Miracle-dz/UniFAR-FTUs huggingface dataset:
A morphological analysis of marsupial mammal higher‐level phylogenetic relationships

Phylogenetic relationships among marsupial taxa have proven to be more complex than the simple grouping of species by continent. Recent marsupials are distributed across the New World, Australia, New Guinea, and certain neighboring islands. Morphological characteristics of various groups bridge different geographical areas. We investigated the origin of these characteristics by assembling a morphological data matrix consisting of a new suite of 149 postcranial characters and incorporated a series of previously published data on the craniodental (76 characters) and soft tissue (5 characters) anatomy. Twenty‐one marsupial terminal taxa representing all the major radiations of marsupials and 10 outgroups, most of which are exceptionally well‐preserved fossils such as Vincelestes, Ukhaatherium, and a few basal metatherian taxa, were investigated. A maximum parsimony analysis was conducted, resulting in one most parsimonious tree. Relationships among outgroups are congruent with current understanding of mammalian phylogeny. All currently accepted marsupial orders were recovered by the analysis. We confirmed previous results showing the South American “monito del monte”Dromiciops nested within the Australasian radiation. Within this australidelphian clade, Dromiciops was closely allied with the Diprotodontia. The South American paucituberculates appeared more closely related to the Australidelphia than to the American Didelphimorphia. The marsupial mole Notoryctes and the Peramelia were closely allied to each other and in turn were the sister group of the Dromiciops plus Diprotodontia clade. This pattern of relationships left Dasyuromorphia as the most basal offshoot of the Australidelphia. Whereas this tree topology recovers some signal that had been detected by previous studies, morphological and/or molecular, some novel hypotheses are also supported.
DIPTERA ASSOCIATED WITH FUNGI IN CZECH AND SLOVAK REPUBLICS

K e y w o r d s: Diptera, insects, fungi, biology, ecology, taxonomy, Czech Republic, Slovakia, Europe. D v o u k ř í d l í v á z a n í n a h o u b y v Č e s k é a S l o v e n s k é r e p u b l i c e Čas. Slez. Muz. Opava (A), 55, suppl.2: 1-84, 2006. A b s t r a k t: V práci jsou shrnuty údaje o 188 druzích dvoukřídlého hmyzu (Diptera) patřících do 26 čeledí, které byly vychovány autorem ze 189 druhů vyšších hub (Fungi) a hlenek (Myxomycetes) nalezených v České a Slovenské republice v letech 1998 až 2006. Nejvíce zaznamenaných druhů patří do čeledi Mycetophilidae (84 druhů), následují čeledi Phoridae (16 dr.), Drosophilidae (12 dr.), Cecidomyiidae (11 dr.), Bolitophilidae (9 dr.), Muscidae (8 dr.) a Platypezidae (8 dr.). Ostatní čeledi byly zastoupeny méně než 5 druhy. Ke každému druhu je podán přehled dosud známých hostitelských hub v České a Slovenské republice, včetně předchozích literárních údajů. Připojen je také systematický přehled hostitelských hub a příslušných druhů hmyzu. Je popsán nový druh čeledi Phoridae, Megaselia sevciki Disney sp. n. , vychovaný z prášivky Bovista pusilla. Poprvé je zaznamenána hostitelská houba pro druhy Discobola parvispinula (Alexander, 1947), Mycetophila morosa Winnertz, 1863 a Trichonta icenica Edwards, 1925. Dva druhy čeledi Mycetophilidae, Mycetophila estonica Kurina, 1992 a Exechia lundstroemi Landrock, 1923, jsou poprvé zaznamenány z České republiky a druhy Allodia (B.) czernyi (Landrock, 1912) a Exechia repanda Johannsen, 1912 ze Slovenska. Uveden je také přehled parazitoidů larev čeledí Mycetophilidae a Phoridae. Author’s address: RNDr. Jan Ševčík, Ph.D., Silesian Museum, Tyršova 1, CZ-746 01 Opava, Czech Republic e-mail: sevcikjan@email.cz Reviewers: PETER J. CHANDLER (Melksham, United Kingdom) JINDŘICH ROHÁČEK (Opava, Czech Republic) Front cover illustration: Ditomyia fasciata (Meigen, 1818) – orig. JINDŘICH ROHÁČEK Illustration on page 5 taken from the New Year’s card by J. Roháček entitled “Only dipterists keep it together”. All photographs by Jan Ševčík.
Metabolite profiling reveals the involvement of aberrant metabolic changes in Gentiana triflora seed showing poor germination

