Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into the ecology of the Black Sea through the qualitative loop analysis of the community structure

Overfishing, excess nutrient load, and invasion of Mnemiopsis leidyi acted on the Black Sea from 1960s to 1990s. Under the effect of these drivers, the ecosystem underwent several transformations that culminated in the shift from a planktonic food chain to a network with most of the energy diverted to jellyfish. The interplay between multiple stressors and the intricate web of trophic interactions make it difficult to understand which causative mechanisms linked the sources of change to the observed variations. To study such interplay, we focused on the structure of the trophic interactions and applied loop analysis to qualitatively predict the response of variables to stressors. Significant variations in biomass trends were identified with statistical analysis and considered as benchmark to validate loop analysis predictions. The results of the comparisons were used to select the most influential trophic interactions that explain the changes observed between 1960 and 1990. The models were applied to test (1) the importance of various environmental drivers and (2) the mechanisms that produced the observed changes. The results suggested that the changes observed before M. leidyi invasion were strongly influenced by the excess nutrient addition, an outcome that challenges the relevance of the trophic cascade as described in literature. The concurrent effect of overfishing, climate, and nutrient enrichment likely triggered the outburst of M. leidyi in the late 1980s. Our work shows the potential of loop analysis to grasp the causal relationships between the drivers, the structure of the interactions, and the responses of the variables.
Towards structural models for the Ebola UTR regions using experimental SHAPE probing data

Next-Generation Sequencing (NGS) technologies have opened new perspectives to refine the process of predicting the secondary structure(s) of structured non-coding RNAs. Herein, we describe an integrated modeling strategy, based on the SHAPE chemistry, to infer structural insight from deep se-quencing data. Our approach is based on a pseudo-energy minimization, incorporating additional information from evolutionary data (compensatory mutations) and SHAPE experiments (reactivity scores) within an iterative procedure. Preliminary results reveal conserved and stable structures within UTRs of the Ebola Genome, that are both thermodynamically-stable and highly supported by SHAPE accessibility analysis.
High-speed video capture of anterior cruciate ligament tearing in human and porcine ex vivo specimens

The tearing of ligaments during sports activities is one of the most common injuries players sustain. Of these ligament tears, the Anterior Cruciate Ligament (ACL) is one of the most prevalent. Although the anteromedial (AM) and posterolateral (PL) bundles of the ACL have been well described, biomechanics research focuses primarily on the strength of the ligament under tension forces. And yet, post-reconstruction tears remain prevalent. To date, no one has captured the tearing of the ACL using high-speed video. We hypothesize that high-speed filming of an artificially induced tear of the human and porcine ACL will reveal the organization of the ligament fibers and provide insight on the ligament’s structural organization and integrity. We filmed scalpel-induced tears of three human and three porcine ACL’s using a high-speed (6000 fps) camera. With the femur fixed securely on a table surface, and the tibia hanging over the edge, resulting in a flexed knee joint at 90 degrees, a 2.2 kg weight was attached to the tibia in order to induce tension on the ACL. The ACL was then cut anteriorly to a depth of approximately 1-3 mm with a scalpel, while a high-speed video camera recorded the unraveling of the anteromedial (AM) and posterolateral (PL) bundle fibers. At the initiation of the human ACL tears, there was a consistent, subtle release of tension visible as a ripple in the most anterior fibers of the AM bundle. Furthermore, the tear pattern revealed that the PL bundle acts as a posterior post, with the AM bundle wrapping tightly around it. In contrast, the porcine bundles were arranged distinctly from one another, with a noticeable, but slight gap of 1-2 mm: Unlike the human ACL, the porcine ACL bundles tore independently. High-speed video of artificially induced ACL tears reveals a distinct difference in the structural arrangement of the AM and PL bundles between human and porcine samples. The independent tearing of the porcine AM and PL bundles suggests that human ACL reconstruction integrity could benefit from a similar two-bundle arrangement. High-speed video of artificially torn human and porcine ACL’s reveal an important difference in the geometric arrangement of the two bundles between the two species: Namely, human ACL bundles are tightly wound, but porcine ACL bundles are arranged as seemingly separate ligaments that tear independently. The video footage suggests that human ACL reconstruction may benefit from a distinct two-bundle geometry. Correspondence to: Jonathan J Wisco, Ph.D., Associate Professor, Brigham Young University, Department of Physiology and Developmental Biology Neuroscience Center Laboratory for Translational Anatomy of Degenerative Diseases and Developmental Disorders (TAD4) 4005 LSB Provo, Utah 84602-5255, USA, Tel: 310-746-6647; 801-422-2402; Fax: 801-422-0004; E-Mail: jjwisco@byu.edu
Clinical course of tracheobronchopathia osteochondroplastica

