An artistic, mythological and documentary study of the Atargatis panel from et-Tannur, Jordan

In 1937 and 1938, a group of high-relief and round statues were uncovered during the joint expedition of the American School of Oriental Research in Jerusalem and the Department of Antiquities in Palestine at the Khirbet et-Tannur Temple, located in Jordan. This expedition was headed by Nelson Glueck (Figs 1, 2). The statues uncovered are important in that they offer considerable information about Nabataean art and religion. This paper concentrates on one of the high-relief statues, called the Atargatis Panel by its excavator, Glueck. It was chosen as a case study for its availability in Amman, Jordan. The other Atargatis statues found at the site are now in the Cincinnati Art Museum in the United States of America. This paper also examines the Nabataean religious beliefs concerning Atargatis and her fertility cult, in addition to the art style of the statue. Furthermore, the digital 3D imaging documentation of the Atargatis statue at The Jordan Museum is presented. Dense image matching algorithms presented a flexible, cost-effective approach for this important work. These images not only provide geometric information but also show the surface textures of the depicted objects. This is especially important for the production of virtual 3D models used as a tool for documentary, educational and promotional purposes

An enthroned Tyche statue from Gadara / Umm Qais, Jordan

The round statue of enthroned Tyche was originally displayed in the middle of the front row of seats in the west theatre of Umm Qais. The statue of high quality is made of ivory coloured marble, while the theatre is constructed of black basalt stone. This contrast of colour and material made the statue stand out and intensified the beauty of the theatre. The statue has been moved by the Department of Antiquities of Jordan and displayed at Umm Qais Archaeological Museum, registered as number 13c. The Gadara Tyche appeared with one of the main symbols of the goddess, the cornucopia. Highly realistic and geometric models of cultural heritage objects are attractive tools for documentation, preservation and promotion purposes. 3D imaging, using dense stereo matching techniques, is used for accurate and realistic modeling of the Tyche statue and the theatre of Umm Qais. Acquiring 3D surfaces with image matching solutions has many advantages related to the flexibility, cost effectiveness of, and need for short data collection time on the site without disturbance to the site’s visitors

Using Interdisciplinary Studies and Analyses in the Conservation of Greco-Roman Cartonnage

This paper describes the multi-analytical techniques and treatment processes that were undertaken in the conservation of two deteriorated cartonnages of the Greek- Roman period. Due to the lack of cartonnage specialists and the complicated nature of the restoration process, cartonnages within Egyptian museums and storage areas suffer from neglect and various other problems. The issue of cartonnage restoration is, so far, still a subject of scientific controversy. The research described in this paper dealt with the conservation and restoration of two mummy cartonnages found in Saqqara. Damage factors were identified and a biological study was conducted aimed at identi­fying the microorganisms that had led to biological infection. Furthermore, spot-stains caused by using resin in the mummification process were also inspected. Scanning electron microscopy (SEM-EDX), X-ray diffraction and Infrared (FTIR) results revealed the cartonnage components. It is clear from the spectra obtained with the blue colored sample that Egyptian blue was used. The white pigment composition appears as a combination of calcite and as calcium silicate mixed with aluminum silicate. FTIR re­vealed the presence of three layers of linen textile, which were made of layers of linen, and sometimes of papyrus, and mounted using animal glue. After examining the condi­tion of the cartonnages and studying the results of the previous analysis, a treatment and restoration plan was developed and applied. Treatments included: strengthening the colors and weak parts, cleaning, removal of previous restoration materials and replacing the missing parts as well as preparing two new display holders.Questo documento descrive le tecniche multi-analitiche e i trattamenti che sono stati intrapresi nella conservazione di due cartonaggi deteriorati del periodo greco-romano. A causa della mancanza di specialisti di cartonnage e della natura complicata del pro­cesso di restauro, i cartonnages all’interno dei musei e delle aree di stoccaggio egizi­ani sono in cattivo stato di conservazione. La questione del restauro del cartonnage è, finora, ancora oggetto di controversie scientifiche. La ricerca descritta in questo documento ha riguardato la conservazione e il restauro di due mummie di cartonaggi trovati a Saqqara. Sono stati identificati i fattori di danno e uno studio biologico è stato condotto per identificare i microrganismi che avevano portato all’infezione biologica. Inoltre, sono state ispezionate anche macchie di macchie causate dall’uso di resina nel processo di mummificazione. La microscopia elettronica a scansione (SEM-EDX), i risultati della diffrazione ai raggi X e dell’infrarosso (FTIR) hanno rivelato i componenti del cartonnage. È chiaro dagli spettri ottenuti con il campione di colore blu che è stato utilizzato il blu egiziano. La composizione del pigmento bianco appare come una com­binazione di calcite e come silicato di calcio mescolato con silicato di alluminio. FTIR ha rivelato la presenza di tre strati di tessuto di lino, che erano fatti di strati di lino e talvolta di papiro e montati con colla animale. Dopo aver esaminato le condizioni dei cartonnages e studiato i risultati dell’analisi precedente, è stato sviluppato e applicato un piano di trattamento e ripristino. Trattamenti: rinforzo dei colori e parti deboli, puli­zia, rimozione dei materiali di restauro precedenti, sostituzione delle parti mancanti e preparazione di due nuovi supporti

