Original Specimens Research Articles

Experimental Study Additional Brantas Sands Of Clay Density

Land functions as a supporting medium for all living activities. The problem that is often encountered is the level of soil stability at each location is different, for this reason the following research is used to determine the parameters of stable soil density when soil structure composed of clay components added 10% of sand from the total weight of the specimen with different diameter variations using proctor testing. The density properties of clay soil after the addition of brantas sand with size variations passed the sieves number 8, 10, 16 and 20 amounting to 10% in perfect solid state the structure of the original soil specimens showed an γd value of 9.61 gr / cm3, in addition of sand 10% with a diameter passing through number 8 shows an γd value of 10.44, at number 10 shows a value of γd 11.77, at number 16 shows the value γd 10.97 and in number 20 shows a value of γd 11.55. the addition of sand to the expansionary structure with low stability can improve the level of stability of the soil structure. Moreover, the addition of sand with a no. 10 sieve diameter shows the value of dry volume density γd of 11.77, the value shows the above average density parameter - average of several other test objects.

The aloes of Friedrich Wilms: notes on Aloe wilmsii Diels ex Hausen, A. affinis A.Berger, and A. cinnabarina Diels ex A.Berger (Asphodelaceae subfam. Alooideae), with a biographical sketch of Wilms

Collections of Aloe L. (Asphodelaceae subfam. Alooideae) made by Friedrich Wilms (1848–1919) are analysed. The identity of material described as Aloe wilmsii Diels ex Hausen about 120 years ago is clarified. This long-overlooked name belongs in the synonymy of Aloe arborescens Mill. The original specimens, also collected by Wilms, on which the names A. affinis A.Berger and A. cinnabarina Diels ex A.Berger are based, are discussed. Lectotypes are designated for A. wilmsii, A. affinis, and A. cinnabarina. Biographical information is provided on Wilms who is commemorated in the specific epithet of Aloe wilmsii.

A reclassification of Acanthocnemoides sukatshevae Zherikhin, 1977 from the mid-Cretaceous Taimyr amber (Coleoptera)

The cleroid beetle Acanthocnemoides sukatshevae Zherikhin, 1977 from the upper Albian Taimyr amber was originally assigned to Acanthocnemidae. New observations of the two original fossil specimens preserved in a single amber piece revealed that A. sukatshevae may be affiliated to Melyridae: Dasytinae and lie in close relation to the basal tribe Danaceini. This is the first and oldest record of the subfamily (former family Dasytidae) and an indication of the presence of flowering plants in an ecosystem of the Begichev Formation.

A new species and emendation of the seldom reported Enterohaematotrema Mehra, 1940 (Digenea: Schistosomatoidea), including a revised phylogenetic hypothesis for turtle blood flukes.

Enterohaematotrema Mehra, 1940 is emended herein based upon a review of the literature and a description of a new species (Enterohaematotrema triettruongi n. sp.) infecting yellow-headed temple turtles, Heosemys annandalii (Boulenger) (Cryptodira: Geoemydidae), in the Mekong River, Vietnam. The new species differs from the published descriptions of its congeners Enterohaematotrema palaeorticum Mehra, 1940 and Enterohaematotrema hepaticum (Simha, 1958) Simha & Chattopadhyaya, 1980 by having two distinctive oesophageal glands, a short and eversible cirrus (vs protrusive with 3 distinct processes), a dorsal common genital pore that is sinistral (vs ventral and medial), a transverse (vs longitudinal) external seminal vesicle, an oviducal seminal receptacle that is sinistral (vs dextral), and a vitellarium distributing from the caecal bifurcation (anterior to the ventral sucker) to the caecal tips (vs vitellarium not extending anteriad beyond ventral sucker in E. palaeorticum or vitellarium wholly posterior to the terminal genitalia in E. hepaticum). A phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) recovered Enterohaematotrema and Platt Roberts & Bullard, 2016 as sister taxa that share a recent common ancestor with the clade comprising Ruavermis Dutton & Bullard, 2020 and Coeuritrema Mehra, 1933. These flukes collectively comprise a monophyletic group of southeast Asian turtle blood flukes. This analysis also indicated that the massive, longitudinal metraterm of species of Enterohaematotrema and Uterotrema Platt & Pichelin, 1994 represents homoplasy (convergent evolution). The present study comprises the first morphological study of original specimens of any species of Enterohematotrema in more than 50 years and is the first molecular phylogenetic placement of the genus among the various turtle blood fluke lineages.