Background Tracheobronchopathia osteochondroplastica (TPO) is characterized by the presence of diffuse cartilaginous or bony submucosal nodules that lead to airway lumen narrowing. So far, there was no study in South Korea analysing a large number of TPO patients. We aimed to elucidate its treatment strategy and clinical course by analysing the characteristics of TPO patients. Methods In this retrospective study, we reviewed the clinical data of 40 patients diagnosed with TPO by bronchoscopy between October 1997 and April 2019 at a single referral hospital. Results Of the 40 patients, 26 (65.0%) were male and the median age was 63.0 years. The most common symptom was cough (n=12, 30%). Pulmonary function test (PFT) revealed an obstructive pattern in 10 (25.7%) patients. Chest computed tomography (CT) scan showed 23 (62.6%) patients with diffuse narrowing and calcified nodules. In bronchoscopy, the entire trachea was found to be involved in 30 (75.0%) patients and airway narrowing was identified in 6 (15.0%) patients. Endobronchial biopsies were obtained from 15 patients and the most common findings included typical cartilaginous and bony tissues (n=14, 93.3%). Since most patients were asymptomatic or had mild symptoms, they did not undergo any specific treatment. Of the 19 symptomatic patients, 2 (5.0%) patients received laser therapy for treating tracheal stenosis. Conclusions TPO is a slowly progressing disease and is well managed with conservative therapies. Although TPO shows a distinctive pattern by bronchoscopy, it follows a benign clinical course.
RegenHeart: A Time-Effective, Low-Concentration, Detergent-Based Method Aiming for Conservative Decellularization of the Whole Heart Organ

Heart failure is the worst outcome of all cardiovascular diseases and still represents nowadays the leading cause of mortality with no effective clinical treatments, apart from organ transplantation with allogeneic or artificial substitutes. Although applied as the gold standard, allogeneic heart transplantation cannot be considered a permanent clinical answer because of several drawbacks, as the side effects of administered immunosuppressive therapies. For the increasing number of heart failure patients, a biological cardiac substitute based on a decellularized organ and autologous cells might be the lifelong, biocompatible solution free from the need for immunosuppression regimen. A novel decellularization method is here proposed and tested on rat hearts in order to reduce the concentration and incubation time with cytotoxic detergents needed to render acellular these organs. By protease inhibition, antioxidation, and excitation–contraction uncoupling in simultaneous perfusion/submersion modality, a strongly limited exposure to detergents was sufficient to generate very well-preserved acellular hearts with unaltered extracellular matrix macro- and microarchitecture, as well as bioactivity.
The Effects of Halogenated Compounds on the Anaerobic Digestion of Macroalgae