ABSTRACT Gentians are alpine plants and two endemic species, Gentiana triflora and G. scabra, are cultivated as ornamentals in Japan. Because most of the Japanese cultivars are F1 hybrids, seed germination rate is an important factor for maintaining these cultivars. However, germination rates frequently differ among cultivars. Poor germination is a severe problem for gentian production, although there is almost no difference in their germination period and growth rate. In this study, we compared seed germination rates among three cultivars of G. triflora. A high rate of seed germination was observed in ‘Majel’ (MJ) and ‘Iwate’ (IW), but a low rate was recorded in ‘Iwate-Yumeminori’ (YM). We conducted a targeted metabolome analysis using these cultivars to elucidate the potential cause of inhibited seed germination. Multivariate analysis revealed that the aberrant accumulation of specific amino acids and a decrease in energy metabolites were observed in YM seed. Furthermore, protein concentrations and proteolytic activities in YM seed were lower than in MJ seed. These results imply that energy depletion was the main reason for the decreased rate of germination and that this depletion inhibited processes involved in seed germination, including de novo synthesis of the proteins necessary for germination.
Synovitis, acne, pustulosis, hyperostosis and osteitis syndrome with trigeminal brainstem involvement

The synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome is defined as the association of characteristic osteoarticular and dermatological manifestations. The diagnosis is based on clinical and radiological aspects, but in the recent years it has been described as an extension of other systems different from the skin and the bones. We report the first case of parenchymal brainstem trigeminal involvement in the context of clinically‐active SAPHO syndrome. We review the literature and discuss the underlying mechanism of this multi‐organ presentation.
The Use of Zeatin to Initiate in Vitro Cultures of Vaccinium Species and

Explants of mature pot-grown Vaccinium corymbosum L. cultivars were tested for initiation of new shoots using two growing conditions and four cytokinin treatments. Initiation tests with 12 genotypes showed significantly higher rates of new shoot growth on modified woody plant (MWPM) medium with 4 mg zeatin/liter at 25C under low light intensity than on any other treatment. Explants at 25C in light with 10 or 15 mg 2iP/iiter initiated at a moderate rate, but significantly lower rates were found for all controls and at 4C in darkness. To determine the utility of zeatin for initiation of diverse genotypes, 96 Vaccinium accessions from the National Clonal Germplasm Repository, representing 22 species and 44 cultivars, were screened using 25C and low light intensity. Initiation rates higher than 60% were achieved for 89 of 96 accessions tested. Chemical name used: N6-(2-isopentenyl)adenine (2iP), 6-(4-hy- droxy-3-methylbut- 2-enylamino )purine (zeatin).
Growth and cropping of ‘Blanquilla’ pear trees treated with paclobutrazol

SummaryThe application of 1000 or 2000 mg l–1 paclobutrazol at full bloom or when shoots were 25 cm long, to trees carrying no crop, inhibited shoot growth, the effect increasing linearly with the concentration applied. However, total tree growth, measured by the relative increase in trunk cross-sectional area, was greatest in the treated trees. The application of paclobutrazol at full bloom resulted in a great reduction of fruit set and in the almost total loss of crop. However, when it was applied in conjunction with GA3, the effect was overcome and a normal crop was obtained. Microscopical observations on flowers sprayed with paclobutrazol showed that growth of ovules and nucellus was slowed down and the maturation of embryo sacs was retarded, effects that were overcome with the application of GA3. Growth of trees treated at bloom time with paclobutrazol was greater than that of trees either sprayed with paclobutrazol and GA3 or left unsprayed, and this was attributed to the loss of crop. Paclobutrazol.
Regulation of B Cell Gene Expression and Function by Ikaros, Helios and Bcl6

