Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential impact of vertebrate and invertebrate herbivores on the reproductive output of Hormathophylla spinosa

Abstract We analyzed herbivory on the reproductive structures (flowers, fruits, and seeds) of Hormathophylla spinosa (Cruciferae) by highly dissimilar species of herbivores, from ungulates to endophagous seed predators and gall-formers, in three different populations from 1988 to 1992. Specific objectives of the study were to quantify (i) the intensity of herbivory on reproductive structures of H. spinosa and the consequent loss of reproductive output; (ii) the frequency of herbivory, and how herbivory varied between years on the same individuals; (iii) spatial, among-population variation in herbivory intensity; and (iv) the relative importance of each herbivore species with respect to the losses in plant reproductive output. All plants of H. spinosa (n = 80) were heavily attacked by herbivores in the high mountains of the Sierra Nevada, where most plants were attacked by different types of herbivores during each year of the study. Plants lost about 50% of their reproductive structures during the study period. However, there was a pronounced difference in the magnitude of damage produced by each herbivore since ungulates accounted for most of the damage, whereas other herbivores caused much lighter damage. Mammalian herbivores appear to be a major ecological factor determining seed production in populations of H. spinosa.
Mise en évidence d’un syndrome inflammatoire génital masculin : l’élastase peut-elle remplacer le Leucoscreen ?

Contexte : l’inflammation genitale est retrouvee chez 20% des hommes de couples infertiles. Elle est determinee par la presence de leucocytes sur le spermogramme a l’aide du LeucoScreen. Cette technique ne detecte pas les polynucleaires neutrophiles actives les plus nocifs, qui liberent des radicaux libres et des proteases dont l’elastase. Objectif : le dosage de l’elastase seminale est-il plus fiable que la leucocytospermie pour detecter une inflammation du tractus genital ? Materiel et methodes : ce travail retrospectif inclut 3489 patients consultant dans notre centre pour infertilite. Le seuil pathologique dans notre population a ete defini a partir d’une courbe ROC. Les caracteristiques spermatiques des patients ayant eu un dosage d’elastase/leucocytospermie ont ete analysees et les correlations etablies a l’aide du test de Spearman : spermogramme (n=2080/n=3780), bacteriologie (n=718), qualite nucleaire (n=198/n=221 pour la fragmentation de l’ADN ; n=190/n=211 pour le stress oxydatif) et biochimie seminale (n=256/n=268). Resultats : la concentration en elastase est fortement correlee a la leucocytospermie (p<0,0001). Le seuil d’elastase de 377 ng/mL est discriminant dans la detection de l’inflammation. Le dosage de l’elastase revele 16% des patients ayant un syndrome inflammatoire sans leucocytospermie. L’elastase est plus discriminante pour detecter une baisse de la mobilite (r=-0,09), une oxydation de l’ADN des spermatozoides (r=0,2) et un deficit de secretion prostatique (citrate r = -0,26, PA r = -0,26, zinc r = -0,21). Conclusion : l’elastase permet d’ameliorer le depistage de l’inflammation genital masculine et d’expliquer des anomalies de la qualite du sperme.
Use of environmental variables to infer gene flow and population structure in the gopher tortoise (Gopherus polyphemus) and predict the seroprevalence of an emerging infectious disease

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Investigation of the Wilms' tumour suppressor protein (WT1)

