedback; inexperienced ideators are less motivated by negative peer feedback but more motivated by positive firm feedback. The results are robust to tests with alternative field data and model specifications, as validated by a controlled laboratory experiment. They also suggest feedback strategies that managers can use to boost customer ideation performance in crowdsourcing contexts.
Effect of compaction, delayed sealing and aerobic exposure on forage choice and short‐term intake of maize silage by goats

Forage choice and intake by ruminants depend on various factors. This study aimed to determine the effects of compaction, delayed sealing and aerobic exposure on forage choice and short‐term dry‐matter intake (DMI) of maize silage by goats. Whole‐crop maize (277 g/kg dry matter [DM]) in 120‐L silos was compacted at either low (194 kg DM/m³) or high (234 kg DM/m³) density, and sealed immediately at day 0 or with a delay at day 2 or day 4 post‐filling, making a total of six treatments. After ensiling for at least 175 days, silages were exposed to air for 6 days. In 2‐day intervals, silages were sampled for chemical analyses and were vacuum‐stored for use in preference trials. During the experimental phase, each possible two‐way combination of the aerobically exposed silages (days 0, 2, 4 and 6 post‐opening) of the treatments and lucerne hay was offered as free choice to goats (n = 5) for 3 hr. Exposing silages to air for >4 days post‐opening caused strong avoidance and lowest intakes. Under the conditions of the study, aerobic exposure after ensiling had a more pronounced effect on silage preference and short‐time DMI than compaction and delayed sealing. Increasing fibre fractions, a deteriorating microbial status and poor silage sensory properties, probably caused by a combination of different fermentation products, can be considered for decrease in preference.
Little-known and phylogenetically obscure South African estuarine microgastropods (Mollusca: Truncatelloidea) as living animals

ABSTRACT Areas of the Knysna estuarine bay in the Western Cape are dominated by three endemic South African truncatelloid microgastropods, temporarily known as ‘Hydrobia’ knysnaensis (Krauss), ‘Assiminea’ capensis (Sowerby) and ‘Assiminea’ globulus Connolly. Although first described 80–170 years ago and present in abundance (up to 100,000 m−2), they remain surrounded by confusion and still await taxonomic assignment, largely because they appear most atypical members of their groups by virtue of anatomy and/or biogeography and/or habitat. This study contributes in-life perspectives to morphological and phylogenetic analyses known to be on-going. At Knysna, they are syntopic: at least two occurring in >85% and all three in >40% of individual 0.0026 m2 samples from their region of dominance. Nevertheless, they tend to greater abundance in divergent microhabitats; ‘A. ’ globulus dominating higher tidal levels, and ‘A. ’ capensis and ‘Hydrobia’ lower ones; the former especially unvegetated sediment, the latter, if anything, seagrass. Interspecific feeding interactions appear unlikely to be responsible for these patterns, other evidence suggesting that all are maintained below carrying capacity. Field biology of ‘H. ’ knysnaensis generally appears equivalent to that of northern-hemisphere intertidal hydrobiids and that of ‘A. ’ globulus is typically assimineid, albeit at atypically low shore height. Unlike assimineids, however, ‘A. ’ capensis is truly aquatic. The success of these truncatelloids in unusual circumstances may be consequent on the absence from South Africa of other microgastropod groups that fill their niches elsewhere in the southern hemisphere.