Energy-dispersive X-ray Spectroscopy for the Quantitative Analysis of Pyrite Thin Specimens

To explore ways to improve the accuracy of quantitative analysis of samples in the micrometer to nanometer range of magnitudes,we adopted analytical transmission electron microscopy(AEM/EDS)for qualitative and quantitative analysis of pyrite materials.Additionally,the k factor of pyrite is calculated experimentally.To develop an appropriate non-standard quantitative analysis model for pyrite materials,the experimentally calculated k factor is compared with that estimated from the non-standard quantitative analytical model of the instrument software.The experimental findings demonstrate that the EDS attached to a TEM can be employed for precise quantitative analysis of micro-and nanoscale regions of pyrite materials.Furthermore,it serves as a reference for improving the results of the EDS quantitative analysis of other sulfides.

Bird specimen number linked with species trait and climate niche breadth

Biological specimens are fundamental for taxonomy and flora/fauna research.More importantly,they also play crucial roles in recording environmental impacts on morphology and behavior,which is vital for biodiversity research and conservation.However,there are few systematic studies on the patterns and drivers of bird specimen number at regional scales.This study is the first attempt to examine the relationships between bird specimen number and species traits as well as climate niche breadth in China,aiming to answer two questions:1)how do species’temperature niche breadth and precipitation niche breadth influence specimen number?2)which trait is most associated with bird specimen number?The associations between bird specimen number and explanatory variables were examined using ordinary least squares,generalized linear models,phylogenetic generalized linear mixed models,and multiple comparisons.The results showed that Muscicapidae was the family with the highest specimen number,and Passeriformes was the order with the highest specimen number.Bird specimen number significantly increased with larger temperature niche breadth and precipitation niche breadth.Specimen number was also positively associated with geographic range size,habitat specificity,hunting vulnerability and clutch size,but negatively associated with body size.These findings suggest that future bird specimen collection should pay more attention to birds with limited ecological niches,large body sizes,and small clutch sizes.This research enhances the use of bird specimen data to study and preserve biodiversity.

Species’ geographical range, environmental range and traits lead to specimen collection preference of dominant plant species of grasslands in Northern China

Many different factors,such as species traits,socio-economic factors,geographical and environmental factors,can lead to specimen collection preference.This study aims to determine whether grassland specimen collection in China is preferred by species traits(i.e.,plant height,flowering and fruiting period),environmental range(i.e.,the temperature and precipitation range)and geographical range(i.e.,distribution range and altitudinal range).Ordinary least squares models and phylogenetic generalized linear mixed models were used to analyze the relationships between specimen number and the explanatory variables.Random Forest models were then used to find the most parsimonious multivariate model.The results showed that interannual variation in specimen number between 1900 and 2020 was considerable.Specimen number of these species in southeast China was notably lower than that in northwest China.Environmental range and geographical range of species had significant positive correlations with specimen number.In addition,there were relatively weak but significant associations between specimen number and species trait(i.e.,plant height and flowering and fruiting period).Random Forest models indicated that distribution range was the most important variable,followed by flowering and fruiting period,and altitudinal range.These findings suggest that future floristic surveys should pay more attention to species with small geographical range,narrow environmental range,short plant height,and short flowering and fruiting period.The correction of specimen collection preference will also make the results of species distribution model,species evolution and other works based on specimen data more accurate.

Direct Pointwise Comparison of FE Predictions to StereoDIC Measurements:Developments and Validation Using Double Edge-Notched Tensile Specimen

To compare finite element analysis(FEA)predictions and stereovision digital image correlation(StereoDIC)strain measurements at the same spatial positions throughout a region of interest,a field comparison procedure is developed.The procedure includes(a)conversion of the finite element data into a triangular mesh,(b)selection of a common coordinate system,(c)determination of the rigid body transformation to place both measurements and FEA data in the same system and(d)interpolation of the FEA nodal information to the same spatial locations as the StereoDIC measurements using barycentric coordinates.For an aluminum Al-6061 double edge notched tensile specimen,FEA results are obtained using both the von Mises isotropic yield criterion and Hill’s quadratic anisotropic yield criterion,with the unknown Hill model parameters determined using full-field specimen strain measurements for the nominally plane stress specimen.Using Hill’s quadratic anisotropic yield criterion,the point-by-point comparison of experimentally based full-field strains and stresses to finite element predictions are shown to be in excellent agreement,confirming the effectiveness of the field comparison process.

