Miracle-dz/UniFAR-FTUs huggingface dataset:
DeepSTL - From English Requirements to Signal Temporal Logic

Formal methods provide very powerful tools and techniques for the design and analysis of complex systems. Their practical application remains however limited, due to the widely accepted belief that formal methods require extensive expertise and a steep learning curve. Writing correct formal specifications in form of logical formulas is still considered to be a difficult and error prone task. In this paper we propose DeepSTL, a tool and technique for the translation of informal requirements, given as free English sentences, into Signal Temporal Logic (STL), a formal specification language for cyber-physical systems, used both by academia and advanced research labs in industry. A major challenge to devise such a translator is the lack of publicly available informal requirements and formal specifications. We propose a two-step workflow to address this challenge. We first design a grammar-based generation technique of synthetic data, where each output is a random STL formula and its associated set of possible English translations. In the second step, we use a state-of-the-art transformer-based neural translation technique, to train an accurate attentional translator of English to STL. The experimental results show high translation quality for patterns of English requirements that have been well trained, making this workflow promising to be extended for processing more complex translation tasks.
Group-Agent Reinforcement Learning with A Distributed Deep Solution

It can largely beneﬁt the reinforcement learning process of each agent if multiple agents perform their separate reinforcement learning tasks cooperatively. These tasks can be not exactly the same but still beneﬁt from the communication behaviour between agents due to task similarities. In fact, this learning scenario is not well understood yet and not well formulated. As the ﬁrst effort, we provide a detailed discussion of this scenario, and propose group-agent reinforcement learning as a formulation of the reinforcement learning problem under this scenario and a third type of reinforcement learning problem with respect to single-agent and multi-agent reinforcement learning. We propose that it can be solved with the help of modern deep reinforcement learning techniques and provide a distributed deep reinforcement learning algorithm called DDA3C (Decentralised Distributed Asynchronous Advantage Actor-Critic) that is the ﬁrst framework designed for group-agent reinforcement learning. We show through experiments in the CartPole-v0 game environment that DDA3C achieved desirable performance with very stable training and has good scalability.
Regularization in network optimization via trimmed stochastic gradient descent with noisy label

Regularization is essential for avoiding over-fitting to training data in network optimization, leading to better generalization of the trained networks. The label noise provides a strong implicit regularization by replacing the target ground truth labels of training examples by uniform random labels. However, it can cause undesirable misleading gradients due to the large loss associated with incorrect labels. We propose a first-order optimization method (Label-Noised Trim-SGD) that uses the label noise with the example trimming in order to remove the outliers based on the loss. The proposed algorithm is simple yet enables us to impose a large label-noise and obtain a better regularization effect than the original methods. The quantitative analysis is performed by comparing the behavior of the label noise, the example trimming, and the proposed algorithm. We also present empirical results that demonstrate the effectiveness of our algorithm using the major benchmarks and the fundamental networks, where our method has successfully outperformed the state-of-the-art optimization methods.
Clinical profile and demographic distribution of pellucid marginal corneal degeneration in India: A study of 559 patients

Purpose: The aim of this study was to describe the clinical profile and demographic distribution of pellucid marginal corneal degeneration (PMD) in patients presenting to a multitier ophthalmology hospital network in India. Methods: This cross-sectional hospital-based study included 2,470,793 new patients presenting between September 2012 and September 2020 (~8 years period). Patients with a clinical diagnosis of PMD in at least one eye were included as cases. The data were collected using an electronic medical record system. Results: Overall, 559 (0.02%) new patients were diagnosed with PMD. The prevalence rates were 0.004% in children (age <16 years) and 0.03% in adults. The majority of patients were males (70.13%) with the bilateral affliction (77.1%). The mean age of the patients was 37.91 ± 13.19 years. The majority (30.23%) of the patients were between 31 and 40 years of age. A significant number of patients were from higher socioeconomic status (93.74%) and from the urban region (45.08%). Of the 990 eyes, the most common clinical signs were ectasia/thinning (58.99%), corneal scar (17.47%), and corneal hydrops (1.01%). The majority of the eyes (87.97%) were managed with either spectacles or contact lenses. Among those who had surgical intervention, collagen cross-linking was the most performed procedure (5.25%) followed by cataract surgery (4.14%). Conclusion: PMD is a rare disease affecting patients seeking eye care in India. It commonly affects adult males and is bilateral in nature. The disease progression is slow and usually occurs beyond 3 years. Conservative management is more common than surgical intervention.
Design and realization of national water environment management information system based on ArcGIS Engine

