Miracle-dz/UniFAR-FTUs huggingface dataset:
Weakly-supervised Temporal Segmentation of Cell-cycle Stages with Center-cell Focus using Recurrent Neural Networks

Training deep-learning models for biomedical images has always been a problem due to the lack of annotated data. Here we propose using a model and a training approach for the weakly-supervised temporal classification of cell-cycle stages during mitosis. Instead of using annotated data, by using an ordered set of classes called transcript, our proposed approach classifies the cell-cycle stages of cell video sequences. The network design helps to propagate information in time using Recurrent Neural Network and helps to focus the features on the center-cell. The algorithm is evaluated on four datasets from LiveCellMiner and has a performance close to the supervised approaches, which is impressive, considering that annotated data is not used in training.
Fully automated detection of dendritic spines in 3D live cell imaging data using deep convolutional neural networks

Dendritic spines are considered a morphological proxy for excitatory synapses, rendering them a target of many different lines of research. Over recent years, it has become possible to image simultaneously large numbers of dendritic spines in 3D volumes of neural tissue. In contrast, currently no automated method for spine detection exists that comes close to the detection performance reached by human experts. However, exploiting such datasets requires new tools for the fully automated detection and analysis of large numbers of spines. Here, we developed an efficient analysis pipeline to detect large numbers of dendritic spines in volumetric fluorescence imaging data. The core of our pipeline is a deep convolutional neural network, which was pretrained on a general-purpose image library, and then optimized on the spine detection task. This transfer learning approach is data efficient while achieving a high detection precision. To train and validate the model we generated a labelled dataset using five human expert annotators to account for the variability in human spine detection. The pipeline enables fully automated dendritic spine detection and reaches a near human-level detection performance. Our method for spine detection is fast, accurate and robust, and thus well suited for large-scale datasets with thousands of spines. The code is easily applicable to new datasets, achieving high detection performance, even without any retraining or adjustment of model parameters.
Protein language model embedded geometric graphs power inter-protein contact prediction

Accurate prediction of contacting residue pairs between interacting proteins is very useful for structural characterization of protein-protein interactions (PPIs). Although significant improvement has been made in inter-protein contact prediction recently, there is still large room for improving the prediction accuracy. Here we present a new deep learning method referred to as PLMGraph-Inter for inter-protein contact prediction. Specifically, we employ rotationally and translationally invariant geometric graphs obtained from structures of interacting proteins to integrate multiple protein language models, which are successively transformed by graph encoders formed by geometric vector perceptrons and residual networks formed by dimensional hybrid residual blocks to predict inter-protein contacts. Extensive evaluation on multiple test sets illustrates that PLMGraph-Inter outperforms five top inter-protein contact prediction methods, including DeepHomo, GLINTER, CDPred, DeepHomo2 and DRN-1D2D_Inter by large margins. In addition, we also show that the prediction of PLMGraph-Inter can complement the result of AlphaFold-Multimer. Finally, we show leveraging the contacts predicted by PLMGraph-Inter as constraints for protein-protein docking can dramatically improve its performance for protein complex structure prediction.
The cancer-specific lncRNA LISR customizes ribosomes to suppress anti-tumour immunity

Responses to anticancer therapies in patients with advanced metastatic disease are often lower than 50% and the majority of patients initially responding develop resistance later on. Therapy resistance often follows an adaptation phase in which cancer cells exit the cell cycle and engage the Integrated Stress Response (ISR). Activation of this pathway induces the emergence of drug-tolerant persister cells via the block of CAP-dependent translation while enhancing translation of select mRNAs that support survival, migration and dampen immunogenicity. Little is known about the molecular mechanisms underlying ISR-dependent immune escape. Searching for transcripts specifically associated with polysomes upon ISR activation we identified the lncRNA LISR. We showed that this untranslated transcript, could suppress the production of putative neoantigens, while promoting translation of PD-L1 and other mRNAs involved in the formation of the glycocalyx. Accordingly, LISR locus is amplified in 60% of melanomas and its expression is increased in patients refractory to Immune Checkpoint Blockade (ICB). Consequently, inhibition of LISR stimulated anti-tumour immune responses both in vitro and in humanized and ICB-resistant patient-derived xenografts. This study establishes a link between lncRNAs, translation rewiring in cancer and immunogenicity, and identifies an RNA-based cancer-specific therapeutic strategy to overcome intrinsic resistance to ICB.
Resting state networks of awake adolescent and adult squirrel monkeys using ultra-high field (9.4T) functional magnetic resonance imaging

