Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Learning-Inferred Multiplex ImmunoFluorescence for IHC Image Quantification

Reporting biomarkers assessed by routine immunohistochemical (IHC) staining of tissue is broadly used in diagnostic pathology laboratories for patient care. To date, clinical reporting is predominantly qualitative or semi-quantitative. By creating a multitask deep learning framework referred to as DeepLIIF, we present a single-step solution to stain deconvolution/separation, cell segmentation, and quantitative single-cell IHC scoring. Leveraging a unique de novo dataset of co-registered IHC and multiplex immunofluorescence (mpIF) staining of the same slides, we segment and translate low-cost and prevalent IHC slides to more expensive-yet-informative mpIF images, while simultaneously providing the essential ground truth for the superimposed brightfield IHC channels. Moreover, a new nuclear-envelop stain, LAP2beta, with high (>95%) cell coverage is introduced to improve cell delineation/segmentation and protein expression quantification on IHC slides. By simultaneously translating input IHC images to clean/separated mpIF channels and performing cell segmentation/classification, we show that our model trained on clean IHC Ki67 data can generalize to more noisy and artifact-ridden images as well as other nuclear and non-nuclear markers such as CD3, CD8, BCL2, BCL6, MYC, MUM1, CD10, and TP53. We thoroughly evaluate our method on publicly available benchmark datasets as well as against pathologists’ semi-quantitative scoring. The code, the pre-trained models, along with easy-to-run containerized docker files as well as Google CoLab project are available at https://github.com/nadeemlab/deepliif.
Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data

Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. ABSTRACT The kingdom Fungi is highly diverse in morphology and ecosystem function. Yet fungi are challenging to characterize as they can be difficult to culture and morphologically indistinct. Overall, their description and analysis lag far behind other microbes such as bacteria. Classification of species via high-throughput sequencing is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. With the rapid development of sequencing technologies, however, standardized procedures for taxonomic assignment of long sequence reads have not yet been well established. Focusing on nanopore sequencing technology, we compared classification and community composition analysis pipelines using shotgun and amplicon sequencing data generated from mock communities comprising 43 fungal species. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungal-specific database. During the assessment of classification algorithms, we found that applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. We also generated draft genome assemblies for three fungal species from nanopore data which were absent from genome databases. Our study improves sequence-based classification and estimation of relative sequence abundance using real fungal community data and provides a practical guide for the design of metagenomics analyses focusing on fungi. IMPORTANCE Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. Although great progress has been made on bacterial community compositions, microbial eukaryotes such as fungi clearly lag behind. Our study provides a detailed breakdown of strategies to improve species identification with immediate relevance to real-world studies. We find that real-life data sets do not always behave as expected, distinct from reports based on simulated data sets.
The Transactional Analysis Review Survey: An Investigation Into Self-Reported Practices and Philosophies of Psychotherapists

Abstract Since the creation of transactional analysis (TA) in the 1950s, almost 50,000 handbooks, theoretical articles, and personal perspectives have been published about it. However, the application of TA has not been systematically studied. The research described in this article involved an online survey titled the Transactional Analysis Review Survey (TARS), which consisted of ten open and 45 closed questions. Items were derived from the most frequently cited TA publications and focused on the psychotherapist’s perspective on metalevel reflection, a central clinical phenomenon, etiology of psychological problems, therapeutic mechanisms, and therapist competencies. Data were analyzed with thematic analysis, principal component analysis, and latent class analysis. The survey was filled out by 238 TA therapists, and most reported seeing TA as a therapeutic approach, a general attitude and view of the world, and their preferred model in their practice. According to their reports, TA focused on the client’s ego states and transactions, social functioning, and self-efficacy, which helped improve their psychological health, self-realization, and general and behavioral well-being. Clients’ most frequently reported problems were seen as caused by negative messages early in life (scripts), lack of development of mature coping mechanisms, transgenerational messages, life events, denial of existential givens, and genetics/temperament. Individuals were understood to have some choice in accepting or rejecting the negative impact of these messages and life events via behavior, emotions, and cognitive styles. TA was viewed as helping clients via the therapeutic work with their ego states, social functioning, and self-efficacy. The changes were facilitated by the therapist competencies of positive client-practitioner relationship, working at experiential depth in the here and now, etiological analysis, and providing treatment structure. Thus, TA seems to offer a coherent conceptual framework for psychotherapeutic practice. Further empirical validation of this framework is required.
A conserved Guided Entry of Tail-anchored pathway is involved in the trafficking of tail-anchored membrane proteins in Plasmodium falciparum