Conditional cell reprogramming for modeling host-virus interactions and human viral diseases.

Conventional cancer and transformed cell lines are widely used in cancer biology and other fields within biology. These cells usually have abnormalities from the original tumor itself, but may also develop abnormalities due to genetic manipulation, or genetic and epigenetic changes during long‐term passages. Primary cultures may maintain lineage functions as the original tissue types, yet they have a very limited life span or population doubling time because of the nature of cellular senescence. Primary cultures usually have very low yields, and the high variability from any original tissue specimens, largely limiting their applications in research. Animal models are often used for studies of virus infections, disease modeling, development of antiviral drugs, and vaccines. Human viruses often need a series of passages in vivo to adapt to the host environment because of variable receptors on the cell surface and may have intracellular restrictions from the cell types or host species. Here, we describe a long‐term cell culture system, conditionally reprogrammed cells (CRCs), and its applications in modeling human viral diseases and drug discovery. Using feeder layer coculture in presence of Y‐27632 (conditional reprogramming, CR), CRCs can be obtained and rapidly propagated from surgical specimens, core or needle biopsies, and other minimally invasive or noninvasive specimens, for example, nasal cavity brushing. CRCs preserve their lineage functions and provide biologically relevant and physiological conditions, which are suitable for studies of viral entry and replication, innate immune responses of host cells, and discovery of antiviral drugs. In this review, we summarize the applications of CR technology in modeling host‐virus interactions and human viral diseases including severe acute respiratory syndrome coronavirus‐2 and coronavirus disease‐2019, and antiviral discovery.

An unusual papier-mâché replica of a fossil (?) from the Free Church of Scotland College collection

A puzzling item of hollow painted papier-m�ch�, apparently a replica of a fossil and purportedly made about 1837, was acquired by the then Royal Scottish Museum in 1966 from the Free Church of Scotland College, Edinburgh, presumably from the latter�s natural sciences teaching collection. It resembles a fossil reptile vertebra or chunk of plant root, but the original specimen and identification remain unknown. The replica does not appear to be a cast from a mould. The inherent limitations and potentials of the technique used, apparently combining three-dimensional modelling and accentuated paintwork, raise the possibility that it was made for Professor John Fleming by his wife Melville Christie as a teaching aid for his lectures at King�s College, Aberdeen, or the Free Church College. The use of papier-m�ch� and paper to make replicas of fossils is briefly discussed.

Conditionally Reprogrammed Human Normal Airway Epithelial Cells at ALI: A Physiological Model for Emerging Viruses.

Cancer cell lines have been used widely in cancer biology, and as biological or functional cell systems in many biomedical research fields. These cells are usually defective for many normal activities or functions due to significant genetic and epigenetic changes. Normal primary cell yields and viability from any original tissue specimens are usually relatively low or highly variable. These normal cells cease after a few passages or population doublings due to very limited proliferative capacity. Animal models (ferret, mouse, etc.) are often used to study virus-host interaction. However, viruses usually need to be adapted to the animals by several passages due to tropism restrictions including viral receptors and intracellular restrictions. Here we summarize applications of conditionally reprogrammed cells (CRCs), long-term cultures of normal airway epithelial cells from human nose to lung generated by conditional cell reprogramming (CR) technology, as an ex vivo model in studies of emerging viruses. CR allows to robustly propagate cells from non-invasive or minimally invasive specimens, for example, nasal or endobronchial brushing. This process is rapid (2 days) and conditional. The CRCs maintain their differentiation potential and lineage functions, and have been used for studies of adenovirus, rhinovirus, respiratory syncytial virus, influenza viruses, parvovirus, and SARS-CoV. The CRCs can be easily used for air-liquid interface (ALI) polarized 3D cultures, and these coupled CRC/ALI cultures mimic physiological conditions and are suitable for studies of viral entry including receptor binding and internalization, innate immune responses, viral replications, and drug discovery as an ex vivo model for emerging viruses.

