Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparison of Branching Diagrams Derived by Various Phenetic and Cladistic Methods

Data for 20 binary characters for 18 hypothetical evolutionary units, members of "Dendrogrammaceae," have been analyzed using various phenetic and cladistic methods. Phenograms from single link, complete link, UPGMA, and WPGMA cluster analysis, shortest spanning tree diagrams, and cladograms from groundplan-divergence, Wagner tree, and character compatibility analyses were con- structed. The phenograms and cladograms derived from these analyses were com- pared with respect to topological distance matrices derived from each. Shortest span- ning tree phenograms and cladograms were compared for the number and sequence of character changes occurring on each. From these comparisons, the advantages and limitations of each method as a means for expressing evolutionary relationships among organisms are discussed and a series of recommendations is outlined. Each method can contribute to the development of an estimate of the evolutionary history for a group of organisms and no single method is best for such studies. Quantitative methods for the examination of similarities and differ- ences among organisms have been developed to assist systematic biolo- gists in assesssing relationships. These methods have usually been ap- plied to morphological data, but geographical distribution, occurrence of chemical compounds, and genetic data have also been used. These methods are operational interpretations of two approaches to the for- mulation of classifications and the estimation of evolutionary relation- ships: phenetics and cladistics. Phenetic methods summarize similarities and differences among organisms without consideration of the number and sequence of changes in characters that have occurred during the evolution of the group being studied (Colless 1967). Cladistic methods attempt to express similarities and differences in terms of the number and sequence of character changes that have occurred during evolution (Estabrook 1972). In both phenetic and cladistic approaches, the results of the assessment of similarities and differences are most frequently ex- pressed as branching diagrams. Diagrams resulting from phenetic meth- 264
MOLECULAR DIAGNOSIS OF THE VIRUSES ASSOCIATED WITH CHIRKE AND FOORKEY DISEASES OF LARGE CARDAMOM

Chirke and foorkey diseases are important constraints of large cardamom cultivation in eastern sub-Himalayan mountains. However the genome of the chirke virus has not been fully characterized and molecular diagnostics were not available. In this study 3’ terminal genome sequence (5961 nucleotides) of the virus associated with chirke disease containing the partial CI, 9k, NIa-VPg, NIaPro, NIb, CP and the 3' terminal untranslated region (UTR) was determined. The partial polyprotein nucleotides (4401) and amino acids (1346) containing the 9k, NIa-VPg, NIa-Pro, NIb and CP showed maximum sequence identity of 41.4 % and 69.2 % with Cardamom mosaic virus (CdMV) causing katte disease in small cardamom, respectively. The deduced amino acids sequences of the 9K protein showed a maximum sequence identity of 83.7 % with CdMV. The viral genome contains the RNA helicase motif, conserved tyrosine residue, Cysteine protease, GDD motif as found in the macluraviruses and potyviruses. Phylogenetic analysis based on the five polyproteins showed that virus was closer to CdMV, Alpinia mosaic virus, and Chinese yam necrotic mosaic virus subclade. The deduced amino acid sequence of putative coat protein (CP) gene showed maximum similarity of 65.8% with the CdMV and other macluraviruses. The results suggest that the virus associated with the chirke disease of large cardamom is a new species under the genus Macluravirus in the family Potyviridae for which the name large cardamom chirke virus (LCCV) is proposed. Purification of LCCV from large cardamom tissues is difficult and therefore immunodiagnostic reagents were not available. In the present study, we have successfully expressed CP gene of LCCV in Escherichia coli. The purification of expressed protein by Ni-NTA affinity chromatography was inefficient due to precipitation of protein during renaturation. We have optimized a simple, inexpensive and efficient method for purification of the expressed CP through gel extraction with 5% SDS followed by renaturation in Milli-Q water, which resulted in high yield (4.7 mg/ml) and good quality of the protein. A higher titer (1:256,000) polyclonal antibody (PAb) to the recombinant CP was produced, which strongly recognized LCCV in crude leaf extract and showed minimal
Rapid Prescreening for Antiviral Agents against HIV-1 Based on Their Inhibitory Activity in Site-Directed Immunoassays. Approaches Applicable to Epidemic HIV-1 Strains