Resting state networks (RSNs) are increasingly forwarded as candidate biomarkers for neuropsychiatric disorders. Such biomarkers may provide objective measures for evaluating novel therapeutic interventions in nonhuman primates often used in translational neuroimaging research. This study aimed to characterize the RSNs of awake squirrel monkeys and compare the characteristics of those networks in adolescent and adult subjects. Twenty-seven squirrel monkeys (n=12 adolescents [6 male/6 female] ∼2.5 years and n=15 adults [7 male/8 female] ∼9.5 years) were gradually acclimated to awake scanning procedures; whole-brain fMRI images were acquired with a 9.4 Tesla scanner. Group level independent component (IC) analysis (30 ICs) with dual regression was used to detect and compare RSNs. Twenty ICs corresponding to physiologically meaningful networks representing a range of neural functions, including motor, sensory, reward (e.g., basal ganglia), and cognitive processes were identified in both adolescent and adult monkeys. Significant age-related differences between the adult and adolescent subjects (adult > adolescent) were found in two networks of interest: (1) the right upper occipital region with an OFC IC and (2) the left temporal cortex, bilateral visual areas, and cerebellum with the cingulate IC. These results demonstrate that squirrel monkey RSNs are stable and consistent with RSNs previously identified in humans, rodents, and other nonhuman primate species. These data also identify several networks in adolescence that are conserved and others that may change into adulthood. Significance Statement Functional magnetic resonance imaging procedures have revealed important information about how the brain is modified by experimental manipulations, disease states, and aging throughout the lifespan. Preclinical neuroimaging, especially in nonhuman primates, has become a frequently used means to answer targeted questions related to brain resting-state functional connectivity. The present study characterized resting state networks (RSNs) in adult and adolescent squirrel monkeys; twenty RSNs corresponding to networks representing a range of neural functions were identified. The RSNs identified here can be utilized in future studies examining the effects of experimental manipulations on brain connectivity in squirrel monkeys. These data also may be useful for comparative analysis with other primate species to provide an evolutionary perspective for understanding brain function and organization.
Adaptive evolution of carnivory in Nepenthes pitcher plants: a comparative transcriptomics and proteomics perspective

While trait diversity associated with evolutionary radiations is easily recognized, their function and adaptive relevance often remain elusive. Here we study the evolution of carnivory genes in Nepenthes, an iconic radiation of carnivorous pitcher plants. We investigate 13 species chosen to represent the diversity of nutrient acquisition strategies, geography and climates covered by the genus. Using a combination of proteomics and transcriptomics, we discovered that Nepenthes secrete hundreds of enzymes and antimicrobial proteins into their digestive fluids. Further genes related to plant carnivory were uncovered by analyses of gene expression changes induced by experimental feeding of starved Nepenthes traps. Feeding status appears to affect the relative abundance of nearly 35% of all expressed genes, and may be accompanied by a strong physiological shift away from photosynthesis towards heterotrophy, proteolysis, and protein synthesis. Among the many thousand genes showing signatures of adaptive evolution in sequence or expression level within the Nepenthes radiation, the secreted pitcher fluid proteins and the carnivory-related genes were over-represented. A bias towards carnivory genes, and towards trap-expressed genes versus leaf-expressed genes, was also observed among the genes differing in expression in a young pair of sister species. Together, our results suggest that the molecular basis of the carnivorous syndrome was disproportionally targeted by positive selection during the Nepenthes radiation. This study demonstrates how the evolutionary relevance of putative key traits can be tested at the level of underlying genes.
Ex-situ mycoremediation of petroleum polluted soils in Ogoniland, Nigeria