Jukka Alinikula Regulation of B Cell Gene Expression and Function by Ikaros, Helios and Bcl6 Department of Medical Microbiology and Immunology Turku Graduate School of Biomedical Sciences (TuBS) Annales Universtitatis Turkuensis Turku, Finland 2010 B lymphocytes constitute a key branch of adaptive immunity by providing specificity to recognize a vast variety of antigens by B cell antigen receptors (BCR) and secreted antibodies. Antigen recognition activates the cells and can produce antibody secreting plasma cells via germinal center reaction that leads to the maturation of antigen recognition affinity and switching of antibody effector class. The specificity of antigen recognition is achieved through a multistep developmental pathway that is organized by interplay of transcription factors and signals through BCR. Lymphoid malignancies arise from different stages of development in abnormal function of transcriptional regulation. To understand the B cell development and the function of B cells, a thorough understanding of the regulation of gene expression is important. The transcription factors of the Ikaros family and Bcl6 are frequently associated with lymphoma generation. The aim of this study was to reveal the targets of Ikaros, Helios and Bcl6 mediated gene regulation and to find out the function of Ikaros and Helios in B cells. This study uses gene targeted DT40 B cell lines and establishes a role for Ikaros family factors Ikaros and Helios in the regulation of BCR signaling that is important at developmental checkpoints, for cell survival and in activation. Ikaros and Helios had opposing roles in the regulation of BCR signals. Ikaros was found to directly repress the SHIP gene that encodes a signaling lipid-metabolizing enzyme, whereas Helios had activating effect on SHIP expression. The findings demonstrate a balancing function for these two Ikaros family transcription factors in the regulation of BCR signaling as well as in the regulation of gene expression. Bcl6 was found to repress plasma cell gene expression program while maintaining gene expression profile of B cells. Analysis of direct Bcl6 target genes suggested novel mechanisms for Bcl6-mediated suppression of plasma cell differentiation and promoting germinal center phenotype.
Performance evaluation of sugarcane stripper for trash recovery.

The limited resources of fossil fuels and increasing prices of electricity has resulted severe energy crises in Pakistan. Being an agricultural country, Pakistan has huge potential of biomass that can be used as alternate energy source. The shortage of energy has led to search for alternate sources of energies. In, Pakistan sugarcane trashes can be used as a source of biomass for energy production. The manual removal of trash is a labor extensive and time wasting process. In the meanwhile, sugar cane stripper can be used to remove trashes from the sugarcane stalks. A sugarcane stripper was designed and developed by Agricultural Mechanization Research Institute (AMRI) Wing, Faisalabad. In this study, the performance evaluation of sugarcane stripper has been carried out for the recovery of sugar cane trashes for energy production as well as to improve the socio- economic condition of the rural community. The experiments were conducted on three varieties of sugarcane V1 (COL1148), V2 (FH-237), V3 (MO-240), three sprocket speeds NS1 (250 rpm), NS2 (200 rpm), NS3 (150 rpm) and three blower speeds NB1 (750 rpm), NB2 (1000 rpm) NB3 (1500 rpm). The cost comparison of sugarcane stripper has also been carried out in comparison with conventional method of de-trashing. The result shows that the best combination to get maximum sugarcane stripper efficiency of 79% was using sprocket speed of NS3 (150rpm) and blower speed of NB3 (1500rpm) for all varieties of sugarcane. The operation cost of sugarcane stripper and conventional method were calculated as Rs. 17120 and Rs. 19200 respectively. Keywords—Sugarcane stripper, Sprocket speeds, Blower speeds, Trash removal rate.
Development of a novel cell-based screening platform to identify inhibitors of viral interferon antagonists from clinically important viruses

i All viruses encode for at least one viral interferon (IFN) antagonist, which is used to subvert the cellular IFN response, a powerful antiviral innate immune response. Numerous in vitro and in vivo studies have demonstrated that IFN antagonism is crucial for virus survival, suggesting that viral IFN antagonists could represent promising therapeutic targets. This study focuses on Respiratory Syncytial Virus (RSV), an important human pathogen for which there is no vaccine or virus-specific antiviral drug. RSV encodes two IFN antagonists NS1 and NS2, which play a critical role in RSV replication and pathogenicity. We developed a high-throughput screening (HTS) assay to target NS2 via our A549.pr(ISRE)GFP-RSV/NS2 cell-line, which contains a GFP gene under the control of an IFN-stimulated response element (ISRE) to monitor IFNsignalling pathway. NS2 inhibits the IFN-signalling pathway and hence GFP expression in the A549.pr(ISRE)GFP-RSV/NS2 cell-line by mediating STAT2 degradation. Using a HTS approach, we screened 16,000 compounds to identify small molecules that inhibit NS2 function and therefore relinquish the NS2 imposed block to IFN-signalling, leading to restoration of GFP expression. A total of twenty-eight hits were identified; elimination of false positives left eight hits, four of which (AV-14, -16, -18, -19) are the most promising. These four hit compounds have EC50 values in the single μM range and three of them (AV-14, -16, -18) represent a chemically related series with an indole structure. We demonstrated that the hit compounds specifically inhibit the STAT2 degradation function of NS2, not the function of NS1 or unrelated viral IFN antagonists. At the current time, compounds do not restrict RSV replication in vitro, hence hit optimization is required to improve their potency. Nonetheless, these compounds could be used as chemical tools to determine the unknown mechanism by which NS2 mediates STAT2 degradation and tackle fundamental questions about RSV biology.
GENETIC DIVERGENCE AMONG CHICKPEA CULTIVARS