Tail-anchored (TA) proteins are defined by the absence of N-terminus signal sequence and the presence of a single transmembrane domain (TMD) proximal to their extreme C-terminus. They play fundamental roles in cellular processes including vesicular trafficking, protein translocation and quality control. Accordingly, TA proteins are post-translationally integrated by the Guided Entry of TA (GET) pathway to the cellular membranes; with their N-terminus oriented towards the cytosol and C-terminus facing the organellar lumen. The TA repertoire and the GET machinery have been extensively characterized in the yeast and mammalian systems, however, they remain elusive in the human malaria parasite Plasmodium falciparum. In this study, we bioinformatically predicted a total of 63 TA proteins in the P. falciparum proteome and revealed the association of their subset with the P. falciparum homolog of Get3 (PfGet3). In addition, our proximity labelling studies either definitively identified or shortlisted the other eligible GET constituents, and our in vitro association studies validated associations between PfGet3 and the corresponding homologs of Get4 and Get2 in P. falciparum. Collectively, this study reveals the presence of proteins with hallmark TA signatures and the involvement of evolutionary conserved GET trafficking pathway for their targeted delivery within the parasite. Synopsis Tail-anchored (TA) proteins, characterized by an absence of N-terminal signal sequence and the presence of a transmembrane domain near the C-terminus, are post-translationally inserted at organellar membranes by the conserved multi-component Guided Entry of TA (GET) pathway. Here, we identified the putative homologs of GET machinery in the human malaria parasite Plasmodium falciparum and revealed their association with a subset of bioinformatically predicted 63 putative TA proteins, thereby validating the functional existence of this trafficking pathway within the apicomplexan parasite. Graphical Abstract
Development of an open source program to identify the size of objects using bright-field microscopy - an automated calibration tool

In light microscopy, eyepiece graticules are commonly used to gauge the size of objects at the micron scale. While this is a relatively simple tool to use, not all microscopes possess this feature. Furthermore, calibrating an eyepiece graticule with a stage micrometer can be time-consuming, particularly for inexperienced microscopists. Similarly, calculating the size of individual objects may also take some time. We present an open-source program to determine the size of objects under a microscope using Python and OpenCV. Taking photos of a stage micrometer under a microscope, we identify gradations on the micrometer and calculate the distance between lines on the micrometer in pixels. From this, we can infer the size of objects from bright-field microscopy images. We believe this will improve access to quantitative microscopy techniques and increase the speed at which samples may be analyzed by light microscopy. Future studies may aim to integrate this with machine learning for object identification.
The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Zoonotic avian influenza A viruses pose a constant threat to global health, and they have the potential to cause pandemics. Species variations in host factor ANP32A play a key role in supporting the activity of avian influenza A virus RNA polymerases in mammalian hosts. ABSTRACT Influenza A viruses are negative-sense RNA viruses that rely on their own viral replication machinery to replicate and transcribe their segmented single-stranded RNA genome. The viral ribonucleoprotein complexes in which viral RNA is replicated consist of a nucleoprotein scaffold around which the RNA genome is wound, and a heterotrimeric RNA-dependent RNA polymerase that catalyzes viral replication. The RNA polymerase copies the viral RNA (vRNA) via a replicative intermediate, called the cRNA, and subsequently uses this cRNA to make more vRNA copies. To ensure that new cRNA and vRNA molecules are associated with ribonucleoproteins in which they can be amplified, the active RNA polymerase recruits a second polymerase to encapsidate the cRNA or vRNA. Host factor ANP32A has been shown to be essential for viral replication and to facilitate the formation of a dimer between viral RNA polymerases. Differences between mammalian and avian ANP32A proteins are sufficient to restrict viral replication. It has been proposed that ANP32A is only required for the synthesis of vRNA molecules from cRNA but not vice versa. However, this view does not match recent molecular evidence. Here we use minigenome assays, virus infections, and viral promoter mutations to demonstrate that ANP32A is essential for both vRNA and cRNA synthesis. Moreover, we show that ANP32A is not only needed for the actively replicating polymerase, but not for the polymerase that is encapsidating nascent viral RNA products. Overall, these results provide new insights into influenza A virus replication and host adaptation. IMPORTANCE Zoonotic avian influenza A viruses pose a constant threat to global health, and they have the potential to cause pandemics. Species variations in host factor ANP32A play a key role in supporting the activity of avian influenza A virus RNA polymerases in mammalian hosts. Here we show that ANP32A acts at two stages in the influenza A virus replication cycle, supporting recent structural experiments, in line with its essential role. Understanding how ANP32A supports viral RNA polymerase activity and how it supports avian polymerase function in mammalian hosts is important for understanding influenza A virus replication and the development of antiviral strategies against influenza A viruses.
Lasing peculiarities in cholesteric multilayer structure with dye-doped polymer film depending on the concentration of laser dye and pumping energy

