Miracle-dz/UniFAR-FTUs huggingface dataset:
A Theoretical Model for Utilizing Mammalian Pharmacology and Safety Data to Prioritize Potential Impacts of Human Pharmaceuticals to Fish

Due to the potential for long-term, low-level exposure of environmental species to pharmaceuticals in the environment, concerns over chronic ecotoxicity have been raised. Pharmaceuticals typically have specific enzyme and receptor-based modes of action, which are extensively studied in mammals during drug development. A survey of the literature demonstrated that there is conservation of many enzyme/receptor systems between mammalian and teleost systems. Based on this conservation of enzyme/receptor systems across teleost species, a model has been developed to utilize the information from mammalian pharmacology and toxicology studies to evaluate the potential for chronic receptor mediated responses in fish. In this model, a measured human therapeutic plasma concentration (HTPC) is compared to a predicted steady state plasma concentration (FSSPC) in fish, and an effect ratio (ER = HTPC/FSSPC) is computed. The lower the ER, the greater the potential for a pharmacological response in fish. Data collection and model validation will strengthen the applicability of this approach as a viable tool for prioritizing research initiatives that examine the potential impact of pharmaceuticals on fish.
The pattern of neonatal admissions and mortality at a regional and district hospital in the Upper West Region of Ghana; a cross sectional study

Background High global neonatal deaths have triggered efforts to improve facility-based care. However, the outcomes achievable at different levels of care are unclear. This study compared morbidity and mortality patterns of newborns admitted to a regional and a district hospital in Ghana to determine outcome, risk and modifiable factors associated with mortality. Objective This study compared morbidity and mortality patterns of newborns admitted to a regional and a district hospital in Ghana to determine outcome, risk and modifiable factors associated with mortality Methods A cross-sectional study involving a records-review over one year at the Upper West Regional Hospital, and three years at St Joseph’s District Hospital, Jirapa was carried out. Age, sex, gestational age, weight, duration of admission, diagnosis, among others were examined. The data were analysed and statistical inference made. Results Altogether, 2004 newborns were examined, comprising 1,241(62%) from St Joseph’s District Hospital and 763(38%) from Upper West Regional Hospital. The proportion of neonatal deaths was similar, 8.94% (St Joseph’s District Hospital) and 8.91% (Upper West Regional Hospital). Prematurity, neonatal sepsis, birth asphyxia, low birth weight, neonatal jaundice and pneumonia contributed the most to mortality and suspected infections including malaria accounted for almost half (45.5%). Mortality was significantly associated with duration of stay of 48 hours, being premature, and being younger than 3 days. Conclusion Majority of the mortality among the neonates admitted was due to preventable causes. Better stabilization and further studies on the epidemiology of sepsis, prematurity, low birth weight, including the contribution of malaria to these and outcome of transferred neonates are needed.
Whale sharks increase swimming effort while filter feeding, but appear to maintain high foraging efficiencies

ABSTRACT Whale sharks (Rhincodon typus) – the largest extant fish species – reside in tropical environments, making them an exception to the general rule that animal size increases with latitude. How this largest fish thrives in tropical environments that promote high metabolism but support less robust zooplankton communities has not been sufficiently explained. We used open-source inertial measurement units (IMU) to log 397 h of whale shark behavior in Yucatán, Mexico, at a site of both active feeding and intense wildlife tourism. Here we show that the strategies employed by whale sharks to compensate for the increased drag of an open mouth are similar to ram feeders five orders of magnitude smaller and one order of magnitude larger. Presumed feeding constituted 20% of the total time budget of four sharks, with individual feeding bouts lasting up to 11 consecutive hours. Compared with normal, sub-surface swimming, three sharks increased their stroke rate and amplitude while surface feeding, while one shark that fed at depth did not demonstrate a greatly increased energetic cost. Additionally, based on time-depth budgets, we estimate that aerial surveys of shark populations should consider including a correction factor of 3 to account for the proportion of daylight hours that sharks are not visible at the surface. With foraging bouts generally lasting several hours, interruptions to foraging during critical feeding periods may represent substantial energetic costs to these endangered species, and this study presents baseline data from which management decisions affecting tourist interactions with whale sharks may be made. Summary: Tail beat kinematics and foraging behavior of filter feeding whale sharks off the Yucatán Peninsula indicate that stroke effort increases with filter feeding, particularly at the surface.
Positive epistasis between viral polymerase and the 3′ untranslated region of its genome reveals the epidemiologic fitness of dengue virus