Genetic divergence among 23 cultivars of chickpea was estimated using D2 statistic for 7 yield traits. The cultivars were grouped into 6 clusters. Maximum genetic distance was recorded between clusters III and VI, followed by that between clusters IV and VI, suggesting wide diversity among these groups. Considering cluster means and the genetic distances, crosses between the cultivar of VI (ICCL 84225) with those of clusters III (ICCL 84217, ICCL 84219) and IV (ICCL 82108, ICCL 83214) are likely to recombine the genes for high yield.
CHARACTER‐STATE WEIGHTING FOR DNA RESTRICTION SITE DATA: ASYMMETRY, ANCESTORS AND THE ASTERACEAE

Brent D. Mishler, Victor A. Albert, Mark W. Chase, Per Ola Karis and Kȧre Bremer University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, California 94720, U.S.A. , Department of Physiological Botany, Department of Systematic Botany, Uppsala University, Villavägen 6, S-752 36 Uppsala, Sweden, Laboratory of Molecular Systematics, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, U.K. and Department of Phanerogamic Botany, Swedish Museum of Natural History, Box 50007, S-104 05 Stockholm, Sweden
Time and Energy Costs of Copulation for the Sphinx Moth, Manduca sexta

In some insects copulation may represent a significant fraction of reproductive effort, yet its energetics are unexamined. The hawkmoth Manduca sexta, recognized for its endothermy and high metabolic scope (> 100), was largely quiescent during copulation, which averaged about 3 h (n = 31). However, we occasionally observed long bouts of abdominal pumping by both sexes, suggesting elevated respiratory rates. The CO₂ production of 1-d-old copulating pairs was recorded in an open-flow respirometry system and averaged 0.508 cc g⁻¹ h⁻¹ (n = 6). Comparison of these rates with the resting metabolic rates of the same males and females on the days before (0.545 cc g⁻¹ h⁻¹) and after (0.495 cc g⁻¹ h⁻¹) copulation shows that metabolic rates during copulation are not different from resting rates. Thoracic temperatures of mating moths averaged 0.31°C above ambient temperatures (n = 11), also indicating resting metabolism. Body mass measurements before and after copulation suggest that males transfer a maximum of about 0.16g, or 7% of body mass. We conclude that copulation in Manduca, while representing a substantial time investment, is metabolically inexpensive.
Calendar Effect and Returns of Listed Companies on the Ghana Stock Exchange: A DOLS and GARCH Modelling

This study investigated the existence of a day-of-the-week, January, and turn-of-the-month effects on the stock returns from the financial institutions and manufacturing companies listed on the Ghana Stock Exchange. Daily stock-price data, sourced from the Ghana Stock Exchange website, and accounting data for shareholder/net tangible asset value, sourced from audited financial statements of listed firms, was collected and analyzed with Fama and French? s three-factor model and dynamic ordinary least square regression. In addition, a time-varying effect was examined with the generalized autoregressive conditional heteroskedasticity model. No evidence was found for day-of-the-week, January, or turn-of-the-month effects in the manufacturing sector; however, effects from day of the week and January were found to exist in the financial sector. With regard to time-varying, neither sector showed evidence of conditional volatility.
Detection for p21 Gene Expression in Bovine Oocytes Maturation and Construction of Eukaryotic Expression Vector pVenus-P21