Rank-based edge reconstruction for scale-free genetic regulatory networks

<p>Abstract</p> <p>Background</p> <p>The reconstruction of genetic regulatory networks from microarray gene expression data has been a challenging task in bioinformatics. Various approaches to this problem have been proposed, however, they do not take into account the topological characteristics of the targeted networks while reconstructing them.</p> <p>Results</p> <p>In this study, an algorithm that explores the scale-free topology of networks was proposed based on the modification of a rank-based algorithm for network reconstruction. The new algorithm was evaluated with the use of both simulated and microarray gene expression data. The results demonstrated that the proposed algorithm outperforms the original rank-based algorithm. In addition, in comparison with the Bayesian Network approach, the results show that the proposed algorithm gives much better recovery of the underlying network when sample size is much smaller relative to the number of genes.</p> <p>Conclusion</p> <p>The proposed algorithm is expected to be useful in the reconstruction of biological networks whose degree distributions follow the scale-free topology.</p

An enthroned Tyche statue from Gadara / Umm Qais, Jordan

The round statue of enthroned Tyche was originally displayed in the middle of the front row of seats in the west theatre of Umm Qais. The statue of high quality is made of ivory coloured marble, while the theatre is constructed of black basalt stone. This contrast of colour and material made the statue stand out and intensified the beauty of the theatre. The statue has been moved by the Department of Antiquities of Jordan and displayed at Umm Qais Archaeological Museum, registered as number 13c. The Gadara Tyche appeared with one of the main symbols of the goddess, the cornucopia. Highly realistic and geometric models of cultural heritage objects are attractive tools for documentation, preservation and promotion purposes. 3D imaging, using dense stereo matching techniques, is used for accurate and realistic modeling of the Tyche statue and the theatre of Umm Qais. Acquiring 3D surfaces with image matching solutions has many advantages related to the flexibility, cost effectiveness of, and need for short data collection time on the site without disturbance to the site’s visitors