Wilms’ tumour is a paediatric nephroblastoma which affects 1: 10,000 live births, and is the most common form of solid tumour in children under 5 years of age. Approximately 10-20% of cases have a mutated wt1 gene. Wilms’ tumour suppressor protein (WT1) is a transcription factor which has a proline and glutamine rich N-terminus and four contiguous zinc fingers of the Cys2His2 type in the Cterminus. WT1 is important in kidney, gonad, and heart development and is associated with Wilms’ tumour and other diseases such as WAGR (Wilms’ tumour, Anirida, Genitourinary, and mental Retardation), DDS (Denys-Drash syndrome), AML (acute myeloid leukaemia), and Frasier syndrome. WT1 has four functional domains (suppression, activation, self-association, and zinc finger domain) and as a result of alternative splicing, can form 24 potential isoforms. The WT1 protein has both tumour suppressor and oncogenic properties and its functional role has been further complicated by reports that WT1 function is plasmid, vector and/or cell line specific. Understanding the structure and function of WT1 will help us in elucidating its role in Wilms’ tumour and other related diseases. This project consisted of two parts. First we investigated the N-terminus of WT1 to determine the minimal region required for self association. This included a four step process: 1) Clone truncations of the WT1 Nterminal region using the Invitrogen Gateway cloning system 2) Express the constructs in E.coli cell lines 3) Batch purify the protein with GST sepharose beads 4) Conduct pull down experiments to test for self association. All the N-terminus WT1 constructs contained an N-terminal 3c protease cleavage site linked to a GST tag. The constructs 68-180 a.a. , 2-135 a.a. , and 2-180 a.a. were successfully expressed in the BL21 (DE3) Star pLysS cell line. The constructs were batch purified and pull down experiments were conducted. The second part of this project was to design a functional assay to determine the DNA binding fractional activity of the WT1 zinc finger domain variants used by Fagerlund (2009). This also included a four step process 1) Purify the zinc finger domain variants 2) Conduct electrophoretic mobility shift assay to determine protein: DNA interaction 3) Design a
noic acid (ATRA) in congenital clubfoot (CCF)-like deformities in in vivo models, the essential cellular and molecular targets and the signaling mechanisms for ATRA-induced CCF-like deformities remain to be eluci-

Despite the well-established role of all-trans-retinoic acid (ATRA) in congenital clubfoot (CCF)-like deformities in in vivo models, the essential cellular and molecular targets and the signaling mechanisms for ATRA-induced CCF-like deformities remain to be elucidated. Recent studies have demonstrated that p53 and p21, expressed in the hindlimb bud mesenchyme, regulate cellular proliferation and differentiation, contributing to a significant proportion of embryonic CCF-like abnormalities. The objective of the present study was to investigate the mechanisms for ATRA-induced CCF, by assessing ATRA-regulated chondrogenesis in rat embryo hindlimb bud mesenchymal cells (rEHBMCs) in vitro. The experimental study was based on varying concentrations of ATRA exposure on embryonic day 12.5 rEHBMCs in vitro. The present study demonstrated that ATRA inhibited the proliferation of cells by stimulating apoptotic cell death of rEHBMCs. It was also observed that ATRA induced a dose-dependent reduction of cartilage nodules compared with the control group. Reverse transcription-polymerase chain reaction and western blotting assays revealed that the mRNA and protein expression of cartilage‐specific molecules, including aggrecan, Sox9 and collagen, type II, α 1 (Col2a1), were downregulated by ATRA in a dose-dependent manner; the mRNA levels of p53 and p21 were dose-dependently upregulated from 16 to 20 h of incubation with ATRA, but dose-dependently downregulated from 24 to 48 h. Of note, p53 and p21 were regulated at the translational level in parallel with the transcription with rEHBMCs treated with ATRA. Furthermore, the immunofluorescent microscopy assays indicated that proteins of p53 and p21 were predominantly expressed in the cartilage nodules. The present study demonstrated that ATRA decreases the chondrogenesis of rEHBMCs by inhibiting cartilage‐specific molecules, including aggrecan, Sox9 and Col2al, via regulating the expression of p53 and p21.
Molecular Systems Biology Peer Review Process File Rapid Neurogenesis through Transcriptional Activation in Human Stems Cells Transaction Report