The objectives of this study were to determine expression of p21 gene during IVM of bovine oocytes,and construct a eukaryotic expression vector pVenus-P21.Firstly,the RT-PCR and immunohistochemical staining were applied to check the expression of p21 mRNA and protein at different maturation stages of bovine oocytes.Then the p21 gene was cloned from bovine fibroblasts by RT-PCR,and a eukaryotic expression vector pVenus-P21 was constructed.After pVenus-P21 mediated by Lipofectamine 2000,it was transfected into Hela cells,it was efficiently expressed,which was identified by Fluorescence microscopy observation and RT-PCR.In addiation,the cRNA of p21-venus transcripted in vitro was microinjected into bovine oocytes,and the expression and location was observed under fluorescence microscopy.In conclusion,these data demonstrate that p21 mRNA and protein are expressed at defferent stages of bovine oocytes.Besides,the recombinant vector pVenus-P21 is successfully constructed.After transfection or microinjection,the fusion protein could be expressed efficiently and localized accurately both in Hela cells and bovine oocytes.This greatly facilitates the further study of P21,especially its role on oocytes maturation and early embryo development.
Body Weight, Intestinal Morphometry and Cell Proliferation of Broiler Chickens Submitted to Cyclic Heat Stress

To investigate the effects of heat stress on body weight, intestinal length, mucous area, crypt's depth, villus height and percentage of cells in proliferation activity in male broiler chickens, one hundred birds of Avian Farms strain were housed in cages and divided into two groups, the reared under heat stress and in thermoneutrality. The group reared under heat stress was submitted daily, from 12-13 h, to 38 C from first o to 27th day old and 40 C from 28 to 42nd day. The group reared in thermoneutrality was maintained for 24 o h in comfort temperature. The body weight of ten birds of each group was obtained weekly from the first until 42nd day old. Each week, five birds from each group were euthanased by cervical dislocation to obtai n intestinal length, the mucous area, crypt's depth, villus height and percentage of cells in proliferation activity. A completely randomized design was used in a factorial schema 6 x 2 (six ages: one, seven, 14, 21, 28 and 42 days and two ambient temperatures: thermoneutral and heat stress). Data were analyzed by analysis of variance and means compared by Tukey test at 5%. The birds stressed by heat presented less crypt depth, mucous area and villus height of duodenum and lower intestinal length at 42 days old. However, heat stress did not influence the percentage of PCNA positive cells, the area of the mucosa, crypt's depth and villus height in jejunum and ileum.
Expression and clinical significance of hepatoma-derived growth factor in breast cancers patients

Aim To investigate the relationship between the expression of hepatoma-derived growth factor(HDGF)and its clinical significance in human breast cancer tissues.Methods The expression of HDGF mRNA was detected in 24 human fresh breast cancer cases and the corresponding adjacent normal mammary tissues by reverse transcriptase-polymerase chain reaction(RT-PCR),and immunohistochemistry was used to detect HDGF protein expression in 75 human breast cancer cases and the corresponding adjacent normal mammary tissues Results The expression of HDGF gene in cancer tissues and benign mammary tissues was 2.00±0.85 and 0.67±0.37 than that of housekeeping gene.The expression of HDGF mRNA in breast cancer was significant higher than that of normal mammary tissues(P0.001). Compared with primary breast cancers,a significant reduction in expression of HDGF protein was noted in benign mammary lesions(P0.001). The expression level of HDGF in high-stage breast cancers was higher than that of low-stage breast cancers.Moreover,the expression of HDGF protein was markedly increased in breast cancers with lymph node metastasis compared with those without metastasis(P0.05). Conclusion Increased expression of HDGF may play a role in the pathogenesis and metastasis of breast cancer.
Mating Behavior of Ceratitis capitata on a Field-Caged Host Tree

We systematically observed the mating behavior of wild Ceratitis capitata (Wiedemann) flies released on a field-caged host tree (coffee) growing naturally in a plantation in Guatemala. The principal site of attempted copulation was the bottom surface of leaves. During late morning and early afternoon, males stationed themselves at this site, often forming leks, and released sex pheromone, thereby attracting virgin or otherwise receptive females. An additional important site of copulation attempts, particularly among already-mated females, and particularly during mid-morning and mid- to late afternoon, was the fruit, where males were arrested by oviposition-deterring pheromone deposited by females after egg laying. The principal strategy of males at this site appeared to be attempted seduction or rape of alreadymated or otherwise rather unreceptive females exhibiting oviposition behavior and little or no attraction to sex pheromone emitted by males on leaves. Possible selective advantages to males of each type of mate encounter pattern are discussed.
Erratum

In the published article by Clark et al1 included in the January 2019 issue of Clinical Endocrinology, ‘Large divergence in testosterone con‐ centrations between men and women: Frame of reference for elite athletes in sex‐specific competition in sports, a narrative review’, it has been brought to the authors’ attention there were some anoma‐ lies that required further clarification within Table 2, Figure 1 and the References. The authors have investigated these issues and have made the following revisions: Changes made in Table 2 are written below: