Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of DNA Barcodes in Asian Tropical Trees – A Case Study from Xishuangbanna Nature Reserve, Southwest China

Background Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world. Methodology and Principal Findings A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH–psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH–psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6–58.1%) and genus (72.8–76.2%) identification. With trnH–psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7–28.5% and 31.6–35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas. Conclusions/Significance Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH–psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.
STUDIES ON PRIMARY CULTURES OF DIFFERENTIATED FETAL LIVER CELLS

A method for culturing non- or slowly growing, differentiated fetal rat liver cells is described. It involves the use of collagenase as a digesting agent and of a selective medium deficient in arginine which suppresses the growth of nonparenchymal liver cells. Evidence is presented that surviving cells (a) retain liver-specific urea cycle functions measured by their capacity to transform ornithine into arginine, (b) synthesize DNA in glucose-deficient medium, and (c) synthesize and secrete albumin. This primary cell culture responds to partially hepatectomized rat serum and may be an appropriate assay system for the study of mechanisms which regulate liver regeneration.
Scheduled-Step-Size Affine Projection Algorithm

An approach for scheduling the step sizes of an adaptive filter using the affine projection algorithm (APA) is proposed so that its mean-square deviation (MSD) learning curve can be guided along a pre-designed trajectory. This approach eliminates the parameter-tuning process and does not require estimating unmeasurable stochastic quantities. Furthermore, a step-size lower bound is derived in random-walk-modeled environments that leads the adaptive filter to achieve the smallest steady-state MSD, while in stationary environments, the closer to zero the step size is, the smaller the steady-state MSD. For efficient memory usage in practice, the schedule is modified from full-table step sizes to a few down-sampled step sizes without performance degradation. In a simulation, the scheduled-step-size APA exhibits fast convergence and produces small steady-state error not only for a white signal but also for various colored input signals for a properly chosen projection order. The proposed algorithm also demonstrates greater robustness over different signal-to-noise ratios than the existing variable-step-size APAs.
Oxidative Stress and Paraoxonase 1 Activity Predict Contrast-Induced Nephropathy in Patients With ST-Segment Elevation Myocardial Infarction Undergoing Primary Percutaneous Coronary Intervention

Reactive oxygen species have been implicated in the pathogenesis of contrast-induced nephropathy (CIN). We investigated the relationship between CIN with paraoxonase 1 (PON-1) activity and oxidative stress markers (total antioxidant status [TAS], total oxidant status [TOS], and oxidative stress index [OSI]) in patients with anterior ST-segment elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention; 289 consecutive patients with STEMI were prospectively included. The patients were divided into 2 groups: CIN (n = 69) and non-CIN (n = 220). Activity of PON-1 and TAS levels were significantly lower and OSI and TOS levels were significantly higher in patients with CIN compared to the non-CIN group (P < .05, for all). On multivariate logistic regression analysis, PON-1 activity and OSI as well as the amount of contrast medium and diabetes were independent predictors for CIN in patients with anterior STEMI. Activity of PON-1 and oxidative stress may play a role in the pathogenesis of CIN.
Antibiotic Susceptibility of Biofilm Cells and Molecular Characterisation of Staphylococcus hominis Isolates from Blood

Objectives We aimed to characterise the staphylococcal cassette chromosome mec (SCCmec) type, genetic relatedness, biofilm formation and composition, icaADBC genes detection, icaD expression, and antibiotic susceptibility of planktonic and biofilm cells of Staphylococcus hominis isolates from blood. Methods The study included 67 S. hominis blood isolates. Methicillin resistance was evaluated with the cefoxitin disk test. mecA gene and SCCmec were detected by multiplex PCR. Genetic relatedness was determined by pulsed-field gel electrophoresis. Biofilm formation and composition were evaluated by staining with crystal violet and by detachment assay, respectively; and the biofilm index (BI) was determined. Detection and expression of icaADBC genes were performed by multiplex PCR and real-time PCR, respectively. Antibiotic susceptibilities of planktonic cells (minimum inhibitory concentration, MIC) and biofilm cells (minimum biofilm eradication concentration, MBEC) were determined by the broth dilution method. Results Eighty-five percent (57/67) of isolates were methicillin resistant and mecA positive. Of the mecA-positive isolates, 66.7% (38/57) carried a new putative SCCmec type. Four clones were detected, with two to five isolates each. Among all isolates, 91% (61/67) were categorised as strong biofilm producers. Biofilm biomass composition was heterogeneous (polysaccharides, proteins and DNA). All isolates presented the icaD gene, and 6.66% (1/15) isolates expressed icaD. This isolate presented the five genes of ica operon. Higher BI and MBEC values than the MIC values were observed for amikacin, vancomycin, linezolid, oxacillin, ciprofloxacin, and chloramphenicol. Conclusions S. hominis isolates were highly resistant to methicillin and other antimicrobials. Most of the detected SCCmec types were different than those described for S. aureus. Isolates indicated low clonality. The results indicate that S. hominis is a strong biofilm producer with an extracellular matrix with similar composition of proteins, DNA and N-acetylglucosamine; and presents high frequency and low expression of icaD gene. Biofilm production is associated with increased antibiotic resistance.
Turning Data into People: Player Perspectives on Game Addiction