Optimisation of Shear and Lateral–Torsional Buckling of Steel Plate Girders Using Meta-Heuristic Algorithms

The shear buckling of web plates and lateral–torsional buckling are among the major failure modes of plate girders. The importance of the lateral–torsional buckling capacity of plate girders was further evidenced when several plate girders of a bridge in Edmonton, Alberta, Canada failed in 2015, because insufficient bracing led to the lateral buckling of the plate girders. In this study, we focus on the optimisation of the cross-sections of plate girders using a well-known and extremely efficient meta-heuristic optimisation algorithm called the harmony search algorithm. The objective of this optimisation is to design the cross-sections of the plate girders with the minimum area that satisfies requirements, such as the lateral–torsional buckling load and ultimate shear stress. The base geometry, material properties, applied load and boundary conditions were taken from an experimental study and optimised. It was revealed that the same amount of load-carrying capacity demonstrated by this model can be achieved with a cross-sectional area 16% smaller than that of the original specimen. Furthermore, the slenderness of the web plate was found to have a decisive effect on the cost-efficiency of the plate girder design.

Impact of neutron irradiation on the strength and ductility of pure and ZrC reinforced tungsten grades

The strength and ductility of two tungsten products, developed for application in nuclear fusion environment, are studied before and after neutron irradiation using uniaxial tensile tests. The first product is a commercially pure tungsten, produced by AT&M company according to ITER specification, and the second one is reinforced with zirconium carbide (W–ZrC) particles. The addition of ZrC particles leads to a reduction of the ductile to brittle transition temperature (DBTT) in non-irradiated conditions down to 50–100 °C without loss of strength and of other attractive properties of tungsten.The neutron irradiation was performed in the range 625–700 °C up to 1.125 dpa. The tests were performed to screen the shift of the DBTT as well as to characterize the evolution of the strength and ductility at the irradiation temperature. In addition, a series of interrupted tensile tests were performed in order to determine the variation of the yield strength as a function of temperature using an original single specimen test method.The neutron irradiation causes the reduction of the total elongation of both tungsten products. The DBTT range, which was evaluated from the tensile test results, of W–ZrC lies in the 300–500 °C range (while it is ∼100 °C in non-irradiated state). The DBTT range of pure tungsten is between 400 and 575 °C i.e. higher than that of W–ZrC. The irradiation hardening, measured at ∼600 °C, which is close to the irradiation temperature, leads to an increase of the proof stress by a factor of two in both studied grades. Despite that the irradiation induced hardening, both products retain a total elongation of about 10% prior to fracture. W–ZrC exhibits a similar total elongation at 500 °C, thus maintaining a significant ductility resource, while pure W becomes brittle at 500 °C and below.

Incidence, Risk Factors and Outcomes of Cancer of the Anal Transitional Zone in Patients with Ulcerative Colitis.