(Note: With the exception of the correction of typographical or spelling errors that could be a source of ambiguity, letters and reports are not edited. The original formatting of letters and referee reports may not be reflected in this compilation.) Thank you again for submitting your work to Molecular Systems Biology. We have now heard back from two of the three referees whom we asked to evaluate your manuscript. Since their recommendations are very similar, I prefer to make a decision now rather than further delaying the process. As you will see from the reports below, the referees raise substantial concerns on your work, which, I am afraid to say, preclude its publication in Molecular Systems Biology. In line with the increasing interest in developing direct differentiation protocols that circumvent intermediate differentiation states (Wapinski et al., Cell 2013, Liu et al., Nature Communications 2013), the reviewers acknowledge that the presented fast and efficient protocol for the differentiation of iPS cells into neurons is a potentially useful tool for directed neuronal differentiation. However, they raise significant concerns regarding the analysis and interpretation of the transcriptomics data and they are not convinced that the study provides sufficiently conclusive functional and mechanistic insights into the regulatory network underlying the neuronal differentiation of stem cells. While they find the network analysis potentially interesting, they point out that as it stands, it relies on heavy filtering (Ingenuity Pathway Analysis) and it remains unclear whether it can conclusively explain (or predict) the observed dynamics and robustness of the differentiation protocol. As such, both reviewers indicated that they would not support publication in Molecular Systems Biology. Considering these rather substantial concerns and the overall low level of support, we feel that we have no choice but to return this manuscript with the message that we cannot offer to publish it. Nevertheless, we recognise that, as indicated by the reviewers, your efficient differentiation protocol using PGP iPS cells represents a strong aspect of the study and understanding the systems-level mechanisms underlying the fast and robust neuronal differentiation would be interesting. As such, we would not be opposed to considering a revised and extended study that would include further experimental data to conclusively address one of the following issues:-Provide experimentally validated insights into the mechanisms that underlie the dynamics of the direct differentiation process and its robustness. This would include a more systematical perturbation analysis of the initial/central regulatory …
Anti-viral Capacity Of Quillaja Saponaria Molina Extract Against Vaccinia AndHerpes simplex Virus-1

ANTI-VIRAL CAPACITY OF QUILLAJA SAPONARIA MOLINA EXTRACT AGAINST VACCINIA AND HERPES SIMPLEX VIRUS-1 Publication No. ______ Matthew Sean Spinks, M.S. The University of Texas at Arlington, 2006 Supervising Professor: Michael Roner It is well known that Quillaja saponins have the ability to elicit a strong immune response when used as an adjuvant in an ISCOM matrix. However, to date, the antiviral capability of Quillaja saponins has not been documented. Using extracts from the Chilean Soap Bark Tree (Quillaja Saponaria Molina) we document the anti-viral capacities of Quillaja saponins against HSV-1 and Vaccinia. The saponin was ineffective against Vaccinia Virus, however neutralized HSV-1 in a time and temperature dependent manner. In addition, Quillaja Saponins were determined capable of preventing cell-to-cell spread when introduced in solution to cell monolayers.
Indicators of postoperative pain in cats and correlation with clinical criteria.

OBJECTIVE To identify clinical indicators that may help identity postoperative pain in cats after ovariohysterectomy. ANIMALS Healthy, laboratory animal source cats. PROCEDURE Clinical indicators of pain were identified, and relief from pain in response to butorphanol was studied in 5 groups of cats. 10 cats had 1 hour of general anesthesia only, followed by recovery without additional medication. 10 cats had general anesthesia and ovariohysterectomy, followed by recovery without additional medication. 10 cats had general anesthesia, ovariohysterectomy, and postoperative administration of 0.1 mg of butorphanol/kg of body weight. Another 10 cats had general anesthesia, ovariohysterectomy, and postoperative administration of 0.3 mg butorphanol/kg. 10 cats received 0.1 mg of butorphanol/kg, IM, only. Samples and recorded data were obtained before, during, and after the anesthesia period. Clinical variables measured included heart rate, blood pressure, respiratory rate, rectal temperature, PCV, and blood glucose concentration. Results were compared with changes in norepinephrine, epinephrine, and cortisol concentrations. RESULTS Cats that did not receive analgesics had higher cortisol concentration than did cats without surgery and cats that received butorphanol after surgery. Systolic blood pressure measured by ultrasonic Doppler was found to be predictive of cortisol concentration, using a multiple linear regression model. CONCLUSIONS Cortisol concentration increased in response to surgical stress and pain, and this increase was diminished by use of butorphanol. CLINICAL RELEVANCE Systolic blood pressure was the best clinical predictor of postoperative pain.
Combined effects of GSTM1 and GSTT1 polymorphisms on breast cancer risk