Several compounds, including the triphenylmethane derivative aurintricarboxylic acid (ATA) and porphyrins, were reported to inhibit the binding of anti-V3 loop-specific antibodies to the V3 loop of gp120 from HIV-1 III-B and to have antiviral activity, probably due to interference with the biological function of the V3 loop. However, these compounds can be applied to antiviral chemotherapy only if they interact with envelope glycoproteins from a multitude of epidemic HIV-1 strains and inhibit their replication. Since recombinant envelope glycoproteins, synthetic peptides and anti-V3 monoclonal antibodies may not be available for these HIV-1 strains, alternative assays are needed to prescreen different compounds for potential antiviral activity against these viruses. Results presented here indicate that: (1) virions of HIV-1 MN, most closely related to primary HIV-1 isolates from European and North American countries, and human anti-HIV-1 antibodies, can also be used for rapid prescreening of antiviral agents, (2) compounds with antiviral activity against HIV-1 MN, discerned by site-directed immunoassays, inhibited the reaction of human anti-HIV-1 with a V3 loop consensus peptide corresponding to European/North American HIV-1 isolates, and (3) meso-tetra (4-carboxyphenyl) porphine (MTCPP), one of the most potent inhibitors of HIV-1 replication selected on the basis of site-directed immunoassays, preferentially attached to the V3 loop of gp120.
Identification of novel gating mechanisms underlying pharmacological potentiation of NMDA receptors

Excitatory neurotransmission mediated by N-methyl-D-aspartate receptors (NMDARs) is known to play an important role in synaptic plasticity, learning and memory. Moreover, NMDAR dysfunction may contribute to a variety of neuropsychiatric and neurological disorders including schizophrenia, epilepsy, stroke and trauma. Pregnenolone sulfate (PS) is one of the most commonly occurring neurosteroids in the central nervous system and influences function of several receptors. PS modulates NMDARs and has been shown to have both positive and negative modulatory effects on NMDAR currents generally in a subtype-selective manner. We assessed the gating mechanism of PS modulation of GluN1/GluN2A receptors transiently expressed in HEK 293 cells using whole-cell and single-channel electrophysiology. Only a modest effect on the whole-cell responses was observed by PS in dialyzed (non-perforated) whole-cell recordings. Interestingly, in perforated conditions, PS was found to increase the whole-cell currents in the absence of nominal extracellular Ca2+ whereas PS produced an inhibition of the current responses in the presence of 0.5 mM extracellular Ca2+. The Ca2+-binding DRPEER motif and GluN1 exon-5 were found to be critical for the Ca2+-dependent bidirectional effect of PS. Single-channel cell-attached analysis demonstrated that PS primarily affected the mean open time to produce its effects, with positive modulation mediated by an increase in duration of open time constants while negative modulation mediated by a reduction in the time spent in a long-lived open state of the receptor. Further kinetic modeling of the single-channel data suggested that the positive and negative modulatory effects are mediated by different gating steps which may represent GluN2 and GluN1 subunit-selective conformational changes respectively. Our studies provide a unique mechanism of modulation of NMDARs by an endogenous neurosteroid which has implications for identifying state-dependent molecules. UBP (University of Bristol Pharmaceuticals) series compounds act at allosteric binding sites on the NMDARs and have been able to achieve subtype-selectivity. We found that UBP684 significantly increased the whole-cell current and mean open time and reduced the mean shut time for GluN1/GluN2A receptors. Mutagenesis studies suggest that UBP684 can stabilize the closed cleft of the LBD and drive the receptor into the more stable open states.
Status of the ROSSINI project at GSI

Since the end of the Apollo missions, human spaceflight concentrated on missions in Low Earth Orbit thus reducing one of the major risk for man in space radiation. Due to Earth’s magnetic field, astronauts are largely protected from cosmic radiation originating from the sun or outside our galaxy. This situation will change significantly when the final destination is beyond this protection and deeper into the solar system. The feasibility of missions into deep space is strongly connected to the capability of protecting astronauts from the harsh radiation environment in interplanetary space [1]. Passive shielding, a well known technique in radiation protection, shows great promises in reducing the health risk induced by the space radiation environment.
Novel permissive cell lines for a complete propagation of hepatitis C virus