Performing a mucosectomy with a hand-sewn ileal pouch-anal anastomosis [IPAA] for ulcerative colitis [UC] theoretically reduces the risk of carcinoma arising from the anal transitional zone [ATZ]. Although current guidelines suggest a stapled anastomosis due to the low incidence of cancer after pouch surgery in UC patients, only a few small series have addressed the oncological advantage of mucosectomy. Therefore, we aimed to investigate the incidence of ATZ/pouch cancer. A total of 1970 UC patients who underwent surgery between April 1987 and December 2018 were included. We retrospectively analysed the incidences of primary ATZ cancer in the original operative specimen and de novo ATZ/pouch cancer after surgery. Possible risk factors for primary ATZ cancer and the pouch survival rate were assessed. Fourteen [6.4%] primary ATZ cancers developed in 220 UC-colorectal cancer [CRC] cases. Multiple (odds ratio [OR] = 8.79, 95% confidence interval [CI] 2.77-27.83, p < 0.01) and rectal [OR = 6.48, 95% CI 1.41-29.7, p = 0.01] cancers were identified as independent risk factors for primary ATZ cancer. Four of 1970 [0.2%] patients developed de novo ATZ/pouch cancer and dysplasia. The 10-year estimated cumulative pouch survival rate was not significantly different between stapled IPAA and hand-sewn IPAA cases [95.9% and 97.3%, p = 0.25]. The risk of de novo ATZ/pouch cancer and dysplasia was rare. The decision to perform a hand-sewn or a stapled IAA should be made on a case-by-case basis. However, the relatively high incidence of primary ATZ cancer in UC patients with CRC suggests that mucosectomy should be recommended for this patient group.

Decoupling Functional and Morphological Convergence, the Study Case of Fossorial Mammalia

The original specimens are stored at the Tsukuba Natural History Museum, Tsukuba, Japan; Los Angeles County Natural History Museum, US; Wien Natural History Museum, Austria, Paris Natural History Museum, France; Lyon Natural History Museum, France; Lisbon Natural History Museum, Portugal.

Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources

ObjectivesTo establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2.MethodsThe most efficient pool size was determined to be five specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 µL from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 µL each) for a total volume of 250 µL. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12 pools.ResultsAll 25 pools were positive with cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that 2 pools were positive followed by identification of 2 individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions.ConclusionsWhen the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.

Tragopogon abbreviatus (Asteraceae): a little-known species inferred from morphological and molecular analysis

Tragopogon porrifolius occurs in Turkey with 3 taxonomically confused subspecies: T. porrifolius subsp. eriospermus, T. porrifolius subsp. longirostris, and T. porrifolius subsp. abbreviatus. In the present paper, T. porrifolius subsp. abbreviatus endemic to Turkey is raised at specific level based on morphological and molecular analysis. After detailed assessment of original herbarium specimens and literature studies, we found that this name is not typified yet. Thus, a lectotype is provided together with an emended diagnosis; synonym, distribution map, and conservation status for the first time. Additionally, a preliminary phylogenetic position of this little-known taxon is given on several newly sequenced data.

Characterisation of Steinernema surkhetense and Its Symbiont Xenrorhabdus stockiae and A Note on Its Geographical Distribution

Two cultured populations of Steinernema surkhetense are described from India. Morphologically and morphometrically this material agrees with other species of the Carpocapsae-group (presence of short juveniles), especially with S. surkhetense. The morphology was somewhat similar to the original description with the distinguishing feature being the presence of anal swelling in second-generation female specimens but absent in the original specimens. The morphometric measurements were in close proximity to those in the original specimens and the PCA analysis of important morphometric characters demonstrated some variability within the test populations. Molecular studies based on 28S and ITS rDNA confirmed the Indian material is well conspecific Nepali populations of S. surkhetense, however, with Nepali populations, two base pair differences were observed at 376 and 713 positions only in ITS rDNA gene. We performed a molecular and biochemical characterization of the bacterial symbiont of S. surkhetense and the symbiont is closely related to Xenorhabdus stockiae, which is widespread among South Asian nematodes from the ‘‘carpocapsae’’ group. Finally, we mapped its geographical distribution using a meta-analysis of the ITS GenBank records. The distribution of S. surkhetense based on a meta-analysis of the GenBank records showed its presence in the three Asian countries—India, China, and Nepal, with maximum records from the Indian subcontinent. This species is indigenous to the Indian subcontinent, thus could be tested and later used in the biocontrol of insect pests in India

Designing an Herbarium Digitisation Workflow with Built-In Image Quality Management.