The urgent need to replace fossil fuels has seen macroalgae advancing as a potential feedstock for anaerobic digestion. The natural methane productivity (dry weight per hectare) of seaweeds is greater than in many terrestrial plant systems. As part of their defence systems, seaweeds, unlike terrestrial plants, produce a range of halogenated secondary metabolites, especially chlorinated and brominated compounds. Some orders of brown seaweeds also accumulate iodine, up to 1.2% of their dry weight. Fluorine remains rather unusual within the chemical structure. Halogenated hydrocarbons have moderate to high toxicities. In addition, halogenated organic compounds constitute a large group of environmental chemicals due to their extensive use in industry and agriculture. In recent years, concerns over the environmental fate and release of these halogenated organic compounds have resulted in research into their biodegradation and the evidence emerging shows that many of these compounds are more easily degraded under strictly anaerobic conditions compared to aerobic biodegradation. Biosorption via seaweed has become an alternative to the existing technologies in removing these pollutants. Halogenated compounds are known inhibitors of methane production from ruminants and humanmade anaerobic digesters. The focus of this paper is reviewing the available information on the effects of halogenated organic compounds on anaerobic digestion.
Screening of Human Phycotoxin Poisoning Symptoms in Coastal Communities of Nigeria: Socio-Economic Consideration of Harmful Algal Blooms

A screening of human phycotoxin poisoning symptoms was done in the coastal communities of Nigeria, every quarter for one year, using structured questionnaires. A multi-stage sampling technique consisting of cluster, snowballing, convenience purposive and random sampling was applied in the study. Based on the responses, a total of 17 Harmful algal toxin-related poisoning symptoms were recorded from respondents, who experienced these symptoms from seafood consumption. The symptoms were Balance difficulty, Breathing difficulty, Burning sensation, Chills, Confusion, Diarrhea, Dizziness, Body itching, Headache, Memory loss, Mouth tingling, Muscle pain, Nausea, Rashes, Abdominal pain, Tiredness and Vomiting. These could be grouped into five categories of diseases namely, Respiratory, Gastrointestinal, Neurological, Dermatological, and Musculo-Skeletal symptoms. The most commonly experienced symptoms were vomiting (24%), mouth tingling (21%), Nausea (14%), diarrhea (11%), headache (10%), tiredness (9%) and body itching (8%) and the least were muscle pain, rashes, confusion, chills, dizziness, balance difficulty burning sensation, breathing difficulty and abdominal pain. Statistical analyses revealed a nexus and significant relationship between visible symptoms and: seafood; season; water colour; habitats/environment of dead seafood and age of respondents. Symptoms enlisted are reminiscent of harmful algal blooms, with grave consequences for public health, commercial fisheries, recreation, tourism, monitoring/management. Therefore, preventive measures, requiring routine monitoring of water bodies, coupled with greater public awareness is suggested for early detection of occurrence of toxin-producing symptoms.
COMPASS III: automated fitting workflows and extension to ionic liquids

ABSTRACT The ability to automatically extend and improve molecular force fields to accurately describe an ever wider range of compounds is a key enabler for the application of molecular modelling of chemicals and materials in industry. In this work we have developed a set of tools to process structural data available in well-known databases, to find deficiencies in the force field, and where necessary, automatically fit force- field parameters to on-the-fly calculated quantum data based on Density Functional Theory, supplemented by experimental data. The protocols have been applied to structures from the Maybridge, PoLyInfo and ILThermo databases, covering drug-like molecules, polymers and ionic liquids respectively. We demonstrate that the new version of the force field can type all structures in the extended data set without missing parameters, with a similar high-quality prediction of geometry (bonds, angles, torsions), energy and forces of earlier versions.
Studies on Sertoli cell function using in vivo and in vitro models