The study investigated the mycoremediation oil-polluted soil from Ogoniland (at the B-dere/Nabem community). The mushroom, Pleurotus tuberregium was exposed to this soil as principal remediation component.While the fungus grew undisturbed, weeds were also allowed to grow from soil seed bank.Dominant weeds identified in the study include Mariscus sp, Pepperomia pellucida, Synedrella nodiflora, Cyperus sp. , and Oldenlandia corymbosa. Survival and growth of microorganisms in the polluted soils were monitored.Bacterial species identified were Escherichia coli, Micrococcus varians, Pseudomonas aeruginosa, P. vulgaris, Bacillus pumilis, Clostridum sp. , Klebsiellasp. , andAzotobacter sp. The fungi species included Mucormucedo, Aspergillus sp. , Penicillin sp. , Rhizopus sp. , Trichoderma harzianum, and Fusarium solani. The degradation of the petroleum pollutant wasmonitored through laboratory determination using the Gas Liquid Chromatographic methods. The determinations showed the gradual but steady decline in the concentration of the petroleum hydrocarbon pollutants in the Ogoni soil within the 4-month observation period. Significant reduction in heavy metal concentration of the soils was also evidenced.
Stabilization for Quantized Feedback Control Systems: An LMI Approach

This paper addresses the feedback stabilization problem for quantized feedback control systems, where sensors and controllers are connected by a digital communication channel. A dynamic, logarithmic quantization scheme is proposed. It is shown that quantized feedback control problems can be converted to robust control problems. The proof techniques rely on the LMI approach. Simulation results show the validity of the proposed quantization policy.
In reply

We thank Dr Glick and Dr Machlin for their thoughtful comments about our audit. The aim of the Stop Before You Block (SB4YB) campaign is to reduce the incidence of wrong-side block. For the SB4YB campaign to be considered a success, we believe two criteria must be met. First, it needs to be demonstrated that it is possible for institutions to achieve a very high level of compliance with a preblock ‘time out’ moment. Second, it needs to be shown that maintenance of this high level of compliance over the long term is associated with a lower incidence of wrong-side block compared with a control group. Our primary aim was to demonstrate that the first of these criteria was achievable. Prior to our study, the highest compliance rate in the published literature that we identified was 57%. Our post-intervention compliance rate of 91% is a big improvement on this, and we hope that future audits will be able to demonstrate compliance rates closer to the theoretically ideal 100%. We disagree with the suggestion that anything less than 100% is inadequate. Introduction of the World Health Organization Surgical Safety Checklist resulted in a reduction in surgical mortality and morbidity despite post-intervention compliance with all six safety indicators being only 56.7%. In the rare and concerning event of a wrong-side block occurring, significant persistent patient harm is actually unlikely to result from the block itself. The reason for taking them so seriously is that they may be suggestive of systemic problems with pre-block quality assurance processes. The rationale for persisting with the comprehensive checklist is that it mitigates risk for wrong-side blocks as well as other complications that are similarly rare and serious but preventable. Examples include blocking the wrong patient, performing a neuraxial block on a patient taking anticoagulants, giving a drug that a patient is known to be allergic to, or failing to have equipment to manage over-sedation or local anaesthetic systemic toxicity. In each of these examples there is a direct link between adherence to a point on the checklist and risk mitigation. With the exception of wrong-side block, for immediate complications that occurred during our audit there is no corresponding point on the checklist. It is therefore spurious to suggest that failure of the checklist to protect against immediate complications is somehow evidence that the checklist would also fail to protect against wrong-side blocks. Whether it is best to emphasise a single SB4YB moment, or whether it is better to persist with a broad checklist is a question that should be answered through further scientific enquiry. Given that the SB4YB campaign has so far failed to reduce the risk of wrong-side block since its inception eight years ago, we think it is reasonable to explore other options.
A Review of Artificial Intelligence and Remote Sensing for Archaeological Research