Stability of SARS Coronavirus in Human Specimens and Environment and Its Sensitivity to Heating and UV Irradiation

Objective The causal agent for SARS is considered as a novel coronavirus that has never been described both in human and animals previously. The stability of SARS coronavirus in human specimens and in environments was studied. Methods Using a SARS coronavirus strain CoV-P9, which was isolated from pharyngeal swab of a probable SARS case in Beijing, its stability in mimic human specimens and in mimic environment including surfaces of commonly used materials or in household conditions, as well as its resistances to temperature and UV irradiation were analyzed. A total of 106 TCID50 viruses were placed in each tested condition, and changes of the viral infectivity in samples after treatments were measured by evaluating cytopathic effect (CPE) in cell line Vero-E6 at 48 h after infectionn. Results The results showed that SARS coronavirus in the testing condition could survive in serum, 1:20 diluted sputum and feces for at least 96 h, whereas it could remain alive in urine for at least 72 h with a low level of infectivity. The survival abilities on the surfaces of eight different materials and in water were quite comparable, revealing reduction of infectivity after 72 to 96 h exposure. Viruses stayed stable at 4℃, at room temperature (20℃) and at 37℃ for at least 2 h without remarkable change in the infectious ability in cells, but were converted to be non-infectious after 90-, 60- and 30-min exposure at 56℃, at 67℃ and at 75℃, respectively. Irradiation of UV for 60 min on the virus in culture medium resulted in the destruction of viral infectivity at an undetectable level. Conclusion The survival ability of SARS coronavirus in human specimens and in environments seems to be relatively strong. Heating and UV irradiation can efficiently eliminate the viral infectivity.

Unusual histopathological findings in appendectomy specimens from patients with suspected acute appendicitis

AIM: To investigate the prevalence and implications of unusual histopathological findings in appendectomy specimens from patients with suspected acute appendicitis. METHODS: The demographic and histopathological data of 1621 patients (≥ 16 years-old) who underwent appendectomy to treat an initial diagnosis of acute appendicitis between January 1999 and November 2011 were retrospectively assessed. Microscopic findings were used to classify the patients under six categories: appendix vermiformis, phlegmonous appendicitis, gan- grenous appendicitis, perforated appendicitis, supurative appendicitis, and unusual histopathologic findings. The demographic and clinicopathologic characteristics of patients with unusual histopathologic findings were evaluated in detail, and re-analysis of archived resected appendix specimens was carried out. RESULTS: A total of 912 males and 709 females, from16 to 94 years old, were included in the study and comprised 789 cases of suppurative appendicitis, 370 cases of appendix vermiformis, 243 cases of perforated gangrenous appendicitis, 53 cases of flegmaneous appendicitis, 32 cases of gangrenous appendicitis, and 134 (8.3%) cases of unusual histopathological findings. The unusual histopathological findings included fibrous obliteration (n = 62), enterobius vermicularis (n = 31), eosinophilic infiltration (n = 10), mucinous cystadenoma (n = 8), carcinoid tumor (n = 6), granulomatous inflammation (n = 5), adenocarcinoma (n = 4; one of them mucinous), and mucocele (n = 3), adenomatous polyp (n = 1), taenia sup (n = 1), ascaris lumbricoides (n = 1), appendiceal diverticula (n = 1), and B cell non-hodgkin lymphoma (n = 1). None of the 11 patients with subsequent diagnosis of tumor were suspected of cancer prior to the appendectomy. CONCLUSION: Even when the macroscopic appearance of appendectomy specimens is normal, histopathological assessment will allow early diagnosis of many unusual diseases.

Development of a reverse-transcription loop-mediated isothermal amplification assay to detect avian influenza viruses in clinical specimens

In recent years,the avian influenza has brought not only serious economic loss to the poultry industry in China but also a serious threat to human health because of the avian influenza virus(AIV) gene recombination and reassortment.Until now,traditional RT-PCR,fluorescence RT-PCR and virus isolation identification have been developed and utilized to detect AIV,but these methods require high-level instruments and experimental conditions,not suitable for the rapid detection in field and farms.In order to develop a rapid,sensitive and practical method to detect and identify AIV subtypes,4 specific primers to the conserved region of AIV M gene were designed and a loop-mediated isothermal amplification(RT-LAMP) method was established.Using this method,the M gene of H1–H16 subtypes of AIV were amplified in 30 min with a water bath and all 16 H subtypes of AIV were able to be visually identified in presence of fluorescein,without cross reaction with other susceptible avian viruses.In addition,the detection limit of the common H1,H5,H7,and H9 AIV subtypes with the RT-LAMP method was 0.1 PFU(plaque-forming unit),which was 10 times more sensitive than that using the routine RT-PCR.Further comparative tests found that the positivity rate of RT-LAMP on detecting clinical samples was 4.18%(14/335) comparing with 3.58%(12/335) from real-time RT-PCR.All these results suggested that the RT-LAMP method can specifically detect and identify AIV with high sensitivity and can be considered as a fast,convenient and practical method for the clinic test and epidemiological investigation of AIV.