Hepatitis C virus (HCV) is a major etiologic agent of chronic liver diseases. Although the HCV life cycle has been clariﬁed by studying laboratory strains of HCV derived from the genotype 2a JFH-1 strain (cell culture-adapted HCV [HCVcc]), the mecha-nisms of particle formation have not been elucidated. Recently, we showed that exogenous expression of a liver-speciﬁc microRNA, miR-122, in nonhepatic cell lines facilitates efﬁcient replication but not particle production of HCVcc, suggesting that liver-spe-ciﬁc host factors are required for infectious particle formation. In this study, we screened human cancer cell lines for expression of the liver-speciﬁc (cid:2) -fetoprotein by using a cDNA array database and identiﬁed liver-derived JHH-4 cells and stomach-derived FU97 cells, which express liver-speciﬁc host factors comparable to Huh7 cells. These cell lines permit not only replication of HCV RNA but also particle formation upon infection with HCVcc, suggesting that hepatic differentiation participates in the expression of liver-speciﬁc host factors required for HCV propagation. HCV inhibitors targeting host and viral factors exhibited different antiviral efﬁcacies between Huh7 and FU97 cells. Furthermore, FU97 cells exhibited higher susceptibility for propagation of HCVcc derived from the JFH-2 strain than Huh7 cells. These results suggest that hepatic differentiation participates in the expression of liver-speciﬁc host factors required for complete propagation of HCV. for efﬁcient replication of HCV RNA and formation of infectious particles. In this study, we screened human cancer cell lines for expression of the liver-speciﬁc (cid:2) -fetoprotein by using a cDNA array database and identiﬁed novel permissive cell lines for complete propagation of HCVcc without any artiﬁcial ma-nipulation. In particular, gastric cancer-derived FU97 cells exhibited a much higher susceptibility to HCVcc/JFH-2 infection than observed in Huh7 cells, suggesting that FU97 cells would be useful for further investigation of the HCV life cycle, as well as the development of therapeutic agents for chronic hepatitis C.
Correlations of power output fluctuations in an offshore wind farm using 
high-resolution SCADA data

Abstract. The correlation of power output fluctuations of wind turbines in free field are investigated, taking into account the challenge of varying correlation states due to variable flow and wind turbine conditions within the wind farm. Based on eight months of 1 Hz SCADA data, measured at an offshore wind farm with 80 wind turbines, the influence of different parameters on the correlation of power output fluctuations is analysed. It is found that the correlation of power output fluctuations of wind turbines depends on the location of the wind turbines within the wind farm as well as the inflow conditions (free-stream or wake). Wind direction investigations show that the correlation is highest for streamwise aligned pairs and decreases towards spanwise pairs. Most importantly, the highly variable measurement data in a free-field wind farm has considerable influence on the identification of different correlation states. To account for that, the clustering algorithm k-means is used to group wind turbine pairs with similar correlations. The main outcome is that next to the location of a wind turbine pair in the wind farm the standard deviation in their power output and their power differences are suitable parameters to describe the correlation of power output fluctuations.
Antigenic properties of methylcholanthrene-induced tumors in mice of the strain of origin.

Summary Experiments are described in which it was shown that immunity of C3H-He mice resulted following ligation and atrophy of methylcholanthrene-induced sarcomas which arose in mice of this inbred strain. The results are discussed in relation to previously reported experiments in which C3H-He mice were not immunized against mammary carcinoma by similar methods.
Influence of Digital Divide and Experience on Nigerian University Students’ Attitude Towards the Use of Information Communication Technologies for Learning