Internet gaming disorder, also known as video game addiction and pathological gaming, has officially been proposed as a psychiatric disorder. Numerous studies have investigated the prevalence of the disorder, but the prevalence rates that they arrive at vary in the extreme (from 0.6% to 44.5%). This discrepancy between studies inevitably raises questions about what they actually measure. To explore this further five young men who were candidates for this new diagnosis where asked to fill out a questionnaire probing pathological gaming and interviewed about how they understood the questions and their thoughts on video game addiction in general. Thus, this paper presents the results of a qualitative investigation of the face-validity of quantitative research on video game addiction. The interviews showed that the respondents often misunderstood the intention of the questions, misjudged the severity of the negative effects that the questions probed and often interpreted the questions very differently. Only one of the respondents believed pathological gaming to be a primary disorder, but he also believed it to promote more positive than negative effects. The rest of the respondent either did not believe in the disorder at all or believed it to be secondary to other problems, such as anxiety or depression.
Knockout of Insulin-Like Growth Factor-1 Receptor Impairs Distal Lung Morphogenesis

Background Insulin-like growth factors (IGF-I and -II) are pleiotropic regulators of somatic growth and development in vertebrate species. Endocrine and paracrine effects of both hormones are mediated by a common IGF type 1 receptor (IGF-1R). Lethal respiratory failure in neonatal IGF-1R knockout mice suggested a particular role for this receptor in pulmonary development, and we therefore investigated the consequences of IGF-1R inactivation in lung tissue. Methods and Findings We first generated compound heterozygous mutant mice harboring a hypomorphic (Igf1rneo) and a null (Igf1r−) allele. These IGF-1Rneo/− mice express only 22% of normal IGF-1R levels and are viable. In adult IGF-1Rneo/− mice, we assessed lung morphology and respiratory physiology and found normal histomorphometric characteristics and normal breathing response to hypercapnia. We then generated homozygous IGF-1R knockout mutants (IGF-1R−/−) and analyzed their lung development during late gestation using histomorphometric and immunohistochemical methods. IGF-1R−/− embryos displayed severe lung hypoplasia and markedly underdeveloped diaphragms, leading to lethal neonatal respiratory distress. Importantly, IGF-1R−/− lungs from late gestation embryos were four times smaller than control lungs and showed markedly thickened intersaccular mesenchyme, indicating strongly delayed lung maturation. Cell proliferation and apoptosis were significantly increased in IGF-1R−/− lung tissue as compared with IGF-1R+/+ controls. Immunohistochemistry using pro-SP-C, NKX2-1, CD31 and vWF as markers revealed a delay in cell differentiation and arrest in the canalicular stage of prenatal respiratory organ development in IGF-1R−/− mutant mice. Conclusions/Significance We found that low levels of IGF-1R were sufficient to ensure normal lung development in mice. In contrast, complete absence of IGF-1R significantly delayed end-gestational lung maturation. Results indicate that IGF-1R plays essential roles in cell proliferation and timing of cell differentiation during fetal lung development.
Scalable and systolic Montgomery multiplier over GF(2m) generated by trinomials

A Montgomery's algorithm in GF(2m) based on the Hankel matrix–vector representation is proposed. The hardware architecture obtained from this algorithm indicates low-complexity bit-parallel systolic multipliers with irreducible trinomials. The results reveal that the proposed multiplier saves approximately 36% of space complexity as compared to an existing systolic Montgomery multiplier for trinomials. A scalable and systolic Montgomery multiplier is also developed by applying the block-Hankel matrix–vector representation. The proposed scalable systolic architecture is demonstrated to have significantly less time–area product complexity than existing digit-serial systolic architectures. Furthermore, the proposed architectures have regularity, modularity and local interconnectability, making them highly appropriate for VLSI implementation.
Effect of deposition site and sperm number on the fertility of sheep inseminated with liquid semen

The effect of the deposition site and the numbers of sperm on the fertility of sheep was tested in a field trial in which 1292 Norwegian crossbred ewes aged between six months and five-and-a-half years from 52 farms were inseminated with liquid semen after natural oestrus. Cervical insemination with 150 x 106 and 75 x 106 spermatozoa resulted in 25-day non-return rates of 63.7 and 56.1 per cent, and vaginal insemination gave non-return rates of 63.3 and 56.6 per cent, respectively. There was no significant difference between the cervical and vaginal inseminations, but the inseminations with 150 x 106 spermatozoa gave significantly higher non-return rates (P=0.004). There were significant differences between the non-return rates for different rams (P<0.0001) and farmers (P=0.0002) but the age of the ewe had no significant effect.
Bamboo–Polylactic Acid (PLA) Composite Material for Structural Applications

Developing an eco-friendly industry based on green materials, sustainable technologies, and optimum processes with low environmental impact is a general societal goal, but this remains a considerable challenge to achieve. Despite the large number of research on green structural composites, limited investigation into the most appropriate manufacturing methodology to develop a structural material at industrial level has taken place. Laboratory panels have been manufactured with different natural fibers but the methodologies and values obtained could not be extrapolated at industrial level. Bamboo industry panels have increased in the secondary structural sector such as building application, flooring and sport device, because it is one of the cheapest raw materials. At industrial level, the panels are manufactured with only the inner and intermediate region of the bamboo culm. However, it has been found that the mechanical properties of the external shells of bamboo culm are much better than the average cross-sectional properties. Thin strips of bamboo (1.5 mm thick and 1500 mm long) were machined and arranged with the desired lay-up and shape to obtain laminates with specific properties better than those of conventional E-Glass/Epoxy laminates in terms of both strength and stiffness. The strips of bamboo were bonded together by a natural thermoplastic polylactic acid (PLA) matrix to meet biodegradability requirements. The innovative mechanical extraction process developed in this study can extract natural strip reinforcements with high performance, low cost, and high rate, with no negative environmental impact, as no chemical treatments are used. The process can be performed at the industrial level. Furthermore, in order to validate the structural applications of the composite, the mechanical properties were analyzed under ageing conditions. This material could satisfy the requirements for adequate mechanical properties and life cycle costs at industrial sectors such as energy or automotive.
The effect of linguistic constraints on the large scale organization of language

This paper studies the effect of linguistic constraints on the large scale organization of language. It describes the properties of linguistic networks built using texts of written language with the words randomized. These properties are compared to those obtained for a network built over the text in natural order. It is observed that the "random" networks too exhibit small-world and scale-free characteristics. They also show a high degree of clustering. This is indeed a surprising result - one that has not been addressed adequately in the literature. We hypothesize that many of the network statistics reported here studied are in fact functions of the distribution of the underlying data from which the network is built and may not be indicative of the nature of the concerned network.
Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran

The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates. The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program. The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types. This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.
Relationship between Protein Expression of VEGF-C, MMP-2 and Lymph Node Metastasis in Papillary Thyroid Cancer

Papillary thyroid cancer (PTC) is a common malignancy and has a good prognosis after appropriate treatment. PTC cells spread mainly by lymph node metastasis (LNM), but the mechanism is not well understood. Expression of vascular endothelial growth factor C (VEGF-C) and matrix metalloproteinase 2 (MMP-2) protein was studied immunohistochemically from the archived specimens of 65 PTC patients who initially presented without LNM. In this retrospective study, the frequency of expression differed significantly between thyroid cancer tissue and adjacent normal follicular epithelium (VEGF-C 78.5% and 20.0%, respectively; MMP-2 81.5% and 36.7%, respectively). LNM developed in 35 of the patients during 5–15 years of follow-up, by the end of which the frequencies of expression of VEGF-C and MMP-2 protein expression were 91.4% and 94.3%, respectively. Both VEGF-C and MMP-2 protein expression were significantly more frequent in PTC with LNM than without LNM. VEGF-C and MMP-2 protein expression levels were significantly correlated with LNM and it is, therefore, feasible that VEGF-C and MMP-2 may be useful as tumour markers of PTC with cervical LNM.
Primary Sclerosing Cholangitis in Patients With Inflammatory Bowel Disease in Turkey