Catalog of insect type specimens preserved at the Kunming Institute of Zoology,Chinese Academy of Science with corrections of some specimens

This article presents a list of insect types preserved in Kunming Natural History Museum of Zoology （KNHMZ）. As of March, 2015, 3412 type specimens belonging to 266 species/subspecies of 37 families in 9 orders （Odonata, Isoptera, Mantodea, Orthoptera, Hemiptera, Coleoptera, Diptera, Hymenoptera and Lepidoptera） are included. Information corrections of some specimens are provided in this article.

Catalogue of the Type Specimens of Amphibians and Reptiles in the Herpetological Museum of Chengdu Institute of Biology, Chinese Academy of Sciences: I. Rhacophoridae(Anura, Amphibia)

In order to facilitate herpetological research for all the herpetologists both in and outside of China, we will report all the type specimens of amphibia and reptilia deposited in the Herpetological Museum of Chengdu Institute of Biology(CIB), Chinese Academy of Sciences in series. This report focuses on the family Rhacophoridae of Anura in Amphibia, including 13 species. The contents of the report include synonym lists and generic transfer of type species, measurements of type specimens, particularly for those with no previously published measurement data, and chromosomal data for each species.

Histopathological characteristics of needle core biopsy and surgical specimens from patients with solitary hepatocellular carcinoma or intrahepatic cholangiocarcinoma

BACKGROUND Pathological manifestations of hepatic tumours are often associated with prognosis. Although surgical specimens(SS) can provide more information,currently, pre-treatment needle core biopsy(NCB) is increasingly showing important value in understanding the nature of liver tumors and even in diagnosis and treatment decisions. However, the concordance of the clinicopathological characteristics and immunohistochemical(IHC) staining between NCB and SS from patients with hepatic tumours were less concerned.AIM To introduce a more accurate method for interpreting the IHC staining results in order to improve the diagnostic value of hepatic malignancy in NCB samples.METHOD A total of 208 patients who underwent both preoperative NCB and surgical resection for hepatocellular carcinoma(HCC) or intrahepatic cholangiocarcinomaRESULTS Morphologically, the presence of compact tumour nests or a cord-like structure in NCB was considered the primary cause of misdiagnosis of HCC from ICC. The kappa statistic showed a moderate agreement in histomorphology(k = 0.504) and histological grade(k = 0.488) between NCB and SS of the tumours. A 4-tier(+++,++, +, and-) scoring scheme that emphasized the focal neoplastic cell immunoreactivity of tumour cells revealed perfect concordance of CK19, GPC3 and HepPar1 between NCB and SS(k = 0.717; k = 0.768; k = 0.633). Furthermore,with the aid of a binary classification derived from the 4-tier score, a high concordance was achieved in interpreting the IHC staining of the three markers between NCB and final SS(k = 0.931; k = 0.907; k = 0.803), increasing the accuracy of NCB diagnosis C(k = 0.987; area under the curve = 0.997, 95%CI: 0.990-1.000; P< 0.001).CONCLUSION These findings imply that reasonable interpretation of IHC results in NCB is vital for improving the accuracy of tumour diagnosis. The simplified binary classification provides an easy and applicable approach.

A CATASTROPHE ANALYSIS ON THE STABILITY OF THE CRACK GROWTH IN THREE-POINT BENDING SPECIMENS

This paper presents an attempt at the application of catastrophe theory to the stability analysis of J-controlled crack growth in three-point bending specimens. By introducing the solutions of J-integral in the completely yielding state for the ideal plastic material, the critical condition of losing stability for the crack propagation in the specimen is obtained, based on the cusp catastrophe theory. The process of the crack growth from geometrical sense is described.