Recent studies have shown that factors influencing technology use include, but are not limited to, accessibility and availability. Several studies in developed countries revealed that digital division and experience significantly influence students’ attitude towards ICT utilization. However, there is lack of empirical evidence to show that such variables do influence ICT utilization by Nigerian students. This study examined the influence of digital divide and experience on Nigerian university students’ utilization of information communication technologies. Two research hypotheses were formulated for the study. A self-constructed and validated twenty-fiveitem instrument was used to gather information from one thousand and five hundred randomly selected respondents in three public universities in Ogun State, southwestern Nigeria, while t-test statistical method was used to analyze the data collected. Findings revealed that there is a significant difference in the perception of digital native and digital immigrant students in attitude towards ICT utilization (t = 3.25, p<0.05). The findings of this study also showed that there is no significant difference in the perception of digitally experienced and less experienced students in attitude towards ICT utilization(t = 1.16, p>0.05). Based on the findings, it was recommended that postgraduate students in Nigerian universities should be further encouraged not to allow age to influence their perception towards ICT utilization negatively. Also, Nigerian Government should subsidize the cost of ICT devices in order to make them affordable to all students.
Differential Privacy Spatial Decomposition via Flattening Kd-Tree

The key problem of using differential privacy is controlling sensitivity. Almost all papers focus on processing sensitivity, but the efficiency of the algorithm is also very important. Therefore, this paper hopes to improve efficiency as much as possible under the premise of ensuring utility. In this paper, decomposition and reconstruction via flattening kd-tree (DRF) is proposed based on differential privacy, which applies a flattening kd-tree to process the adjacency matrix. Firstly, by adjusting the vertex labeling, the set of labeling form dense areas and sparse areas as much as possible in the adjacency matrix. The adjacency matrix is then decomposed by flattening kd-tree, and each sub-region is anonymously operated using differential privacy. Finally, each subregion is reconstructed to obtain a complete anonymous graph. At the end of the article, experiments are conducted over real-world datasets. According to the results, DRF has a significant improvement in efficiency, the time complexity of DRF is 𝑶 (| 𝑽 |), and DRF has a good performance in degree distribution, degree centrality and cutting query.
Diagnosis of Head and Neck Cancer in Developing Countries Using a Stacked Ensemble Model

Head and neck cancers (HNC) are indicated when cells grow abnormally. The incidence of HNC is on the increase owing to several factors. There is often late presentation that can result in loss of lives (mortality) especially in Africa due to paucity of specialists. These challenges prompted the development of a stacked ensemble model for diagnosis of HNC to facilitate prompt referral. The data were collected which consists of 1473 instances with 18 features. Information Gain was used for selecting important features and three supervised learning algorithms were deployed for the base learners: Decision Tree (C4.5), K-Nearest Neighbors and Naïve Bayes. The predictions of the base learners were combined and passed to meta learners: Logistic Model Tree (LMT). The result showed that Information Gain method with stacked LMTwas 95.11%. It was deduced that both Information Gain with stacked MLR produced higher accuracy that the base learners’ results. Hence, this stacked model can be used for diagnosis of HNC in healthcare systems.
Anti-Oxidant Activity of Polyphenols from Phyllanthus debilis Klein ex Willd

Phyllanthus debilis Klein ex Willd. (Euphorbiaceae) usually used as substitute/adulterant to Phyllanthus amarus , a hepatoprotective drug. However, the phytochmeical investigation of P.debilis has not been performed much. In the present study, five compounds were isolated from the ethyl acetate extract of aerial parts of P.debilis and they were identified as Gallic acid, Rutin, Corilagin, Furosin and Geraniin. All the constituents have been reported for the first time from this plant. Their structures were elucidated by spectral techniques. Furthermore, the phenolic compounds were tested for antioxidant activity against DPPH (1,1-diphenyl picrylhydrazyl) and by the phosphomolybdenum method. Ascorbic acid is used as the reference standard. From the isolated compounds, the Geraniin had showed highest activity in DPPH assay and Gallic acid in phosphomolybdenum method.
Ultrafiltration as a simple purification method of a water extract of common bean seed as a natural coagulant