Abstract We have experimentally investigated lasing peculiarities in a cholesteric liquid crystal – dye-doped polymer layer – cholesteric liquid crystal three-layer wedge-cell system with different laser dye concentration changing pumping energy. It was theoretically and experimentally shown that there are photonic defect modes in cholesteric photonic bandgap of the wedge-cell system. The problem was solved by Ambartsumian’s layer addition modified method. It was shown that in the mentioned above system it is possible to obtain lasing generation and it should be noted that in our case the observed lasing peculiarities are not because of the isotropic defect (planar polymer layer) but the observed features are due to the cholesterics, namely by changing the thickness of the layer of cholesterics, we are able to ensure a change in the laser wavelength, due to the pitch jumps and therefore helix pitch gradient. The advantage of our experiment is the continuous change in the thickness of the cholesteric liquid crystal layer. To prevent degradation of the molecules, decrease of the fluorescence output as well as to except convective flows for higher pumping energies the dye concentration in the polymer was chosen 10−4mol/l. We have experimentally shown the dependences of the intensity and displacement of the lasing peaks’ on the pumping power.
Modulated TRPC1 expression predicts sensitivity of breast cancer to doxorubicin and magnetic field therapy: segue towards a precision medicine approach

Background Chemotherapy is the mainstream treatment modality for invasive breast cancer. Nonetheless, chemotherapy-associated adverse events can result in a patient terminating treatment. We show that transient receptor potential channel 1 (TRPC1) expression level predicts breast cancer sensitivity to doxorubicin (DOX) and pulsed electromagnetic field (PEMF) therapies. Methods The effects of PEMFs were examined with respect to: 1) the growth of MCF-7 cells in vitro; 2) MCF-7 tumors implanted into a chicken chorioallantoic membrane (CAM) model and; 3) patient-derived and MCF-7 breast cancer xenografts in mice. Potential synergisms between DOX and PEMF therapies were examined in these model systems and under conditions of TRPC1 overexpression or silencing in vitro. Results PEMF exposure impaired the survival of MCF-7 cells, but not that of nonmalignant MCF10A breast cells. The effects of PEMF- and DOX-therapies synergized in vitro at compromising MCF-7 cell growth. Synergism could be corroborated in vivo with patient-derived xenograft mouse models, wherein PEMF exposure alone or in combination with DOX reduced tumor size. Stable overexpression of TRPC1 enhanced the vulnerability of MCF-7 cells to both DOX and PEMF exposure and promoted proliferation, whereas chronic DOX exposure reduced TRPC1 expression, induced chemoresistance, precluded response to PEMF exposure and mitigated proliferation. Markers of metastasis including SLUG, SNAIL, VIMENTIN, and E-CADHERIN as well as invasiveness were also positively correlated with TRPC1 channel expression. Conclusion The presented data supports a potential role of PEMF-therapy as an effective companion therapy to DOX-based chemotherapy for the treatment of breast cancers characterized by elevated TRPC1 expression levels.
VHF high-power tunable low-pass filter based on nested coupled helical inductor

ABSTRACT In this paper, a novel VHF high-power tunable low-pass filter based on nested coupled helical inductors is reported. By analysing the theory of nested coupled spiral inductors, a proposed VHF low-pass filter based on a set of nested coupled spiral inductors is realised, which is equivalent to a third-order low-pass filter with a transmission zero. The resulting filter offers advantages of compact structure, low insertion loss, high power and wide adjustable range. As a demonstration, a new VHF high-power tunable low-pass filter with two sets of nested coupled spiral inductors is designed and fabricated. The measured results show that the filter having a size of 30 mm×20 mm×20 mm× an insertion loss of less than 1.0 dB, a tuning range of 50% from 150 MHz to 250 MHz, with a band rejection greater than 10 dB, and that can withstand a power of at least 47 dBm.
Comparison of the rheological and the thermal behaviour of a neat asphalt binder and a wood-based binder for pavement surface layer

The decrease of crude oil availability, typically used to produce asphalt binders, is a concern among the pavement materials researchers. Binders from alternative sources have been studied as total or partial replacement of asphalt binder in asphalt mixtures more intensively in the past decade. However, the characterisation of these new materials, in order to determine how their properties affect the mixture performance, remains a challenge. This paper presents a comparison between one neat asphalt binder and a bio-binder from renewable resource (for 100% replacement of the asphalt binder), in terms of the linear viscoelastic characterisation, permanent deformation susceptibility, fatigue resistance and thermo-gravimetric characterisation. Results show that the bio-binder studied presents similar behaviour in terms of stiffness and permanent deformation susceptibility to the neat asphalt binder, that was taken as the reference for wearing course pavement layer application. Nevertheless, in terms of fatigue life, the bio-binder showed lower performance.
A Systematic Review of Psychometric Transactional Analysis Instruments