The adult testis consists of two compartments, the seminiferous tubules and interstitium; the seminiferous tubules contain Sertoli cells (SC) each in close association with a complement of germ cells (GC) and are the site of GC maturation from diploid spermatogonia to haploid spermatozoa. The interstitium contains Leydig cells (LC), peritubular myoid cells (PTM), macrophages and blood vessels. In addition to producing haploid GC, the other essential function of the testis is synthesises of steroids hormones (primarily androgens and oestrogens). Sertoli cells are essential for support of GC development, but support of spermatogenesis is dependent upon expression ofAR in SC, which they express in a stage-specific pattern. The SCs also express oestrogen receptor P (ER(S). The association between SC and adjacent GC and SC are mediated by junctional complexes, including gap junctions, tight junctions, ectoplasmic specialisations, and tubulobulbar complexes. The aims of this thesis were; 1) to investigate androgen and oestrogen responses in SC using the immortalised SKI 1 cell line, 2) determine the effectiveness of an adenoviral vector for introduction of transgenes into SC in vivo and in vitro, and 3) investigate androgen-dependent gene and protein expression in testosterone depleted testes of EDStreated rats. SKI 1 cells had detectable expression of ER/3 mRNA, and activated an ERE-luciferase reporter construct in response to a range of oestrogenic ligands. In contrast endogenous AR expression was low, but transfection with mouse AR cDNA resulted in sufficient AR expression to activate a luciferase reporter under control of the Rhox5 proximal promoter in response to androgen treatment. However transfected SKI 1 cells could not stimulate endogenous Rhox5 mRNA expression under similar conditions. Infection of SKI 1 cells with an adenoviral construct in vitro resulted in efficient transgene expression in 80-100% of cells, and was associated with excellent cell survival. In vivo infection in mouse testes with an adenoviral vector containing a GFP transgene,
Isn’t it iconic? Brand iconicity and distilled spirits: An exploratory study

ABSTRACT This exploratory study uses both qualitative and quantitative data to reveal insights used to proffer a new definition for iconicism as related to distilled spirits: A distilled spirit brand that has reached the pinnacle of its category through quality product, widespread brand recognition in the marketplace, brand insistence from its consumers, and an extended product life cycle. The study found that package and brand name recognizability was the most important attribute for a distilled spirit to be considered iconic, followed by longevity, the story the brand tells, cultural relevance, status and lastly celebrity endorsement. Additionally, the research revealed specific brands in each distilled spirit category that respondents considered to be iconic. The main contribution of this work is furthering the research on both iconicism and distilled spirits in academia and providing useful insights to industry professionals.
Dark Ammonium Transformations in the Pearl River Estuary During Summer

Growing human activities in recent decades have collectively resulted in large amounts of nutrients export into coastal oceans. As the most reactive nitrogen species, ammonium ( NH4+ ) plays the critical role in biogeochemical cycles in estuaries and the coastal ocean. In the highly polluted Pearl River Estuary (PRE), NH4+ predominates to be the energy source for nitrification and to be the material source for bacteria and phytoplankton to grow. Both above processes are affected by light, yet in opposite ways. Nevertheless, rare studies paid attention to dual NH4+ transformation processes specifically during dark conditions. By using nitrogen isotope tracer technique, we quantitatively and simultaneously differentiated two distinctive NH4+ consumption pathways, that is, NH4+ oxidation (AOD) and assimilation (AAD) rates, especially under dark conditions along the PRE during the 2015 and 2017 summer cruises when biological activities were the highest. We found the NH4+ transformations display a bilayer structure with AAD > AOD in almost all the surface waters and vice versa in all bottom waters, suggesting bacteria and phytoplankton (mainly bacteria) control NH4+ consumption in surface during the night while nitrifiers are the major NH4+ consumer in the bottom waters. Through redundancy analysis, we found that both processes are mainly driven by NH4+ in the PRE during summer. In addition, in the downstream PRE during two cruises, AOD at most contributed 27% and 8% of the water column community dissolved oxygen (DO) consumption assuming the Redfield stoichiometry has no direct effect on hypoxia formation in the PRE during summer.
Impact of cardiovascular risk factors on the clinical presentation and survival of pulmonary embolism without identifiable risk factor