A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments

<p>Abstract</p> <p>Background</p> <p>The incorporation of prior biological knowledge in the analysis of microarray data has become important in the reconstruction of transcription regulatory networks in a cell. Most of the current research has been focused on the integration of multiple sets of microarray data as well as curated databases for a genome scale reconstruction. However, individual researchers are more interested in the extraction of most useful information from the data of their hypothesis-driven microarray experiments. How to compile the prior biological knowledge from literature to facilitate new hypothesis generation from a microarray experiment is the focus of this work. We propose a novel method based on the statistical analysis of reported gene interactions in PubMed literature.</p> <p>Results</p> <p>Using Gene Ontology (GO) Molecular Function annotation for reported gene regulatory interactions in PubMed literature, a statistical analysis method was proposed for the derivation of a likelihood of interaction (LOI) score for a pair of genes. The LOI-score and the Pearson correlation coefficient of gene profiles were utilized to check if a pair of query genes would be in the above specified interaction. The method was validated in the analysis of two gene sets formed from the yeast Saccharomyces cerevisiae cell cycle microarray data. It was found that high percentage of identified interactions shares GO Biological Process annotations (39.5% for a 102 interaction enriched gene set and 23.0% for a larger 999 cyclically expressed gene set).</p> <p>Conclusion</p> <p>This method can uncover novel biologically relevant gene interactions. With stringent confidence levels, small interaction networks can be identified for further establishment of a hypothesis testable by biological experiment. This procedure is computationally inexpensive and can be used as a preprocessing procedure for screening potential biologically relevant gene pairs subject to the analysis with sophisticated statistical methods.</p

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data

<p>Abstract</p> <p>Background</p> <p>Bayesian Network (BN) is a powerful approach to reconstructing genetic regulatory networks from gene expression data. However, expression data by itself suffers from high noise and lack of power. Incorporating prior biological knowledge can improve the performance. As each type of prior knowledge on its own may be incomplete or limited by quality issues, integrating multiple sources of prior knowledge to utilize their consensus is desirable.</p> <p>Results</p> <p>We introduce a new method to incorporate the quantitative information from multiple sources of prior knowledge. It first uses the Naïve Bayesian classifier to assess the likelihood of functional linkage between gene pairs based on prior knowledge. In this study we included cocitation in PubMed and schematic similarity in Gene Ontology annotation. A candidate network edge reservoir is then created in which the copy number of each edge is proportional to the estimated likelihood of linkage between the two corresponding genes. In network simulation the Markov Chain Monte Carlo sampling algorithm is adopted, and samples from this reservoir at each iteration to generate new candidate networks. We evaluated the new algorithm using both simulated and real gene expression data including that from a yeast cell cycle and a mouse pancreas development/growth study. Incorporating prior knowledge led to a ~2 fold increase in the number of known transcription regulations recovered, without significant change in false positive rate. In contrast, without the prior knowledge BN modeling is not always better than a random selection, demonstrating the necessity in network modeling to supplement the gene expression data with additional information.</p> <p>Conclusion</p> <p>our new development provides a statistical means to utilize the quantitative information in prior biological knowledge in the BN modeling of gene expression data, which significantly improves the performance.</p

Efficacy and safety of two neutralising monoclonal antibody therapies, sotrovimab and BRII-196 plus BRII-198, for adults hospitalised with COVID-19 (TICO): a randomised controlled trial