Significance Dengue affects approximately one-half of the world’s population. While it causes regular and cyclical outbreaks throughout the tropical world, the molecular mechanisms that determine its epidemic potential remain poorly defined. The present work provides insight into the molecular determinants of epidemiologic fitness, which is critical for surveillance to identify dengue virus strains with a potential to cause outbreaks. This will allow for better implementation of control measures to intercept impending outbreaks before many lives are affected. Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world. While low herd immunity levels to any one of the four antigenic types of DENV predispose populations to outbreaks, viral genetic determinants that confer greater fitness for epidemic spread is an important but poorly understood contributor of dengue outbreaks. Here we report that positive epistasis between the coding and noncoding regions of the viral genome combined to elicit an epidemiologic fitness phenotype associated with the 1994 DENV2 outbreak in Puerto Rico. We found that five amino acid substitutions in the NS5 protein reduced viral genomic RNA (gRNA) replication rate to achieve a more favorable and relatively more abundant subgenomic flavivirus RNA (sfRNA), a byproduct of host 5′-3′ exoribonuclease activity. The resulting increase in sfRNA relative to gRNA levels not only inhibited type I interferon (IFN) expression in infected cells through a previously described mechanism, but also enabled sfRNA to compete with gRNA for packaging into infectious particles. We suggest that delivery of sfRNA to new susceptible cells to inhibit type I IFN induction before gRNA replication and without the need for further de novo sfRNA synthesis could form a “preemptive strike” strategy against DENV.
Autologous chondrocyte implantation with a Reveille cartilage processor for articular cartilage injury: a case report

Abstract Autologous chondrocyte implantation (ACI) is an important operative option when repairing cartilage defects of the knee. This report introduces a new product development with one-stage ACI using a Reveille Cartilage Processor (Reveille CP) as well as the assessment of MRI and clinical results at a 1-year follow-up. The report compared cases between a 42-year-old female who underwent ACI surgery using Reveille CP and a 51-year old female who received treatment with two-stage ACI of tissue-engineered cartilage-like tissue (J-TEC Autologous Chondrocyte Cultured Cartilage [JACC]). One year after JACC, magnetic resonance imaging (MRI) showed signal intensity area in the grafted area, while patients with Reveille CP showed greater thickness than the surrounding healthy cartilage. The Lysholm, pain and QOL scores of Knee Injury and Osteoarthritis Outcome (KOOS) at one 1 year after surgery with Reveille CP were higher than JACC.
Supervised machine learning for coronary artery lumen segmentation in intravascular ultrasound images

Intravascular ultrasound (IVUS) has been widely used to capture cross sectional lumen frames of inner wall of coronary arteries. This kind of medical imaging modalities is capable of providing detailed and significant information of lumen contour shape, which is very important for clinical diagnosis and analysis of cardiovascular diseases. Numerous learning based techniques have recently become very popular for coronary artery segmentation due to their impressive results. In this work, a supervised machine learning method for coronary artery lumen segmentation with high accuracy and minimal user interaction is designed. The fully discriminative lumen segmentation method jointly learning a classifier the weak learners rely on and the features of the classifier is developed. Additionally, the theoretical supports of the Gradient Boosting framework used in this work and its quadratic approximation are presented. The proposed algorithm is tested on the public datasets of boundary detection of lumen in IVUS challenge held in MICCAI 2011 and achieves a higher average Jaccard similarity of 96.8% and a lower mean error distance of 0.55 (in Cartesian coordinates), which shows higher accuracy compared to the existing learning based methods. Moreover, three real patient IVUS datasets are used to evaluate the performance of the proposed coronary artery lumen segmentation algorithm, which is shown to achieve lower percent error of lumen area of 1.861% ± 0.965%, 1.968% ± 0.864%, and 1.671% ± 0.584%, respectively, compared to the manually measured lumen area (ground truth). The proposed lumen segmentation method is found to be superior to the latest learning based segmentation techniques. Given the efficiency and robustness, our method has great potential in IVUS images processing and coronary artery segmentation and quantification.
Characterisation of aroma‐active compounds, chemical and sensory properties of acid‐coagulated cheese: Circassian cheese

The objectives of this study were to determine basic composition, aroma and sensory characteristics of Circassian cheese. Seven Circassian cheeses were provided by local producers. Aroma compounds were extracted by using solid-phase microextraction procedure and determined by gas chromatography-olfactometry system. Water-soluble, trichloroacetic acid-soluble and phosphotungstic acid-soluble nitrogen fractions ranged between 2.30–29.35%, 2.48–9.96% and 3.33–6.26%, respectively. Diacetyl, butyric acid, 2-acetyl-1-pyrroline, 1-octen-3-one and methional were identified at high intensities in cheeses. In addition, ‘cooked’, ‘whey’, ‘creamy’ and ‘fermented’ were defined as characteristic flavour terms for Circassian cheeses.
IncN3 and IncHI2 plasmids with an In1763 integron carrying bla IMP-1 in carbapenem-resistant Enterobacterales clinical isolates from the UK.

Introduction. Imipenemase (IMP) carbapenemase genes are relatively rare among Enterobacterales in the UK. Emergence in multiple hospitals, in different strains and species, prompted an investigation into their genetic context.Aim. Our goal was to identify and describe the elements carrying bla IMP genes in a variety of Enterobacterales from five hospitals in the UK.Methodology. Long-read nanopore sequencing was carried out on 18 IMP-positive isolates belonging to 6 species. The locations of the bla IMP genes and other associated genetic elements were identified.Results. Ten out of 18 isolates carried bla IMP-1 on an IncN3 plasmid (52-57 kb) in an In1763 class 1 integron. These plasmids also contained genes encoding type IV secretion and conjugal transfer proteins. Five out of 18 isolates carried bla IMP-1 in the same In1763 integron in much larger IncHI2 plasmids. A further isolate carried the In1763 integron in a chromosomally located plasmid fragment. Two isolates carried bla IMP-4 in IncHI2 plasmids. The isolates included three representatives of sequence type 20 of Klebsiella pneumoniae, with one carrying a distinct plasmid from the other two.Conclusion. Highly similar IncN3 plasmids were found in a range of Enterobacterales, mostly K. pneumoniae and the Enterobacter cloacae complex, from three of four London hospitals, with the same In1763 integron carrying bla IMP-1 also being found in IncHI2 plasmids and chromosomally. These plasmids carried multiple elements facilitating self-transmission. Strain typing alone was not sufficient to investigate cross-infection among this set of isolates, many of which appeared to be unrelated until plasmid analysis was undertaken, and vice versa.
A Novel Detector Based on Convolution Neural Networks for Multiscale SAR Ship Detection in Complex Background

Convolution neural network (CNN)-based detectors have shown great performance on ship detections of synthetic aperture radar (SAR) images. However, the performance of current models has not been satisfactory enough for detecting multiscale ships and small-size ones in front of complex backgrounds. To address the problem, we propose a novel SAR ship detector based on CNN, which consist of three subnetworks: the Fusion Feature Extractor Network (FFEN), Region Proposal Network (RPN), and Refine Detection Network (RDN). Instead of using a single feature map, we fuse feature maps in bottom–up and top–down ways and generate proposals from each fused feature map in FFEN. Furthermore, we further merge features generated by the region-of-interest (RoI) pooling layer in RDN. Based on the feature representation strategy, the CNN framework constructed can significantly enhance the location and semantics information for the multiscale ships, in particular for the small ships. On the other hand, the residual block is introduced to increase the network depth, through which the detection precision could be further improved. The public SAR ship dataset (SSDD) and China Gaofen-3 satellite SAR image are used to validate the proposed method. Our method shows excellent performance for detecting the multiscale and small-size ships with respect to some competitive models and exhibits high potential in practical application.
Computational NMR Spectroscopy of Ionic Liquids: [C4C1im]Cl/Water Mixtures

In this work, I have analyzed the structure of binary mixtures of 1-butyl-3-methylimidazolium chloride ionic liquid, [C4C1im]Cl, and water, using computational NMR spectroscopy. The structure of the complex fluid phase, where the ionic and hydrophobic nature of ionic liquids is further complicated by the addition of water, is first generated by classical Molecular Dynamics (MD) and then validated by calculating the NMR properties with DFT at the ONIOM(B3LYP/cc-pVTZ//B3LYP/3-21G) on clusters extracted during the MD trajectories. Three ionic liquid/water mixtures have been considered with the [C4C1im]Cl mole fraction of 1.00, 0.50, and 0.01, that is the pure ionic liquid [C4C1im]Cl, the equimolar [C4C1im]Cl/water mixture, and a diluted solution of [C4C1im]Cl in water. A good agreement is obtained with published experimental data that, at the same time, validates the structural features obtained from the MD and the force field used, and provides an example of the power of NMR spectroscopy applied to complex fluid phases.
Progressive Metabolic Dysfunction and Nutritional Variability Precedes Necrotizing Enterocolitis

Necrotizing Enterocolitis (NEC) is associated with prematurity, enteral feedings, and enteral dysbiosis. Accordingly, we hypothesized that along with nutritional variability, metabolic dysfunction would be associated with NEC onset. Methods: We queried a multicenter longitudinal database that included 995 preterm infants (<32 weeks gestation) and included 73 cases of NEC. Dried blood spot samples were obtained on day of life 1, 7, 28, and 42. Metabolite data from each time point included 72 amino acid (AA) and acylcarnitine (AC) measures. Nutrition data were averaged at each of the same time points. Odds ratios and 95% confidence intervals were calculated using samples obtained prior to NEC diagnosis and adjusted for potential confounding variables. Nutritional and metabolic data were plotted longitudinally to determine relationship to NEC onset. Results: Day 1 analyte levels of alanine, phenylalanine, free carnitine, C16, arginine, C14:1/C16, and citrulline/phenylalanine were associated with the subsequent development of NEC. Over time, differences in individual analyte levels associated with NEC onset shifted from predominantly AAs at birth to predominantly ACs by day 42. Subjects who developed NEC received significantly lower weight-adjusted total calories (p < 0.001) overall, a trend that emerged by day of life 7 (p = 0.020), and persisted until day of life 28 (p < 0.001) and 42 (p < 0.001). Conclusion: Premature infants demonstrate metabolic differences at birth. Metabolite abnormalities progress in parallel to significant differences in nutritional delivery signifying metabolic dysfunction in premature newborns prior to NEC onset. These observations provide new insights to potential contributing pathophysiology of NEC and opportunity for clinical care-based prevention.
Diffusion Magnetic Resonance Imaging Phenotypes Predict Overall Survival Benefit From Bevacizumab or Surgery in Recurrent Glioblastoma With Large Tumor Burden.

BACKGROUND Diffusion magnetic resonance (MR) characteristics are a predictive imaging biomarker for survival benefit in recurrent glioblastoma treated with anti-vascular endothelial growth factor (VEGF) therapy; however, its use in large volume recurrence has not been evaluated. OBJECTIVE To determine if diffusion MR characteristics can predict survival outcomes in patients with large volume recurrent glioblastoma treated with bevacizumab or repeat resection. METHODS A total of 32 patients with large volume (>20 cc or > 3.4 cm diameter) recurrent glioblastoma treated with bevacizumab and 35 patients treated with repeat surgery were included. Pretreatment tumor volume and apparent diffusion coefficient (ADC) histogram analysis were used to phenotype patients as having high (>1.24 μm2/ms) or low (<1.24 μm2/ms) ADCL, the mean value of the lower peak in a double Gaussian model of the ADC histogram within the contrast enhancing tumor. RESULTS In bevacizumab and surgical cohorts, volume was correlated with overall survival (Bevacizumab: P = .009, HR = 1.02; Surgical: P = .006, HR = 0.96). ADCL was an independent predictor of survival in the bevacizumab cohort (P = .049, HR = 0.44), but not the surgical cohort (P = .273, HR = 0.67). There was a survival advantage of surgery over bevacizumab in patients with low ADCL (P = .036, HR = 0.43) but not in patients with high ADCL (P = .284, HR = 0.69). CONCLUSION Pretreatment diffusion MR imaging is an independent predictive biomarker for overall survival in recurrent glioblastoma with a large tumor burden. Large tumors with low ADCL have a survival benefit when treated with surgical resection, whereas large tumors with high ADCL may be best managed with bevacizumab.
mHealth Technologies Towards Parkinson's Disease Detection and Monitoring in Daily Life: A Comprehensive Review

Parkinson's disease (PD) can gradually affect people's lives thus attracting tremendous attention. Early PD detection and treatment can help control the disease progress, relief from the symptoms and improve the patients’ life quality. However, the current practice of PD diagnosis is conducted in a clinical setup and administrated by a PD specialist due to the early signs of PD are not noticeable in daily life. According to the report of CDC/NIH, the diagnosed time of PD ranges from 2-10 years after onset. Therefore, a more accessible PD diagnosis approach is urgently demanded. In recent years, mobile health (for short mHealth) technology has been intensively investigated for preventive medicine, particularly in chronic disease management. Notably, many types of research have explored the possibility of using mobile and wearable personal devices to detect the symptom of PD and shown promising results. It provides opportunities for transforming early PD detection from clinical to daily life. This survey paper attempts to conduct a comprehensive review of mHealth technologies for PD detection from 2000 to 2019, and compares their pros and cons in practical applications and provides insights to close the performance gap between state-of-the-art clinical approaches and mHealth technologies.
Serological Survey and Molecular Typing Reveal New Leptospira Serogroup Pomona Strains among Pigs of Northern Italy

Swine act as both maintenance and incidental hosts of pathogenic Leptospira spp. Here, a serological test was performed on 131,660 pig sera collected between 2002 and 2017 from 4715 farms in Northern Italy. A positivity rate of 13.05% was determined. Australis was the most frequently identified serogroup (77.29%), followed by Pomona (18.47%), Tarassovi (1.51%) and Icterohaemorrhagie (1.40%). Culture isolation and real-time Polymerase chain reaction (PCR) were carried out on 347 kidneys and 470 clinical samples, respectively. Overall, 133 strains were cultured successfully and 43 randomly chosen isolates were identified as serogroup Pomona. Multi-locus sequence typing (MLST) revealed that 41 isolates and 8 DNA extracted from biological samples belonged to sequence type 140. Using a multiple-locus, variable-number tandem repeat analysis, 43 samples produced identical profiles but, after 2014, three new Leptospira interrogans serogroup Pomona genotypes were observed. Interestingly, two isolates showed new MLST profiles and an unclassified identification by monoclonal antibodies. The 16S rRNA gene sequencing clustered them into L. kirschneri species and a core genome MLST analysis revealed an allelic identity of 96% compared with Mozdok strains. Genotyping allowed us to discriminate leptospires and to identify new emerging strains. The accurate identification of infective strains is required for formulating preventive methods and intervention strategies.
Nod factors and cytokinins induce similar cortical cell division, amyloplast deposition and MsEnod12A expression patterns in alfalfa roots

Summary Under nitrogen limitation, Rhizobium meliloti Nod factors induce cell divisions in the inner cortex of alfalfa roots in a still unknown way. These cell division clusters subsequently develop into symbiotically nitrogen-fixing nodules. To study the involvement of plant signals in nodule initiation transgenic alfalfa carrying the promoter of the early nodulin gene MsEnod12A fused to the reporter gene gusA were generated. In untreated plants, low level GUS staining was only found in lateral root primordia and in front of the root apices. After inoculation with R. meliloti or after treatment with purified Nod factors, GUS activity was first induced in the cell division foci of the inner cortex. The GUS staining patterns in nodules and roots were in agreement with the activation of the endogenous MsEnod12A gene as revealed by reverse transcription-PCR analysis, rendering the MsEnod12A-gusA fusion a valuable novel marker for studying the onset of nodule and lateral root developmental processes. Treatment of roots with purified Nod factors and cytokinins induced similar patterns of cortical cell division, GUS staining and amyloplast accumulation while upon application of auxin transport inhibitors and auxins these patterns were different. Like the Nod factor responses, the cytokinin responses required photosynthesis and limiting combined nitrogen supply. Thus, cytokinins and Nod factors may share elements of their signal transduction pathways to the inner root cortex. A model on the possible involvement of cytokinins in coordinating plant metabolism with nodule initiation is proposed.