Background Primary sclerosing cholangitis (PSC), which is a progressive cholestatic liver disease of unknown etiology, is strongly correlated with inflammatory bowel disease (IBD). Goals To determine the prevalence and describe the characteristics of PSC in patients with IBD in Turkey. Study We determined the prevalence of PSC in patients with IBD admitted to our department during a 6-year period. Also, patients with PSC were investigated from an IBD aspect. Regardless of whether the patient had symptoms such as itching, jaundice, and abdominal pain, endoscopic retrograde cholangiopancreatography was performed on those with elevated alkaline phosphatase, and liver biopsy was done if endoscopic retrograde cholangiopancreatography failed to bring about the diagnosis. Results Overall prevalence of PSC was 9 of 386 (2.3%) patients with ulcerative colitis (UC) and 4 of 110 (3.6%) patients with Crohn's disease (CD). Inflammatory bowel disease was established in 13 of 18 (72.2%; UC, 50.0%; CD, 22.2%) patients who were being observed for PSC. The male-to-female ratio was 5:4 in UC and 3:1 in CD patients with PSC. The mean age at diagnosis of PSC was 43.6 years (range, 30–54 years) in patients with UC and 30.5 years (range, 26–41 years) in patients with CD. In patients with UC, the extension of colitis was total in seven patients (7/110, 6.3%) and left-sided in two patients (2/142, 1.4%). In patients with CD, the disease was located in the ileum and colon in one patient (1/47, 2.1%) and in colon alone in three patients (3/21, 14.2%). Conclusions Prevalence of PSC-associated IBD in the Turkish community appear to be similar to the results of western origin studies.
Evolution analysis of low-cost iterative equalization in coded linear systems with cyclic prefixes

This paper is concerned with the low-cost iterative equalization/detection principles for coded linear systems with cyclic prefixes. Turbo frequency-domain-equalization (FDE) is applied to systems that may contain the joint effect of multiple-access interference (MAI), cross-antenna interference (CAI) and inter-symbol interference (ISI). We develop an SNR-variance evolution technique for the performance evaluation of the proposed systems. Numerical results in various channel environments demonstrate excellent agreement between the predicted and simulated system performance.
Altered erythropoiesis and iron metabolism in carriers of thalassemia

The thalassemia syndromes (α‐ and β‐thalassemia) are the most common and frequent disorders associated with ineffective erythropoiesis. Imbalance of α‐ or β‐globin chain production results in impaired red blood cell synthesis, anemia, and more erythroid progenitors in the blood stream. While patients affected by these disorders show definitive altered parameters related to erythropoiesis, the relationship between the degree of anemia, altered erythropoiesis, and dysfunctional iron metabolism has not been investigated in both α‐thalassemia carriers (ATC) and β‐thalassemia carriers (BTC). Here, we demonstrate that ATC have a significantly reduced hepcidin and increased soluble transferrin receptor levels but relatively normal hematological findings. In contrast, BTC have several hematological parameters significantly different from controls, including increased soluble transferrin receptor and erythropoietin levels. These changes in both groups suggest an altered balance between erythropoiesis and iron metabolism. The index sTfR/log ferritin and (hepcidin/ferritin)/sTfR are, respectively, increased and reduced relative to controls, proportional to the severity of each thalassemia group. In conclusion, we showed in this study, for the first time in the literature, that thalassemia carriers have altered iron metabolism and erythropoiesis.
Selective localization of organoclay and effects on the morphology and mechanical properties of LDPE/PA11 blends with distributed and co-continuous morphology

A study was made on the effect of small amounts of organically modified clay on the morphology and mechanical properties of blends of low-density polyethylene and polyamide 11 at different compositions. The influence of the filler on the blend morphology was investigated using wide angle X-ray diffractometry, scanning and transmission electron microscopy and selective extraction experiments. The filler was found to locate predominantly in the more hydrophilic polyamide phase. Although such uneven distribution does not have a significant effect on the onset of phase co-continuity of the polymer components, it brings about a drastic refinement of the microstructure for the blends both with droplets/matrix and co-continuous morphologies. In addition to the expected reinforcing action of the filler, the resulting fine microstructure plays an important role in enhancing the mechanical properties of the blends. This is essentially because of a good quality of stress transfer across the interface between the constituents, which also seems to benefit for a good interfacial adhesion promoted by the filler. Our results provide the experimental evidence for the capabilities of nanoparticles added to multiphase polymer systems to act selectively as a reinforcing agent for specific domains of the material and as a medium able to assist the refinement of the polymer phases during mixing.