Abstract Since the founding of transactional analysis (TA) by Eric Berne in the 1950s, many psychometric instruments have been developed to operationalize TA concepts. Several studies have provided general reviews of these, but the studies are not systematic and do not assess the psychometric quality of the instruments. We conducted a systematic literature review of all psychometric instruments operationalizing TA concepts by searching in Pubmed, Medline, PsycInfo, APA articles, Web-of-Knowledge, and scholar.google. com. The study quality was evaluated with the consensus-based standards for the selection of health measurement instruments (COSMIN). Of the 12,287 initial search hits, we selected 56 instruments in 263 studies. Among those, the Schema Mode Inventory, the Tokyo Egogram, the Adjective Check List, the ANINT-A36, and the Life Position Scale were found to have fair to good overall COSMIN quality. Except for the Life Position Scale, they operationalize ego states (Parent, Adult, Child) and the functional analysis concepts of Critical Parent, Nurturing Parent, and Adapted/Free Child. The Life Position Scale operationalized the positive and negative positions toward self and others. Other questionnaires had poor to fair COSMIN quality, usually because of a lack of studies. Meta-analyses indicated that psychopathology and physical symptoms are associated with strong Critical Parent, strong Adapted Child, weak Integrated Adult, negative coping styles, and negative positions toward oneself and others. Many instruments need further validation and translation into more languages. The Schema Mode Inventory, the Tokyo Egogram, the Adjective Check List, and the Life Position Scale are the best validated questionnaires. These could be used by researchers to test treatment effectiveness and by psychotherapists to examine the problems and etiology of clients.
Fatigue damage monitoring and analysis of aged asphalt concrete using acoustic emission technique

This paper presents an Acoustic Emission characterisation of the damage behaviour of asphalt concrete subjected to bending fatigue loading. An experimental campaign is carried out on an old asphalt concrete extracted from an in-service highway pavement, built-in 2001. Tests were performed in strain-controlled mode with an amplitude of 175 µstrain, a frequency of 25 Hz, and at 10°C. Failure criteria based on modulus decrease are analysed to determine the fatigue lifespan. Acoustic emission measurements are used to investigate the damage and failure processes. A network of eight piezoelectric sensors was used to acquire the acoustic signals. Therefore, different fatigue stages are identified based on the temporal evolution of acoustic activity. Hence, the event’s spatial location is presented to show the crack path propagation. The results show that sensors located at the bottom of the sample register more acoustic activity. The locations of acoustic events were in good agreement with the mechanical background calculations.
The compact Earth system model OSCAR v2.2: description and first results

This paper provides a comprehensive description of OSCAR v2.2, a simple Earth system model. The general philosophy of development is first explained, followed by a complete description of the model's drivers and various modules. All components of the Earth system necessary to simulate future climate change are represented in the model: the oceanic and terrestrial carbon cycles – including a book-keeping module to endogenously estimate land-use change emissions – so as to simulate the change in atmospheric carbon dioxide; the tropospheric chemistry and the natural wetlands , to simulate that of methane; the stratospheric chemistry , for nitrous oxide; 37 halogenated compounds; changing tropospheric and stratospheric ozone; the direct and indirect effects of aerosols; changes in surface albedo caused by black carbon deposition on snow and land-cover change; and the global and regional response of climate – in terms of temperature and precipitation – to all these climate forcers. Following the probabilistic framework of the model, an ensemble of simulations is made over the historical period (1750–2010). We show that the model performs well in reproducing observed past changes in the Earth system such as increased atmospheric concentration of greenhouse gases or increased global mean surface temperature.
g-C3N4 Decorated TiO2 Nanotube Ordered Thin Films as Cathodic Electrodes for the Selective Reduction of Oxalic Acid

Paper Received: 21 May 2020; Revised: 23 December 2020; Accepted: 19 February 2021 Please cite this article as: De Luca F. , Passalacqua R. , Abramo F.P., Perathoner S. , Centi G. , Abate S. , 2021, G-c3n4 Decorated Tio2 Nanotube Ordered Thin Films as Cathodic Elctrodes for the Selective Reduction of Oxalic Acid, Chemical Engineering Transactions, 84, 37-42 DOI:10.3303/CET2184007 CHEMICAL ENGINEERING TRANSACTIONS
Australia's ice epidemic and the detrimental mental health effects of recent use

This work applies propensity score matching to assess the impact of methamphetamine on mental health. Using Australian microdata from the 2013 National Drug Strategy Household Survey, Kessler scores of recent and non-recent methamphetamine users are analysed after controlling for confounding variables. The results support the decision to prepare frontline emergency service workers for the psychological issues present in those consuming methamphetamine. The results also highlight the importance for policy makers to develop effective harm reduction programs. An estimate of the mental health costs associated with methamphetamine abuse is also presented, the findings of which strongly support additional government spending on harm reduction.