Based on ArcGIS Engine 9.0,one of the embedded GIS(Geographic Information System) module systems,a water environment management information system for national key water quality stations has been designed and developed,which includes functions of data storage in database,information inquiry,statistical analysis and graphics visualization of long-term water quality data for more than 160 key water quality stations in the whole country.Some specialized models of water environment have been integrated in the information system,such as water quality assessment,water quality trend analysis and water quality forecasting modeling,thus enhancing the system's professional functions and practicability.The study is very important for the Water Environmental Evaluation Research Center of the Ministry of Water Resources to improve the service quality and efficiency.It would also promote the innovation of water environment management and informationization realization in the sector of water resources.
Quality of Life and Depression in Rheumatoid Arthritis Patients Treated with Biologics – A Single Centre Experience

Introduction Patients with rheumatoid arthritis (RA) often experience depression, which has a very negative impact on the assessment of the quality of life (QoL). However, there are not many studies that assess the relationship between depression and QoL in RA patients. The aim of the study was to assess the level of QoL and determine the mutual relationship between anxiety and depression levels and QoL in patients treated for RA. Material and Methods The study included 101 patients (aged:52.4±16.97), who met the established criteria for a diagnosis of RA and treatment with a biological agent. Only standardized tools were used to examine the patients: WHO-QoL, HADS and the VAS scale. Results The mean RA duration in the group studied was 13.54±9.51 years and the disease activity score was 4.8±0.8. The mean QoL perception score was 3.48± 0.8. Nearly 40% of the respondents could not clearly determine their QoL, perceiving it as neither poor nor good, and 10% believed their QoL is poor or very poor. The correlation analysis revealed that anxiety is significantly and negatively associated with QoL in the psychological domain (r = −0.472, p < 0.001) and social domain (r = −0.298, p = 0.023) and depression is significantly and negatively associated with QoL in the psychological domain (r = −0.322, p = 0.01) and physical health domain (r = −0.209, p = 0.04). In the multiple linear regression model, depression was an independent negative predictor affecting the following domains: perception of QoL and perception of health, and physical health. Conclusion RA patients treated with biologics present a low level of health perception and an average level of QoL perception. Depression and anxiety negatively correlate with QoL domains: the higher the anxiety and depression levels, the poorer the QoL in the psychological and social relationships domains. Depression is an independent determinant of decreased QoL.
HOMELETTE: a unified interface to homology modelling software

Abstract Summary Homology modelling, the technique of generating models of 3D protein structures based on experimental structures from related proteins, has become increasingly popular over the years. An abundance of different tools for model generation and model evaluation is available from various research groups. We present HOMELETTE, an interface which implements a unified programmatic access to these tools. This allows for the assemble of custom pipelines from pre- or self-implemented building blocks. Availability and implementation HOMELETTE is implemented in Python, compatible with version 3.6 and newer. It is distributed under the MIT license. Documentation and tutorials are available at Read the Docs (https://homelette.readthedocs.io/). The latest version of HOMELETTE is available on PyPI (https://pypi.org/project/homelette/) and GitHub (https://github.com/PhilippJunk/homelette). A full installation of the latest version of HOMELETTE with all dependencies is also available as a Docker container (https://hub.docker.com/r/philippjunk/homelette_template). Supplementary information Supplementary data are available at Bioinformatics online.
Drivers of and Barriers to Adherence to Neovascular Age-Related Macular Degeneration and Diabetic Macular Edema Treatment Management Plans: A Multi-National Qualitative Study