Abstract Many molecular epidemiology studies have reported an association between the combined effects of glutathione S-transferase M1 (GSTM1) and glutathione S-transferase T1 (GSTT1) polymorphisms on breast cancer risk. However, the results have been controversial. A meta-analysis was performed to clarify this issue. Meta-analysis of observational studies in epidemiology guidelines was used. Pooled the crude odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model or fixed-effects model. Several subgroup analyses were conducted by ethnicity, source of control, matching, and menopausal status. In addition, we also performed sensitivity analysis and publication bias. Moreover, a false-positive report probability (FPRP) test was applied to assess positive results. A significantly increased breast cancer risk was observed in overall population (GSTM1 null/GSTT1 present [− +] vs GSTM1 present/GSTT1 present [+ +]: OR = 1.19, 95% CI: 1.03–1.36, GSTM1 null/GSTT1 null [− −] vs + +: OR = 1.63, 95% CI: 1.29–2.06, (− +) + GSTM1 present/GSTT1 null (+ −) vs + +: OR = 1.17, 95% CI: 1.05–1.31, (− +) + (+ −) + (− −) vs + +: OR = 1.27, 95% CI: 1.12–1.44, and − − vs (− +) + (+ −) + (+ +): OR = 1.39, 95% CI: 1.17–1.66) and several subgroup analyses, such as Caucasians, Indians, postmenopausal women, and so on. However, positive results were only considered noteworthy in overall population (− − vs + +: FPRP = 0.150 and (− +) + (+ −) + (− −) vs + +: FPRP = 0.162). Moreover, no significant association was observed when we used the trim and fill method to adjust the pooled data from all populations. Further, none of positive results of sensitivity analysis were considered noteworthy (FPRP >0.2). These positive findings should be interpreted with caution and indicate that an increased breast cancer risk may most likely result from false-positive results, rather than from true associations or biological factors on the combined effects of GSTM1 and GSTT1. Future studies should be based on sample sizes well-powered and attention needs to be paid to study design to further identify this issue.
Surface Deformation Of The Whole Netherlands After PSI Analysis

Being a coastal country with low topography, the Netherlands is seriously threatened by the risk of being flooded. Improving our knowledge of the deformation signals affecting the country is therefore a need. Dutch authorities carry out periodic leveling measurements to monitor surface heights. A major country wide campain happens every 20 years, but if we take into account not only first order network campaigns but also higher order ones, heights are measured every 5 to 10 years, area dependent. However, the knowledge we obtain from these observations is very limited because the reduce density of benchmarks, around 1 every 10 km, (area dependent) and the low temporal sampling. A more thorough analysis can be performed with other geodetical techniques, in particular, time-series InSAR. These methods are able to provide with a density of reliable measurements of about 100 per km, although this is case dependent. Furthermore, the archive of the European space Agency (ESA) provide us with an observation every 35 days for the Netherlands, with one year data gap in 1994 and 3 years gap from 2001-2004. To estimate land deformation over the whole of the Netherlands we need to combine InSAR estimates obtained for different tracks (satellite foot-prints), but this operation is not trivial. First, to capture large scale deformation we need to take into account that radar images are usually affected by orbital errors and atmosphere. Second, since InSAR produce deformation maps relative to an area (or pixel) that is part of the observed track, data combination requires to change these relative measurements to a common area or reference point. In this contribution we explore a method for data combination to produce a velocity map of the whole Netherlands that reflect the average rates of the period 19922010). We combine all InSAR tracks available over the country for this period, plus leveling and GPS. These last two techniques help to better constrain the longwavelength deformation signal and remove ramps produce by atmosphere or orbital errors that affects InSAR measurements.
Study of variability and similarities among Lotus corniculatus L. accessions.