Finite size specimens with cracks of icosahedral Al Pd Mn quasicrystals

Icosahedral quasicrystals are the most important and thermodynamically stable in all about 200 kinds of quasicrystals currently observed. Beyond the scope of classical elasticity, apart from a phonon displacement field, there is a phason displacement field in the elasticity of the quasicrystal, which induces an important effect on the mechanical properties of the material and makes an analytical solution difficult to obtain. In this paper, a finite element algorithm for the static elasticity of icosahedral quasicrystals is developed by transforming the elastic boundary value problem of the icosahedral quasicrystals into an equivalent variational problem. Analytical and numerical solutions for an icosahedral A1-Pd-Mn quasicrystal cuboid subjected to a uniaxial tension with different phonon-phason coupling parameters are given to verify the validity of the numerical approach. A comparison between the analytical and numerical solutions of the specimen demonstrates the accuracy and efficiency of the present algorithm. Finally, in order to reveal the fracture behavior of the icosahedral A1-Pd-Mn quasicrystal, a cracked specimen with a finite size of matter is investigated, both with and without phonon-phason coupling. Meanwhile, the geometry factors are calculated, including the stress intensity factor and the crack opening displacement for the finite-size specimen. Computational results reveal the importance of pbonon-phason coupling effect on the icosahedral A1-Pd-Mn quasicrystal. Furthermore, the finite element procedure can be used to solve more complicated boundary value problems.

Epidermal growth factor receptor mutation analysis in cytological specimens and responsiveness to gefitinib in advanced non-small cell lung cancer patients

Background： Epidermal growth factor receptor（EGFR） mutation is the key predictor of EGFR tyrosine kinase inhibitors（TKIs） efficacy in non-small cell lung cancer（NSCLC）. We conducted this study to verify the feasibility of EGFR mutation analysis in cytological specimens and investigate the responsiveness to gefitinib treatment in patients carrying EGFR mutations.Methods： A total of 210 cytological specimens were collected for EGFR mutation detection by both direct sequencing and amplification refractory mutation system（ARMS）. We analyzed EGFR mutation status by both methods and evaluated the responsiveness to gefitinib treatment in patients harboring EGFR mutations by overall response rate（ORR）, disease control rate（DCR） and progression free survival（PFS）.Results： Of all patients, EGFR mutation rate was 28.6%（60/210） by direct sequencing and 45.2%（95/210） by ARMS（P〈0.001） respectively. Among the EGFR wild type patients tested by direct sequencing, 26.7% of them were positive by ARMS. For the 72 EGFR mutation positive patients treated with gefitinib, the ORR, DCR and median PFS were 69.4%, 90.2% and 9.3 months respectively. The patients whose EGFR mutation status was negative by direct sequencing but positive by ARMS had lower ORR（48.0% vs. 80.9%, P=0.004） and shorter median PFS（7.4 vs. 10.5 months, P=0.009） as compared with that of EGFR mutation positive patients by both detection methods. Conclusions： Our study verified the feasibility of EGFR analysis in cytological specimens in advanced NSCLC. ARMS is more sensitive than direct sequencing in EGFR mutation detection. EGFR Mutation status tested on cytological samples is applicable for predicting the response to gefitinib. Abundance of EGFR mutations might have an influence on TKIs efficacy.

An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens

Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. Methods Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure： reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide （random hexamer or non-ribosomal hexanucleotide） primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline. Results NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease （HFMD） and identified other potential viruses or differentiated misdiagnosis events. Conclusion The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.

Fracture analyses of different pre-holed concrete specimens under compression

Crack propagation processes in specially prepared concrete discs and rectangular specimens containing a single cylindrical hole or multiple holes of varying diameters have been studied both experimentally and numerically. In this research, the cracks coalescence paths in Brazilian disc and rectangular specimens made from rock-like material containing multi-holes are investigated. These concrete specimens are specially prepared from an appropriate mixture of Portland Pozzolana Cement （PPC）, fine sands, and water. The pre-holed Brazilian discs and rectangular specimens are experimentally tested under compression. The breakage load in the ring type disc specimens containing an axial hole with varying diameters is measured and the distribution of the induced lateral stress is obtained. The mechanism of cracks propagation in the wall of the ring type specimens is also stud- ied. In the case of multi-hole Brazilian disc and rectangular specimens, the cracks propagation and cracks coalescence are also investigated. These experiments are numerically modeled by a modified higher order displacement discontinuity method. It has been shown that the corresponding experimental and numerical results are in good agreement with each other. The results presented in this research vali date the accuracy and applicability of these crack analyses procedures.