Digitisation of natural history collections has evolved from creating databases for the recording of specimens’ catalogue and label data to include digital images of specimens. This has been driven by several important factors, such as a need to increase global accessibility to specimens and to preserve the original specimens by limiting their manual handling. The size of the collections pointed to the need of high throughput digitisation workflows. However, digital imaging of large numbers of fragile specimens is an expensive and time-consuming process that should be performed only once. To achieve this, the digital images produced need to be useful for the largest set of applications possible and have a potentially unlimited shelf life. The constraints on digitisation speed need to be balanced against the applicability and longevity of the images, which, in turn, depend directly on the quality of those images. As a result, the quality criteria that specimen images need to fulfil influence the design, implementation and execution of digitisation workflows. Different standards and guidelines for producing quality research images from specimens have been proposed; however, their actual adaptation to suit the needs of different types of specimens requires further analysis. This paper presents the digitisation workflow implemented by Meise Botanic Garden (MBG). This workflow is relevant because of its modular design, its strong focus on image quality assessment, its flexibility that allows combining in-house and outsourced digitisation, processing, preservation and publishing facilities and its capacity to evolve for integrating alternative components from different sources. The design and operation of the digitisation workflow is provided to showcase how it was derived, with particular attention to the built-in audit trail within the workflow, which ensures the scalable production of high-quality specimen images and how this audit trail ensures that new modules do not affect either the speed of imaging or the quality of the images produced.

Seismic performance of precast segmental bridge columns repaired with CFRP wraps

Precast segmental bridge columns (PSBCs) have many advantages compared with monolithic bridge columns. However, PSBCs could be severely damaged during an earthquake due to their limited seismic capacity. Rapid repair of the PSBCs and the seismic behavior of the repaired PSBCs are critical to the post-earthquake recovery of bridges with such columns. In this study, an original PSBC specimen is designed, constructed, and tested under cyclic loading. After the cyclic test on the original specimen is carried out, carbon fiber reinforced polymer (CFRP) sheets and sticky steel glue are used to repair the damaged specimen. The repaired PSBC specimen is then tested under the same loading protocol as the original specimen to compare their cyclic performance. Test results show that the concrete damage of the repaired specimen is reduced compared to the original specimen, and the repaired column has a relatively larger energy dissipation and residual displacement than those of the original column. To leverage the test results, detailed three-dimensional finite element models are developed and calibrated with the results from the experiments. Closely replicating the test results, the validated finite element models are used to replace the lab experiments for the parametric modeling of the seismic performance of bridges with PSBCs while capturing effects of CFRP. Specifically, the influence of CFRP design variables, including the CFRP cross-sectional area ratio and the CFRP height ratio, on the seismic performance of the repaired PSBCs is evaluated by using the validated finite element model. It is found that the CFRP cross-sectional area ratio has little effect on the seismic capacity of the repaired PSBCs, and the repaired PSBC with a CFRP height ratio of 2.0 is the most suitable for the repaired PSBCs investigated in this study.

Fatigue behaviors of foreign object damaged Ti-6Al-4V alloys under laser shock peening

Two-sided and simultaneous laser shock peening (TSLSP) was used to strengthen the Ti-6Al-4V titanium alloy. The fatigue crack growth rate of the specimens was investigated by fatigue test. The results show that both direct TSLSP (TSLSP-D) and indirect TSLSP (TSLSP-I) can reduce the fatigue crack growth rate by producing high magnitude compressive residual stress. The maximum fatigue life increases by 94% (TSLSP-D) and 169% (TSLSP-I) compared with the original specimens. Moreover, the TSLSP-D results show decreased resistance to foreign object damage because of decreased plasticity while the TSLSP-I simultaneously achieves superior foreign object damage resistance and fatigue performance.