The documentation and protection of archaeological and cultural heritage (ACH) using remote sensing, a non-destructive tool, is increasingly popular for experts around the world, as it allows rapid searching and mapping at multiple scales, rapid analysis of multi-source data sets, and dynamic monitoring of ACH sites and their environments. The exploitation of remote sensing data and their products have seen an increased use in recent years in the fields of archaeological science and cultural heritage. Different spatial and spectral analysis datasets have been applied to distinguish archaeological remains and detect changes in the landscape over time, and, in the last decade, archaeologists have adopted more thoroughly automated object detection approaches for potential sites. These approaches included, among others, object detection methods, such as those of machine learning (ML) and deep learning (DL) algorithms, as well as convolutional neural networks (CNN) and deep learning (DL) models using aerial and satellite images, airborne and spaceborne remote sensing (ASRS), multispectral, hyperspectral images, and active methods (synthetic aperture radar (SAR) and light detection and ranging radar (LiDAR)). Researchers also refer to the potential for archaeologists to explore such artificial intelligence (AI) approaches in various ways, such as identifying archaeological features and classifying them. Here, we present a review study related to the contributions of remote sensing (RS) and artificial intelligence in archaeology. However, a main question remains open in the field of research: the rate of positive contribution of remote sensing and artificial intelligence techniques in archaeological research. The scope of this study is to summarize the state of the art related to AI and RS for archaeological research and provide some further insights into the existing literature.
It is Time to Bury the Spearman-Brown “Prophecy” Formula for Some Common Applications

The restrictive assumption of classical parallelism for the Spearman-Brown formulas makes them obsolete when the two-part alpha and coefficient alpha formulas can be used. The alpha coefficients require the less restrictive assumption of essential tau-equivalence. Even small reliability differences produced by the Spearman-Brown and alpha coefficient formulas on the same data can result in large applied differences.
Trailing Edge Noise Measurements Using a Large Aperture Phased Array

The primary objective of this study was to obtain measurements of the noise generated by flow over an asymmetric trailing edge in an Anechoic Wind Tunnel (AWT) using a large aperture 40 microphone acoustic array. The sound field was complicated by the presence of unwanted or “parasitic” noise caused by the operation of the AWT. The ability of the array to separate the parasitic noise from the desired sound source was determined through a series of calculations using simulated source data. The bias errors that are caused by these extraneous sources were determined for three different array post processing algorithms: delay-sum (time-domain), weighted beamforming (frequency-domain), and a Deconvolution Approach to Mapping of Acoustic Sources (DAMAS). The results indicate that each method had advantages/disadvantages that were dependent on frequency. As such, different beamforming methods were utilized over different frequency ranges in order to produce the best possible spectral representation of the trailing edge source.
Life Satisfaction and Depression in the Oldest Old: A Longitudinal Study

This study aimed to analyze the effect of individual differences and family variables on life satisfaction and depression in the oldest old compared with the young-old. A total of 1,799 cases from an 8-year period of the Korean Welfare Panel Study (2006–2013) were analyzed. A key finding was that life satisfaction significantly increased with time for the two groups of older adults while depression decreased. Moreover, family relationship satisfaction significantly affected both life satisfaction and depression in both groups. However, its impact was stronger for the oldest old. Finally, individual difference variables, that is, objective life conditions, such as gender, education, and religion, did not have a significant impact on life satisfaction or depression in the oldest old. The results suggest that the oldest old not only face death but also experience continuous growth from a gerotranscendence perspective.
Sleep Problems in Individuals With Intestinal Stomas and Determining the Quality of Sleep