RT-nPCR Assays for Amplification and Sequencing of VP1 Genes in Human Enterovirus A–D from Clinical Specimens

Objective To develop RT-nPCR assays for amplifying partial and complete VP1 genes of human enteroviruses(HEVs)from clinical samples and to contribute to etiological surveillance of HEV-related diseases.Methods A panel of RT-nPCR assays,consisting of published combined primer pairs for VP1 genes of HEV A–C and in-house designed primers for HEV-D,was established in this study.The sensitivity of each RT-nPCR assay was evaluated with serially diluted virus stocks of five serotypes expressed as CCID50 perμL and copies perμL,and the newly established methods were tested in clinical specimens collected in recent years.Results The sensitivity of RT-nPCR assays for amplifying partial VP1 gene of HEVs was 0.1 CCID50 perμL and 10 virus copies perμL,and for the complete VP1 gene was 1 CCID50 perμL and 100 virus copies perμL,using serially-diluted virus stocks of five serotypes.As a proof-of-concept,25 serotypes were identified and complete VP1 sequences of 23 serotypes were obtained by this system among 858 clinical specimens positive for HEVs during the past eight surveillance seasons.Conclusion This RT-nPCR system is capable of amplifying the partial and complete VP1 gene of HEV A–D,providing rapid,sensitive,and reliable options for molecular typing and molecular epidemiology of HEVs in clinical specimens.

Edge crack growth of mortar plate specimens under uniaxial loading tests

In this paper, a compression-to-tension conversion technique is developed by applying predominant mode I loading test, using a servo-controlled compression system. The technique is applied to thin mortar plate specimens of different widths that include a prefabricated crack on either a single side to facilitate unilateral crack propagation, or prefabricated cracks positioned on both sides asymmetrically with respect to the specimen midpoint to facilitate bilateral crack propagation under direct tensile stress with a loading rate of 0.001 mm/s. The results show that the main pathways of unilateral crack propagation governing specimen failure are fluctuated locally, but present an approximately straight line overall in the absence of pre-existing internal defects. However, the pathways of bilateral crack propagation are relatively complex, although they present similar characteristics. Analysis results suggest that bilateral crack propagation can be basically divided into three stages, i.e. a stage of linear propagation, a stage representing deviation from the other crack, and a stage where one crack approaches either the other crack or approaches the opposite edge of the specimen, and thereby forming a continuous crack through the specimen. In addition, the stressestrain curves of bilateral crack specimens do not vary significantly around the point of peak stress prior to specimen failure, which means that the specimens do not fail instantaneously.

A Modified approach for calculating dynamic shear modulus of stiff specimens by resonant column tests

An error analysis of the dynamic shear modulus of stiff specimens from tests performed by a new resonant column device developed by the Institute of Engineering Mechanics, China was conducted. A modified approach for calculating the dynamic shear modulus of the stiff specimens is presented. The error formula of the tests was deduced and parameters that impact the accuracy of the test were identified. Using six steel specimens with known standard stiffness as a base, a revised dynamic shear modulus calculation for stiff specimens was formulated by comparing three of the models. The maximum error between the test results and the calculated results shown by curves from both the free-vibration and the resonant-vibration tests is less than 6%. The free-vibration and resonant-vibration tests for three types of stiff samples with a known modulus indicate that the maximum deviation between the actual and the tested value using the modified approach were less than 10%. As a result, the modified approach presented here is shown to be reliable and the new device can be used for testing dynamic shear modulus of any stiff materials at low shear strain levels

SHORT FATIGUE CRACK BEHAVIOUR IN ISO-STRESS SPECIMENS

Fatigue tests were made on a vibration machine using specially designed specimens to investi- gate the initiation and propagation features of short fatigue cracks in a weld metal.The spec- imens were triangular in shape so that when loaded as a cantilever beam the surface tensile stress is constant.Test results show that short fatigue cracks mainly originate from slip bands within ferrite grains.The development of short fatigue cracks is marked by a gradual increase in crack density with fatigue cycles.Coalescence of short cracks leads to crack propagation and the crack path is predominantly transgranular.

New Cutting Technique of Making Collembola Glass Specimens

A new technique, involving tool making, clearing, staining, cutting and mounting specimens on slides, was described for studying Collembola taxonomy. It could resolve the problem of observing Collembola glass specimens under standard optical microscopy, because the phase-contrast microscope has not been available for all researchers. A type of micro cutting probe （about 1 μm in tip diameter） was designed, and it made the cutting method go from two-handed to one-handed, which was a huge step forward in the cutting method of Collembola. The micro cutting probe was custom designed for Collembola using two electric grinders, followed by ferric tannate staining with a stable blue color, mounting in specialized solutions and sealing with a neutral quick-drying gum. We also described a method to make glass capillary extractor and glass capillary brush to make sure a better condition of cleared specimens.