Background The nature of pulmonary embolism (PE) without identifiable risk factor (IRF) remains unclear. The objective of this study is to investigate the potential relationship between cardiovascular risk factors (CVRFs) and PE without IRF (unprovoked) and assess their role as markers of disease severity and prognosis. Methods A case-control study was performed of patients with PE admitted to our hospital [2010–2019]. Subjects with PE without IRF were included in the cohort of cases, whereas patients with PE with IRF were allocated to the control group. Variables of interest included age, active smoking, obesity, and diagnosis of arterial hypertension, dyslipidemia or diabetes mellitus. Results A total of 1,166 patients were included in the study, of whom 64.2% had PE without IRF. The risk for PE without IRF increased with age [odds ratio (OR): 2.68; 95% confidence interval (CI): 1.95–3.68], arterial hypertension (OR: 1.63; 95% CI: 1.27–2.07), and dyslipidemia (OR: 1.63; 95% CI: 1.24–2.15). The risk for PE without IRF was higher as the number of CVRF increased, being 3.99 (95% CI: 2.02–7.90) for subjects with ≥3 CVRF. The percentage of high-risk unprovoked PE increased significantly as the number of CVRF rose [0.6% for no CVRF; 23.8% for a CRF, P<0.001 (OR: 9.92; 95% CI: 2.82–34.9); 37.5% for two CRFs, P<0.001 (OR: 14.8; 95% CI: 4.25–51.85); and 38.1% for ≥3, P<0.001 (OR: 14.1; 95% CI: 4.06–49.4)]. No significant differences were observed in 1-month survival between cases and controls, whereas differences in 24-month survival reached significance. Conclusions A relationship was observed between CVRF and PE without IRF, as the risk for unprovoked PE increased with the number of CVRF. In addition, the number of CVRF was associated with PE without IRF severity, but not with prognosis.
Development of Sternum and Ribs in White New Zealand Rabbit (Oryctolagus cuniculus)

The bone development and the assessment of the fetal skeletal improvement turn into a basic segment in the behavior of a prenatal toxicity study. The sternum is a unique bone in the distinctive shape and development. This study focuses on the development of the sternum and the ribs attached in the whit New Zealand rabbit, Specimens were collected prenatally (n=30) and postnatally (n=30). A group of specimens were double stained for bone and cartilage using Alizarin Red and Alcian blue. Another group was scanned by CT. The sternum was consisted of manubrium, four sternebrae and xiphoid cartilage. The sternum was in communication with 6 pairs of ribs. 7 ossification centers appeared in the sternum, one for each segment except the fourth one which has two. The first group centers appeared in the manubrium and the first two sternebrae on 22 days old embryos. All primary centers seen before birth. There are no secondary ossification centers for the sternum. Concerning ribs, there are four ossification centers for each except the last two ribs. The ossification centers of the body came from the extension of the transvers process of the thoracic vertebrae and it appears as early as two weeks of gestation. By the end of the third week of pregnancy, the ribs show primary center of ossification from the second to the last one. The second center was designed for the head and it appeared two weeks after birth. The third and fourth centers for the tubercle appeared a month after birth. Complete fusion between these centers takes place in three months old rabbit.
Glycaemic control among Bulgarian children and adolescents with type 1 diabetes – an impact of the social status and the educational level of the parents

ABSTRACT Achievement of optimal glycaemic control in children and adolescents with type 1 diabetes depends on the knowledge of the patients and their parents about the control of the disease and the family support. The aim of this study was to investigate the importance of the social standard of the families determined by the employment of the parents and their educational qualification on the control of diabetes. Two consecutive national multi-centre cross-sectional studies of patients with type 1 diabetes, aged 0–19 years, for HbA1c were conducted in 2012 and in 2014. The first study included 829 patients (422 boys, 407 girls), and the second - 498 patients; 281 patients participated in both studies. The patients whose parents are with primary education showed the highest level of HbA1c in both studies: 9.73% ± 2.38% and 9.27% ± 1.54% in the first, and the second study, respectively. The patients whose parents have university education achieved the best control: HbA1c is 8.45% ± 1.76% and 7.84% ± 1.24%, respectively. The cohorts of diabetic patients whose parents have secondary (p = 0.035) and university education (p < 0.001) showed significant reduction of HbA1c in the second study compared to the first one. The patients in families with unemployed parents or families in which only the mother is employed showed the highest levels of HbA1c. Our results underline the importance of the educational qualification and the social standard of the family for the proper control of this chronic disease.