Natural coagulants from a crude water extract of common bean seed showed very good efficiency of turbidity removal from water of ~89 % under optimal coagulation conditions, which were determined using response surface methodology (RSM). However, they also increased the content of organic matter in treated model water by ~66 %, which is the main drawback of usage of natural coagulants, in general. Thus, ultrafiltration was applied for processing of the crude water extract in order to separate biomolecules, which exhibit the coagulation activity. Four fractions obtained by ultrafiltration were applied in coagulation tests under the same conditions as the crude extract, and the 4 th fraction (molecules with molecular weights >30 kDa) with the predominant content of proteins with molecular weights 50 – 60 kDa, achieved almost as high efficiency of turbidity removal (75 %) as the crude extract. At the same time, the content of organic matter in treated water increased just for 16 % in comparison to the blank (model water processed in the same way but without coagulant). After optimization of process parameters by RSM for usage of the 4 th fraction, the coagulation activity increased further to 80 %.
Comparing temporal patterns in body condition of ringed seals living within their core geographic range with those living at the edge

1 –––––––––––––––––––––––––––––––––––––––– © 2020 The Authors. Ecography published by John Wiley & Sons Ltd on behalf of Nordic Society Oikos This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Subject Editor: Jean-Michel Gaillard Editor-in-Chief: Miguel Araújo Accepted 29 May 2020 43: 1–15, 2020 doi: 10.1111/ecog.04988 43 1–15
Significance of MRI before surgery to remove polyacrylamide hydrogel used for augmentation mamma-plasty

Objective To evaluate the significance of MRI before surgery to remove polyaeryl-amide hydrogel (PAMHG) which has been used for augmentation mammaplasty. Methods Twenty female patients with 40 breasts, having been injected PAMHG as augmentation mammaplasty, under-went bilateral breast axial T1WI, T2WI-fat saturation (FS) and sagittal T2WI-FS by 4-channal phased-assay breast coil at 3.0T (Philips) before removal surgery, in which 8 patients underwent axial multiphase contrast-enhanced MRI with THRIVE after Gd-DTPA (2.0 ml/s, 0.1 mmol/kg) adminis- tration. The results of MRI were compared with that of operation and pathology. Results PAMHG showed iso-intensity compared with breast gland on T1WI and hyperintensity on T2WI-FS. Low signal septa were noted within PAMHG in 40 breasts (20 patients), 90% (36/40) PAMHG without capsule, 10 % (4/40) with smooth capsule which showing homogenous low signal on T1WI and T2WI-FS. Subcutaneous lump of PAMHG was 70 % (28/40), lump of that in breast gland was 20% (8/40). Diffuse gel along spatium intermusculare of pectoralis major was 100 % (40/40), that along spatium intermusculare of intercostal muscle was 10 % (4/40). All PAMHG in breast of the 8 patients showed no enhancement, an irregular enhanced mass was found in gland of 1 patient. All distributions of PAMHG and appearances of its complications on T2WI-FS were consistent with the results of operation. Conclusions T2WI-FS can accurately display the distribution of PAMHG and its complication before removal surgery. MRI plane scan combined with muhiphase contrast-enhanced MRI can differentiate PAMHG from the lesions in the gland and find the breast carcinoma, so that it can guide clinicians before surgery to remove PAMHG used for augmentation mammaplasty. Key words: MRI; Breast; Polyacrylamide hydrogel; Augmentation mammaplast
Optimization for Cutting Conditions of Surface Roughness in Machining Process Using Support Vector Regression and Genetic Algorithm

— This paper considers a machining process in which its surface roughness is influenced by radial rake angle, speed and feed rate cutting condition simultaneously. In previous works, researchers have been used a response surface methodology (RSM), soft-computing techniques based regression model and integration of linear/nonlinear regression and soft-computing techniques to estimate the proper cutting conditions in this machining process. It is noticed that the combined linear regression and genetic algorithm (GA) had limitation regarding to the issue of multicollinearity. While the hybrid of nonlinear regression and GA faced the issue of complexity of the nonlinear regression’s structure since more complex structure of regression can increase the chance of overfitting, In this paper, an alternative techniques based on support vector regression (SVR) and GA is proposed to address the above issuess. SVR employs relatively a new technique, call it structural risk minimization (SRM), to obtain a nonlinearity relationship between the cutting conditions and its surface roughness. The alternative framework gave more accurate prediction model compared to RSM and soft-computing techniques based regression model in a machining dataset, and has less complex structure of regression compared to KPCR and GA.