Purpose Neovascular age-related macular degeneration (nAMD) and diabetic macular edema (DME) patients treated with intravitreally injected anti-vascular endothelial growth factor (anti-VEGF) monotherapies achieve lower vision improvements compared with patients in clinical trials. This qualitative research study aimed to better understand the real-world anti-VEGF treatment experience from nAMD and DME patients’, caregivers’, and retina specialists’ perspectives. Methods One-time, semi-structured, individual interviews were conducted with adult patients with nAMD or DME treated with anti-VEGF injections for ≥12 months, their caregivers, and experienced retina specialists. Interview transcripts were analyzed qualitatively using a thematic analysis approach. Results A total of 49 nAMD and 46 DME patients, 47 nAMD and 33 DME caregivers, and 62 retina specialists were interviewed in the USA, Canada, France, Germany, Italy and Spain. Most (79%) patients and caregivers reported disruptions to their routine on the day before, the day of, or the day after anti-VEGF injection. Seven nAMD patients (14%) and 14 DME patients (30%) reported having missed an injection visit. The most frequently reported driver for adherence for patients was the doctor–patient relationship (n=66, 70%), whereas for caregivers, it was the ease of booking an appointment (n=25, 32%). Retina specialists reported patient education on the treatment (n=28, 45%) as the most important driver. Treatment barriers could be grouped into four categories: tolerability, clinical factors, logistical parameters and human factors. The most frequently reported barrier to adherence for patients and caregivers was related to side effects (pain/discomfort/irritation: n=63, 67% of patients; n=52, 66% of caregivers), whereas for retina specialists it was logistical parameters (travel logistics: n=44, 71%). Conclusion This study highlights the importance of the doctor–patient relationship and patient education as key drivers, and treatment tolerability and logistics as key barriers to treatment adherence. Improved doctor–patient relationship/communication and patient education together with new therapies offering convenience, long-acting effectiveness, and better tolerability may improve treatment adherence.
Transcriptome analysis and molecular characterization of soluble chemical communication proteins in the parasitoid wasp Anagrus nilaparvatae (Hymenoptera: Mymaridae)

Abstract Anagrus nilaparvatae is an important egg parasitoid wasp of pests such as the rice planthopper. Based on the powerful olfactory system of sensing chemical information in nature, A. nilaparvatae shows complicated life activities and behaviors, such as feeding, mating, and hosting. We constructed a full‐length transcriptome library and used this to identify the characteristics of soluble chemical communication proteins. Through full‐length transcriptome sequencing, splicing, assembly, and data correction by Illumina, we obtained 163.59 Mb of transcriptome data and 501,179 items with annotation information. We then performed Gene Ontology (GO) functional classification of the transcriptome's unigenes. We analyzed the sequence characteristics of soluble chemical communication protein genes and identified eight genes: AnilOBP2, AnilOBP9, AnilOBP23, AnilOBP56, AnilOBP83, AnilCSP5, AnilCSP6, and AnilNPC2. After sequence alignment and conserved domain prediction, the eight proteins encoded by the eight genes above were found to be consistent with the typical characteristics of odorant‐binding proteins (OBPs), chemosensory proteins (CSPs), and Niemann‐pick type C2 proteins (NPC2s) in other insects. Phylogenetic tree analysis showed that the eight genes share low homology with other species of Hymenoptera. Quantitative real‐time polymerase chain reaction (RT‐qPCR) was used to analyze the expression responses of the eight genes in different sexes and upon stimulation by volatile organic compounds. The relative expression levels of AnilOBP9, AnilOBP26, AnilOBP83, AnilCSP5, and AnilNPC2 in males were significantly higher than those in females, while the relative expression level of AnilCSP6 was higher in females. The expression levels of AnilOBP9 and AnilCSP6 were significantly altered by the stimulation of β‐caryophyllene, suggesting that these two genes may be related to host detection. This study provides the first data for A. nilaparvatae's transcriptome and the molecular characteristics of soluble chemical communication proteins, as well as an opportunity for understanding how A. nilaparvatae behaviors are mediated via soluble chemical communication proteins.
Comprehensive Characterization of the Genomic Landscape in Chinese Pulmonary Neuroendocrine Tumors Reveals Prognostic and Therapeutic Markers (CSWOG-1901)