PURPOSE: The aim of this study was to determine sleep problems and the sleep quality of individuals with intestinal stomas. DESIGN: Descriptive quantitative design was used. SUBJECTS AND SETTING: The research was carried out from September 2018 to September 2019 at 3 university hospitals with stoma units located in Ankara, Turkey. The study sample comprised 222 individuals with intestinal ostomies who were being monitored in these 3 centers. Approximately half (N = 113, 50.9%) had an ileostomy and 68.5% (N = 152) had a temporary stoma. More than half of the participants (N = 116, 52.3%) reported current sleep problems, 59.5% (N = 132) reported that their stoma affected their sleep, and 64% (N = 142) had problems at night due to their stomas, reporting that they woke up frequently during their main sleep period due to ostomy-related problems. METHODS: Three instruments were used to measure study outcomes: the researcher-designed instrument determining the descriptive characteristics of individuals with intestinal stomas, the Pittsburgh Sleep Quality Index, and Epworth Sleepiness Scale. RESULTS: The mean Pittsburgh Sleep Quality Index score was found to be above 5 (13.42, SD: 3.01) indicating poor sleep quality. The mean Epworth Sleepiness Scale score was 7.54 (SD: 6.37) indicating that participants had daytime sleepiness. The mean Pittsburgh Sleep Quality Index scores of participants with ileostomies (P = .002) and those with temporary stomas (P = .009) were found to be significantly higher. CONCLUSIONS: Study findings indicate that individuals with intestinal stomas have poor sleep quality and problems with daytime sleepiness; those with ileostomies and temporary stomas had the worst quality of sleep.
Comparison of novel anteroposterior short-axis in-plane technique with conventional short-axis out-of-plane technique for ultrasound-guided internal jugular vein cannulation: A randomized-controlled trial

OBJECTIVES: Various ultrasound (US)-guided probe positioning and needle procedures have been described in the literature for cannulation of the internal jugular vein (IJV). In the present study, we compared the conventional short-axis out-of-plane (SAX-OOP) method with a novel anteroposterior short-axis in-plane (APSAX-IP) technique for IJV cannulation under US guidance. The APSAX-IP method of IJV cannulation has not been compared to other IJV cannulation techniques. METHODS: A total of 104 patients above 18-year-old were randomly allocated to one of two groups - APSAX-IP or SAX-OOP and evaluated for US-guided IJV cannulation in either the operating room or critical care unit. The primary outcome of this research was the access time for IJV cannulation using both approaches. The secondary outcomes were the number of attempts of needle insertion, success rate, and complications of IJV cannulation. RESULTS: The access time for IJV cannulation was 13.0 (12.0–15.0) sec in the APSAX-IP group and 13.0 (12.0–14.0) sec in the SAX-OOP group; P = 0.947. The number of successful 1st attempts was 90.91%, and the 2nd attempts were 9.09% in the APSAX-IP group and 85.19% and 14.81% in the SAX-OOP group, respectively. Both techniques did not have any complications. CONCLUSIONS: We conclude that the US-guided APSAX-IP IJV cannulation method has comparable access time to the SAX-OOP technique.
Translation of in, on, at and over into Spanish in a Technical Context

L'auteur etudie quatre prepositions locatives anglaises (in, on, at, over} et leurs traductions espagnoles afin de decouvrir lesquelles sont les plus usitees en anglais, dans un contexte technique et scientifique: elle analyse ensuite les traductions espagnoles possibles de ces prepositions au niveau syntaxique et leur utilisation en contexte selon leur prototypicite.
The lyriform organ of the orb‐weaving spider Araneoussericatus: Vibration sensitivity is altered by bending the leg

The patella of the spider A. sericatus contains a lyriform organ which responds to vibrations applied to the tip of the leg. Single unit activity indicates that this sense organ has an elevated threshold when the leg is bent toward the cepalothorax. The leg appears to function like a mechanical attenuator in which its position determines the efficiency of stimulating the lyriform organ. This system would allow spiders to exert control over the vibrational input by merely varying the position of their legs.
The interrogation of a conventional current transformer using an in-fibre Bragg grating

An alternative approach for measuring large currents at high potentials is presented. The output signal from a conventional current transformer is measured by transducing the voltage developed across the transformer secondary into a shift in the reflected wavelength from an in-fibre Bragg grating using a piezoelectric element. A pseudo-heterodyne detection scheme was used to determine this shift. We demonstrate the scheme's performance over a current range of 700 A. The current resolution was about over a frequency range of about 50 to .