Effect of thermal cycling on mechanical and thermal properties of basalt fibre-reinforced epoxy composites

Current study investigated the effect of thermal fatigue on mechanical and thermal properties of basalt fibre-reinforced polymer (BFRP) composites. To this, basalt fibre textiles in 2/2 twill pattern was used to fabricate BFRP composites. Thermal cycling experiment was carried out between $$-40$$ and $$+120^{\circ }$$ C for 20, 40, 60, 80 and 120 cycles. Moreover, dynamic mechanical analyzer (DMA) was used to evaluate the effect of thermal cycling on thermal properties of BFRPs. Moreover, we compared the extracted viscoelastic characteristics, such as storage modulus, loss modulus and loss factor curves with original thermal-treated BFRP specimens. Based on the results, thermal cycling affected the characteristics of composites in the post-curing stage due to an increase in temperature. Finally, the effect of thermal cycling on water absorption properties of BFRP composites was examined by hydrophobicity test. The results showed that tensile strength, flexural modulus and ILSS values increased with the increase in the number of cycles up to 80 cycles. In other words, an increase in the number of cycles increased the hydrophobicity of BFRP composites by decreasing the contact angles. Finally, the mechanical properties of tested composites were significantly decreased when the number of cycles reached 120. This was due to the mismatch of thermal expansion coefficient and long crack formation in the structure of composite.

The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini)

DNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools and taxonomists will soon not have utility. Here we demonstrate that DNA-based identification is not reliable without the contributions of taxonomic experts. We use ambrosia beetles (Xyleborini), which are known for great diversity as well as global invasions and damage, as a test case. Recent xyleborine introductions have caused major economic and ecological losses, thus timely species identifications of new invaders are necessary. This need is hampered by a paucity of identification tools and a fauna that is only moderately documented. To help alleviate deficiencies in their identification, we created COI and CAD DNA barcode databases (490 and 429 specimens), representing over half of the known fauna of Southeast Asia (165/316 species). Taxonomic experts identified species based on original descriptions and type specimens. Tree, distance, and iterative methods were used to assess the identification and delimitation of species. High intra- and interspecific COI distances were observed for congeneric species and attributed to the beetle’s inbreeding system. Neither of the two markers provided 100% identification success but with the neighbor-joining tree-based method, 80% of species were identified by both genes. As for species delimitation, an obvious barcode gap between intra- and interspecific differences was not observed. Correspondence between distance-based groups and morphology-based species was poor. In a demonstration of iterative taxonomy, we constructed parsimony-based phylogenies using COI and CAD sequences for two genera. Although not all clades were resolved or supported, we provided better explanations for species boundaries in light of morphological and DNA sequence differences. Confident species identifications demonstrated 10–12% COI and/or >2–3% CAD. Involvement of taxonomic experts from the start of this project was essential for the creation of a stable foundation for the DNA identification of xyleborine species. In general, their role in DNA barcoding cannot be underestimated and is further discussed.

On the taxonomy and distribution of Varanus salvator andamanensis Deraniyagala, 1944 (Reptilia: Varanidae), including a redescription of the type specimens and a discussion about its allopatric co-occurrence with V. s. macromaculatus on the Nicobar Islands.

We provide a detailed redescription of the two original type specimens of the little-known, endemic Andaman water monitor, Varanus salvator andamanensis Deraniyagala, 1944. Examination of further voucher specimens allows for an expanded morphological diagnosis of this island taxon and comparison with other currently recognized subspecies of the wide-spread Southeast Asian water monitor. Based on the specimens examined, V. s andamanensis is characterized by a homogenous black dorsal background colour, with five to seven, more or less distinctive transverse rows of small spots or ocelli, light yellowish dots arranged sporadically between transverse spot/ocelli rows on the body, light yellowish coloured spots distributed sporadically throughout both forelimbs and hind limbs; 17-18 prominent rows of light spots continuing from base of tail to its tip dorsally with sporadically arranged dots on lateral sides of tail; and higher scale counts in transverse dorsal scale rows. Based on photographic evidence and examination of museum specimens, V. s. andamanensis inhabits both the Andaman and southern Nicobar Islands, which politically belong to the Republic ofIndia. In addition, we confirm the presence of V. s. macromaculatus in the northern and central Nicobar Islands, thus providing evidence for the allopatric co-occurrence of two different water monitor subspecies in these remote archipelagos.