BACKGROUND: We aimed to assess the efficacy and safety of two neutralising monoclonal antibody therapies (sotrovimab [Vir Biotechnology and GlaxoSmithKline] and BRII-196 plus BRII-198 [Brii Biosciences]) for adults admitted to hospital for COVID-19 (hereafter referred to as hospitalised) with COVID-19. METHODS: In this multinational, double-blind, randomised, placebo-controlled, clinical trial (Therapeutics for Inpatients with COVID-19 [TICO]), adults (aged ≥18 years) hospitalised with COVID-19 at 43 hospitals in the USA, Denmark, Switzerland, and Poland were recruited. Patients were eligible if they had laboratory-confirmed SARS-CoV-2 infection and COVID-19 symptoms for up to 12 days. Using a web-based application, participants were randomly assigned (2:1:2:1), stratified by trial site pharmacy, to sotrovimab 500 mg, matching placebo for sotrovimab, BRII-196 1000 mg plus BRII-198 1000 mg, or matching placebo for BRII-196 plus BRII-198, in addition to standard of care. Each study product was administered as a single dose given intravenously over 60 min. The concurrent placebo groups were pooled for analyses. The primary outcome was time to sustained clinical recovery, defined as discharge from the hospital to home and remaining at home for 14 consecutive days, up to day 90 after randomisation. Interim futility analyses were based on two seven-category ordinal outcome scales on day 5 that measured pulmonary status and extrapulmonary complications of COVID-19. The safety outcome was a composite of death, serious adverse events, incident organ failure, and serious coinfection up to day 90 after randomisation. Efficacy and safety outcomes were assessed in the modified intention-to-treat population, defined as all patients randomly assigned to treatment who started the study infusion. This study is registered with ClinicalTrials.gov, NCT04501978. FINDINGS: Between Dec 16, 2020, and March 1, 2021, 546 patients were enrolled and randomly assigned to sotrovimab (n=184), BRII-196 plus BRII-198 (n=183), or placebo (n=179), of whom 536 received part or all of their assigned study drug (sotrovimab n=182, BRII-196 plus BRII-198 n=176, or placebo n=178; median age of 60 years [IQR 50-72], 228 [43%] patients were female and 308 [57%] were male). At this point, enrolment was halted on the basis of the interim futility analysis. At day 5, neither the sotrovimab group nor the BRII-196 plus BRII-198 group had significantly higher odds of more favourable outcomes than the placebo group on either the pulmonary scale (adjusted odds ratio sotrovimab 1·07 [95% CI 0·74-1·56]; BRII-196 plus BRII-198 0·98 [95% CI 0·67-1·43]) or the pulmonary-plus complications scale (sotrovimab 1·08 [0·74-1·58]; BRII-196 plus BRII-198 1·00 [0·68-1·46]). By day 90, sustained clinical recovery was seen in 151 (85%) patients in the placebo group compared with 160 (88%) in the sotrovimab group (adjusted rate ratio 1·12 [95% CI 0·91-1·37]) and 155 (88%) in the BRII-196 plus BRII-198 group (1·08 [0·88-1·32]). The composite safety outcome up to day 90 was met by 48 (27%) patients in the placebo group, 42 (23%) in the sotrovimab group, and 45 (26%) in the BRII-196 plus BRII-198 group. 13 (7%) patients in the placebo group, 14 (8%) in the sotrovimab group, and 15 (9%) in the BRII-196 plus BRII-198 group died up to day 90. INTERPRETATION: Neither sotrovimab nor BRII-196 plus BRII-198 showed efficacy for improving clinical outcomes among adults hospitalised with COVID-19. FUNDING: US National Institutes of Health and Operation Warp Speed

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

INVESTIGATIONS OF HELLENISTIC MORTAR FROM UMM QAIS (GADARA), JORDAN

Ancient mortars have been widely studied, in connection with both diagnosis and applications required for restoration. This study is primarily based on analyses of different mortar samples from a Hellenistic temple. The study was done by means of a polarizing microscope equipped for observations in transmitted and reflected light; and X-ray powder diffraction (XRD). Scanning Electron Microscopy/Energy Dispersive X-Ray Spectroscopy (SEM-EDS) were also used to confirm and supplement the microscopic data, and wet chemical analyses were performed on the acid filtrate for soluble oxides of Fe, Al, Ca, Mg, S, Na and K. Chemical and petrographic analysis were used to determine chemical composition and physical properties, which in turn provide an in-depth understanding of the structural behavior and durability characteristics as they relate to the composition. The results show that the plaster used was a lime-based mortar. The cementing binder was a lime (identified by spot test) with fossilized shell, very fine grain size quartz, and some other minerals as the aggregate. The EDS analysis showed the presence of calcium and a small proportion of magnesium; in addition, silicon, aluminum, potassium, and iron were detected. Possibly, the silicate compounds contributed to the hydraulic component. We found strong similarities among mortar samples used in the temple. Physical methods provided useful information on the mineralogical compounds and the surface structures of samples, allowing for the postulation of deterioration mechanisms and overall decay, including the identification and crystalline morphology of reaction products and salts. These results aid in both understanding the technology of historic mortars and planning the restoration of these mortars