Summary: In an individual planting 25 birdsfoot trefoil (Lotus corniculatus L.) accessions constituting the Czech collection were assessed. Fourteen accessions were varieties from the world collection and eleven accessions were wild forms obtained during the collecting expeditions in the Czech Republic and abroad. Morphological, yield and qualitative traits were measured on ten plants of each accession. A total of 34 traits were evaluated. From these values point and interval estimates of means and variation coeffi cients were produced for each accession as a measure of variability of each particular trait within and among accessions. Point estimates of mean values of accessions formed a data matrix which was then processed by cluster analysis. Accessions with the highest similarity were determined based on these results.
Comment l'alimentation des poules influence la qualité des oeufs ?

Le producteur est interesse principalement par le poids de l'œuf et la solidite de la coquille. Le poids de l'œuf est conditionne par l'origine genetique et l'âge de la poule, mais aussi par les apports nutritionnels de la poulette puis de la poule. Le poids de la poulette a l'entree en ponte, la concentration energetique de l'aliment, les teneurs en proteines et acides amines (methionine notamment) et en acides gras (acides linoleique et oleique) influencent le poids de l'œuf. Moins etudies, la forme de l'aliment et les modes de distribution sont importants et meritent une attention particuliere pour les recherches a venir. La solidite de la coquille est determinee par l'alimentation calcique tant en termes de quantite de calcium que de taille des particules. Les effets de l'alimentation sur les proportions de l'albumen et du jaune, qui interessent le transformateur, sont marginaux en regard des effets de l'âge de la poule, neanmoins de legers effets sont observes en modifiant les apports en proteines, acides amines ou en acide linoleique. Pour les criteres interessant le consommateur, il est clairement etabli que la composition en acides gras de l'œuf est le reflet de la composition de l'aliment. Il est ainsi possible d'optimiser la valeur nutritionnelle de l'œuf via l'aliment. La composition en macroelements mineraux est invariable mais de nombreux oligoelements (iode, selenium, manganese) peuvent etre modules par l'apport alimentaire tout comme les vitamines liposolubles (E, D 3 , A et K). La couleur du jaune, quant a elle, est dependante des apports alimentaires, la poule ne pouvant synthetiser les carotenoides. Neanmoins l'efficacite de coloration est variable selon les pigments utilises.
Mutation breeding in vegetable crops: A review

Mutation breeding generally plays a very important role in vegetable crops. Among the different present approaches, mutagenesis and mutation breeding and the isolation of improved or novel phenotypes in conjunction with conventional breeding programmes can result in mutant varieties endowed with new and desirable variation of agrometrical traits. Induced mutations and its related technologies play very well in this ground and this overall strategy helps to trace the crop genetic diversity along with its biodiversity maintenance. Such induced mutagenesis, a crucial step in vegetable crop improvement programme, is now successful in application due to the advancement and incorporation of large-scale selection techniques, micro propagation and other in vitro culture methods, molecular biology tools and techniques in modern crop breeding performance. Molecular mutation breeding will significantly increase both the efficiency and efficacy of mutation techniques in crop breeding. Thus, mutation assisted plant breeding will play a crucial role in the generation of ‘designer crop varieties’. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of mutation breeding, and how these tools complement the ones already used in traditional breeding.
JCB_201404066 1..17

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 208 No. 7 931–947 www.jcb. org/cgi/doi/10.1083/jcb.201404066 JCB 931 Correspondence to Sean T. Sweeney: sean.sweeney@york.ac. uk Abbreviations used in this paper: ALS, amyotrophic lateral sclerosis; AP-1, activator protein-1; EPSP, excitatory postsynaptic potential; Eve, even-skipped; FTD, frontotemporal dementia; GMR, glass multimer reporter; Hiw, highwire; JNKKK, JNK kinase kinase; LAMP, lysosome-associated membrane protein; MCC, Mander’s correlation coefficient; mEPSP, miniature EPSP; MVB, multivesicular body; NMJ, neuromuscular junction; PCC, Pearson’s correlation coefficient; P-MAD, phosphorylated MAD; UAS, upstream activation sequence; VNC, ventral nerve cord; Wit, wishful thinking. Introduction