Molecular investigations in date palm genetic structure and diversity among commercially important date palm cultivars (Phoenix dactylifera L.)

2019 Fall.Includes bibliographical references.The date palm, Phoenix dactylifera L. is the notable palm which produces a nutrient-rich edible fruit (the date), well known for its unique attributes of medicine and healthy energy. It is a species that has been cultivated since early civilizations in the fertile crescent and later in the Middle East. It is typically cloned with many cultivars (over 3000). A means of accurately identifying specific clones and an understanding of the relationships among major commercial cultivars would provide valuable information for the maintenance, potentially an improvement and continued conservation of superior genotypes. Phylogenetic relationships amid commercial date cultivars are poorly understood, despite their importance. This research aimed at providing applicable knowledge through an expedient technique, by developing an exclusively tailored Simple Sequence Repeat (SSR) panel, custom-made for date palm fingerprinting and molecular identification also named as 'Dates PalmàPrinting'. This assembled modified genotyping by microsatellite markers provides a standardized approach to cultivar identification and a quality control application in date palm micropropagation production. A deeper understanding and relationship of today's major commercial cultivars is incomplete. Improving the development and productivity of this tree species is restricted due to few genetic resources. Only regionally narrowed studies have been conducted but it is more important to have a broader base of such knowledge. The present research reports on 20 selected, commercially important date palm cultivars, consisting of 18 females and 2 males, which are grown throughout the world. The knowledge of relationships among these cultivars is needed, although the date palm genome has been mostly sequenced (90.2 %) with 41,660 gene models representing an 82,354 scaffold. The relationships among the major cultivars remain unclear. Presently, the information on the characterization of these cultivars requires an assessment to better understand the relationships among the superior genotypes. The use of microsatellites, due to their accuracy and high polymorphic capability, have led to fine scaled phylogenies. The phylogenetic relationships were determined using neighbor joining un-rooted trees correlated with genetic structure clustering. Primer selections were achieved from evaluation of 14 nuclear SSR loci isolated from P. dactylifera. Results revealed a high degree of polymorphism observed in the 20 cultivars with fewer common alleles than anticipated. Within the cultivars studied, a broad heterozygosity across base pair (bp) amplification data has led to an understanding of limited inbreeding, accounting for possible adaptation to environmental changes and revealing conserved extensive array of genomic structure. Population structure analysis suggests a large genetic boundary between Northwest African and Middle Eastern cultivars with 6 subpopulations that represent divergences and fragments of admixture in cultivars present in these regions. The possible selection of potential and good quality parents is achievable for improving cultivars by generating population and structure maps. This analysis documents patterns of relationship and provides genetic structure and diversity of gene pool specificity complexes of date palm cultivars. This study provides insights about the relationships that exist among cultivars of interest through genetic sequence analysis using SSRs, facilitating the development of a standard approach to identification and enhancements to the micropropagation process. Keywords: Microsatellites, Phoenix dactylifera L., Simple sequence repeats, Phylogenetics, Genetic structure, Date palm, Genetic diversit

Characterization and structural properties of bamboo fibre solid foams

In this work, cellulose fibres extracted from bamboo culms were used to fabricate two types of cellular materials: rigid foams and fibrous networks. A relatively simple and low-technology fabrication method is presented, using natural binders and blowing agents to manufacture rigid foams, and fibrillation by partial hydrolysis in H2SO4 to manufacture fibrous networks. The compressive response is related to the internal microstructure and processing parameters. In the case of fibrous networks, the achievable relative density range is determined by the length of initial fibres and extent of external fibrillation. The compressive properties are dictated both by the density of the network and strength of the fibrous bridges, showing a linear stiffness-density relationship due to the length of fibres, and an inverse relationship at increased external fibrillation. The rigid foams showed an orthotropic internal microstructure but nearly isotropic compressive response, due to the influence of the interpenetrating void structure on the deformation and fracture mechanisms. The results show the potential of bamboo-fibre porous materials as low cost, lightweight structural materials

Cutibacterium (formerly Propionibacterium) acnes clavicular infection.

Cutibacterium (formerly Propionibacterium) acnes13, 16 is a slow growing, gram-positive bacteria that is naturally found in higher concentrations as skin flora on the chest and back, as well as in other areas with greater numbers of hair follicles.25, 37 Most of the reported cases of C. acnes shoulder girdle infection follow arthroplasty surgery,18, 20, 26, 27, 32, 35 which then often requires debridement, administration of intravenous antibiotics, and surgical revision of the implanted device.12, 15, 21, 28-30 In a recent study, 56% of 193 shoulder revisions had a positive culture, 70% of which grew C. acnes.30 Despite the relatively common presumed association of C. acnes humeral osteomyelitis with prosthetic infection, infection of the scapula or clavicle secondary to C. acnes is rare.4, 23, 36 Osteomyelitis of the clavicle involving any organism is also an uncommon event that can arise spontaneously via presumed hematogenous spread, or secondary to open fractures or internal fixation.6, 33 The most commonly found organism in clavicular osteomyelitis is Staphylococcus aureus.9 We here report two cases of clavicular infection secondary to C. acnes that were not associated with implants

Transfer Learning with Deep Convolutional Neural Network (CNN) for Pneumonia Detection using Chest X-ray

Pneumonia is a life-threatening disease, which occurs in the lungs caused by either bacterial or viral infection. It can be life-endangering if not acted upon in the right time and thus an early diagnosis of pneumonia is vital. The aim of this paper is to automatically detect bacterial and viral pneumonia using digital x-ray images. It provides a detailed report on advances made in making accurate detection of pneumonia and then presents the methodology adopted by the authors. Four different pre-trained deep Convolutional Neural Network (CNN)- AlexNet, ResNet18, DenseNet201, and SqueezeNet were used for transfer learning. 5247 Bacterial, viral and normal chest x-rays images underwent preprocessing techniques and the modified images were trained for the transfer learning based classification task. In this work, the authors have reported three schemes of classifications: normal vs pneumonia, bacterial vs viral pneumonia and normal, bacterial and viral pneumonia. The classification accuracy of normal and pneumonia images, bacterial and viral pneumonia images, and normal, bacterial and viral pneumonia were 98%, 95%, and 93.3% respectively. This is the highest accuracy in any scheme than the accuracies reported in the literature. Therefore, the proposed study can be useful in faster-diagnosing pneumonia by the radiologist and can help in the fast airport screening of pneumonia patients.Comment: 13 Figures, 5 tables. arXiv admin note: text overlap with arXiv:2003.1314

Occult Breast Cancer Metastasis Presenting as Acute Liver Failure

CASE: A 45 year-old-female with history of clinically stage IA ER/PR/Her-2 Negative moderately differentiated ductal carcinoma of right breast presented with abdominal pain, abdominal distension, jaundice, and scleral icterus three weeks after laparoscopic cholecystectomy due to acute cholecystitis. Intraoperatively her liver was noted to be cirrhotic and an intraoperative biopsy was done. Upon discharge after surgery her total bilirubin remained elevated. On presentation she showed signs of acute liver failure and coagulopathy with a bilirubin of 10.5, INR was elevated to 2.8, and AST/ALT downtrending. Clinically she continued to have increased abdominal pain and distension, jaundice, and scleral icterus. Intraoperative biopsy pathology showed fragments of benign liver cyst with granulomatous inflammation. During her hospital course she continued to display worsening liver function with elevated AST/ALT, total bilirubin, alkaline phosphatase, and INR. Post-surgical complications including bile leak, viral, autoimmune, and granulomatous causes of acute liver failure were excluded. Further evaluation with transjugular hepatic biopsy was done due to limited diagnostic value of previous biopsy, and revealed cirrhosis. Immunohistochemical staining was positive for GATA-3 immunostain and CK-7 stain, revealing adenocarcinoma most consistent with primary breast carcinoma. DISCUSSION: Acute Liver Failure (ALF) is defined as sudden liver dysfunction manifesting as coagulopathy and any degree of encephalopathy in a patient without preexisting cirrhosis with illness lasting less than 26 weeks\u27 duration. As much as 20-40% of ALF is due to unclear causes. Hepatic metastases have been identified in up to 40% of adults with malignant tumors. In the case of breast cancer metastases,the liver is considered to among the common sites of metastasis, along with lungs and bone. However, most metastases present in the form of a discrete mass, and patients do not usually present with liver disease. Isolated liver metastases from breast cancer is rare and only seen in 5-12% of breast cancer patients. Prior studies have shown that isolated liver involvement prognosis improves if patients have hormone positive cancer, normal liver function, good performance status, and have had a long Disease Free Interval (DFI). Resection of liver metastasis is indicated of helical CT or MRI demonstrates well-circumscribed mass that can be excised without further damaging liver function. Diffuse liver metastasis is very rare and difficult to diagnose as they are not identifiable on routine radiologic diagnostic studies. There are multiple case reports of occult metastatic breast cancer in the liver presenting with acute liver failure, in patients with a history of known and treated breast cancer. The majority of these cases are only identified as metastasis from breast cancer primary upon autopsy, as the prognosis for such a presentation of metastatic breast cancer is appalling. In few reported cases, early diagnosis and treatment resulted in some improvement beyond the 18-24 months expected prognosis in metastatic breast cancer. CONCLUSION: Our patient presents a challenging case in which liver function and performance status was poor prior to diagnosis of metastasis. Helical CT also demonstrated a unique presentation of cirrhotic liver with vastly diffuse metastatic lesions, with no circumscribed mass seen. The findings of this case emphasize the unique presentations of metastatic breast cancer in patients who are in remission, necessitating a broader differential diagnosis at time of presentation.https://scholarlycommons.henryford.com/merf2019caserpt/1123/thumbnail.jp

A Kernel-Based Change Detection Method to Map Shifts in Phytoplankton Communities Measured by Flow Cytometry

1. Automated, ship-board flow cytometers provide high-resolution maps of phytoplankton composition over large swaths of the world\u27s oceans. They therefore pave the way for understanding how environmental conditions shape community structure. Identification of community changes along a cruise transect commonly segments the data into distinct regions. However, existing segmentation methods are generally not applicable to flow cytometry data, as these data are recorded as ‘point cloud’ data, with hundreds or thousands of particles measured during each time interval. Moreover, nonparametric segmentation methods that do not rely on prior knowledge of the number of species are desirable to map community shifts. 2. We present CytoSegmenter, a kernel-based change-point estimation method for segmenting point cloud data. Our method allows us to represent and summarize a point cloud of data points by a single element in a Hilbert space. The change-point locations can be found using a fast dynamic programming algorithm. 3. Through an analysis of 12 cruises, we demonstrate that CytoSegmenter allows us to locate abrupt changes in phytoplankton community structure. We show that the changes in community structure generally coincide with changes in the temperature and salinity of the ocean. We also illustrate how the main parameter of CytoSegmenter can be easily calibrated using limited auxiliary annotated data. 4. CytoSegmenter is generally applicable for segmenting series of point cloud data from any domain. Moreover, it readily scales to thousands of point clouds, each containing thousands of points. In the context of flow cytometry data collected during research cruises, it does not require prior clustering of particles to define taxa labels, eliminating a potential source of error. This represents an important advance in automating the analysis of large datasets now emerging in biological oceanography and other fields. It also allows for the approach to be applied during research cruises