Abstract Background Pulmonary neuroendocrine tumors (pNETs) include typical carcinoid (TC), atypical carcinoid (AC), large cell neuroendocrine carcinoma (LCNEC), and small cell lung carcinoma (SCLC). The optimal treatment strategy for each subtype remains elusive, partly due to the lack of comprehensive understanding of their molecular features. We aimed to explore differential genomic signatures in pNET subtypes and identify potential prognostic and therapeutic biomarkers. Methods We investigated genomic profiles of 57 LCNECs, 49 SCLCs, 18 TCs, and 24 ACs by sequencing tumor tissues with a 520-gene panel and explored the associations between genomic features and prognosis. Results Both LCNEC and SCLC displayed higher mutation rates for TP53, PRKDC, SPTA1, NOTCH1, NOTCH2, and PTPRD than TC and AC. Small cell lung carcinoma harbored more frequent co-alterations in TP53-RB1, alterations in PIK3CA and SOX2, and mutations in HIF-1, VEGF and Notch pathways. Large cell neuroendocrine carcinoma (12.7 mutations/Mb) and SCLC (11.9 mutations/Mb) showed higher tumor mutational burdens than TC (2.4 mutations/Mb) and AC (7.1 mutations/Mb). 26.3% of LCNECs and 20.8% of ACs harbored alterations in classical non-small cell lung cancer driver genes. The presence of alterations in the homologous recombination pathway predicted longer progression-free survival in advanced LCNEC patients with systemic therapy (P = .005) and longer overall survival (OS) in SCLC patients with resection (P = .011). The presence of alterations in VEGF (P = .048) and estrogen (P = .018) signaling pathways both correlated with better OS in patients with resected SCLC. Conclusion We performed a comprehensive genomic investigation on 4 pNET subtypes in the Chinese population. Our data revealed distinctive genomic signatures in subtypes and provided new insights into the prognostic and therapeutic stratification of pNETs.
Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets

Post-weaning diarrhea (PWD) in pigs has mainly an infectious basis and control strategies are centred on antibiotics added to the diet. Given concerns on the spread of multi-resistant bacteria, it is necessary to develop alternative prophylactic approaches to control PWD in piglets. The most promising alternative strategies are based on substances that act indirectly on the bacteria by stimulating the immune system or by improving gut health. The aim of this study was to evaluate the effect on the gut microbiota of feed supplemented with a mixture of essential oils (garlic and oregano) in weaning piglets, compared to traditional PWD management (in-feed antibiotics) and to a control group without any diet supplementation. The study involved 197 piglets from 18 litters in a single farm. The piglets were followed from birth to day 58 of age and were weaned at day 26. During the experimental period, the animals were monitored for weight and growth, average daily gain, morbidity and mortality. For the metataxonomics analysis, rectal samples were collected from 17 piglets from the three experimental groups at 4 different time-points (days 1, 12, 26 and 58). Results revealed that the gut microbiota in pre- and post-weaning piglets was dominated by the phyla Firmicutes (51%), Bacteroidetes (25%) and Proteobacteria (16%), which together make up for over 90% of the entire piglet core gut microbiota. The core microbiota comprised 10 taxa before weaning and 43 taxa after weaning, with 7 taxa overlapping between timepoints: two of them (Prevotella 9, p-value = 0.00095; Solobacterium p-value = 0.00821) were significantly more abundant after weaning. All alpha diversity indexes were significantly different between pre- and post-weaning, while only Shannon and Simpson diversity and equitability were significantly different between treatments. Based on the matrix of Bray-Curtis dissimilarities, samples showed clear clustering per timepoint (before and after weaning, p-value < 0.001) and between treatments by timepoint (p-value = 0.0086). The oil-diet group showed a consistently higher F:B ratio at all timepoints. These results show that the pig gut microbiota changes significantly with weaning, and suggest that the use of essential oils as feed supplementation to control PWD does not seem to alter sgnificantly the microbiota nor the growth parameters of piglets, however modifications of specific taxa may occur.
Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.
Optical Characterization of Bitumen: Inspecting the Quantum Size Effect in the Nanostructured Phase

Bitumen (BIT) is an oil sub-product with many applications. A variety of literature reports the analysis of its optical properties, as the fluorescence and the Fourier transform infrared (FT-IR) optical transmittance (OT). We have performed photoluminescence (PL) on the visible region of the spectrum and OT on the visible-NIR in solutions of BIT in toluene at different concentrations. The results revealed a nonlinear, concentration-dependent effect attributed to intermolecular solvent–solute interactions. PL analysis of pure BIT as a function of the temperature and the laser pumping power pointed to the existence of nanosized crystalline inclusions on the amorphous BIT matrix with noticeable optical properties. The inference was confronted with the results of X-ray diffraction studies and literature reports. The possibility of the occurrence of a quantum size effect governing the luminescence is considered.