Miracle-dz/UniFAR-FTUs huggingface dataset:
The selection, testing and application of terrestrial insects as bioindicators

Although the uses and merits of terrestrial insects as indicators have been extensively discussed, there is a lack of clear definition, goal directedness and hypothesis testing in studies in the field. In an attempt to redress some of these issues and outline an approach for further studies, three categories of terrestrial insect indicators, corresponding to differences in their application, are proposed, i.e. environmental, ecological and biodiversity indicators. The procedures in terrestrial insect bioindicator studies should start with a clear definition of the study objectives and proposed use of the bioindicator, as well as with a consideration of the scale at which the study is to be carried out. Bioindication studies are conducted at a variety of spatial and temporal scales within the context of earth‐system processes, but the objectives of the study will largely determine the scale at which it would be optimally conducted. There is a tendency for studies to be conducted below their space‐time scaling functions, giving them apparent predictability. The selection of potential indicator taxa or groups is then based on a priori suitability criteria, the identification of predictive relationships between the indicator and environmental variables and, most importantly, the development and testing of hypotheses according to the correlative patterns found. Finally, recommendations for the use of the indicator in monitoring should be made. Although advocating rigorous, long‐term protocols to identify indicators may presently be questionable in the face of the urgency with which conservation decisions have to be made, this approach is critical if bioindicators are to be used with any measurable degree of confidence.
Construction and EST Analysis of cDNA Library from Latex in Hevea brasiliensis

In order to isolate and clone the functional genes involved in the latex metabolism,rubber biosynthesis pathway,and jasmonic acid biosynthesis pathway in Hevea brasilensis,a cDNA library was constructed from the la-tex in this research.The latex was collected from the newly tapped clone 7-33-97,RNA was extracted through SDS method,and then to purify by magnetic beads.The primary library had a total of 5×105 phages for the latex,in which above 90 % of the phages were recombinants.Insert sizes mainly ranging from1 000 bp to 2 000 bp were ob-tained.About 3 200 clones were randomly sequenced from the library;the Blast X analysis was carried out with the non-redundant protein database,and afterwards,the genes were made in classification according their functions.The cDNA library was in high quality,which was suitable for the detection and identification of functional genes in-cluding the lowabundance gene in latex.This library would provide a good foundation for investigating the molecu-lar mechanism of rubber biosynthesis and latex metabolism,and it was also an important resource for cloning the im-portant functional genes in latex.
p24 proteins, intracellular trafficking, and behavior: Drosophila melanogaster provides insights and opportunities

Summry— The p24 transmembrane proteins, also known as EMP24/GP25 (endomembrane protein precursor of 24kD (Schimmoller et al., 1995) proteins, are components of coat protein (COP)‐coated vesicles and are present in species as diverse as fungi, plants, flies, worms, and mammals, indicating that they have important conserved functions. Genetic, molecular, and biochemical characterization of these proteins and the loci that encode them has provided insights into their potential cellular roles, including postulated functions in vesicle cargo protein selection and sorting, COPI and COPII vesicle formation and budding, and quality control of proteins that mature through the secretory pathway. Recently, the first mutations in a Drosophila melanogaster p24 gene have been isolated and characterized. These alleles produce an interesting behavioral phenotype in females, affecting their ability to oviposit. This identification and mutant characterization of a p24 locus in Drosophila will pave the way for a better understanding of cell‐type‐specific functions and interactions among p24 proteins.
Introduction of data analytics in the engineering probability course: Implementation and lessons learnt

Data analytics‐based tools are used extensively in industry, business, science, engineering, and medicine. Efforts are being made to transform the undergraduate course in engineering probability by incorporating the data analytics while retaining the concept‐driven topics. The author has been engaged in these efforts since 2017–2018. This manuscript reports on a number of data analytics‐based assignments alongside the traditional ones consisting of exercises requiring proofs, derivations, and calculations created during the fall quarter of 2018–2019. These assignments rely on computational tools and are connected to the theoretical concepts allowing the students to understand and appreciate the use of conceptual topics to practical application in machine vision, robotics, medical diagnostics, and so forth. The details on these assignments along with their implementation, results, and lessons learnt and conclusions drawn are presented.
Allogeneic hematopoietic stem cell transplantation at the first remission for younger adults with FLT3‐internal tandem duplication AML: The JALSG AML209‐FLT3‐SCT study

In this phase II multicenter study (JALSG AML209‐FLT3‐SCT), we aimed to prospectively elucidate the role of allogeneic hematopoietic stem cell transplantation (allo‐HSCT) at first complete remission (CR1) for FLT3‐internal tandem duplication (ITD)‐positive AML. Newly diagnosed de novo AML patients with FLT3‐ITD were enrolled at the achievement of CR1 and received allo‐HSCT as soon as possible after the first consolidation therapy. Mutations of 57 genes in AML cells at diagnosis were also analyzed. Among 48 eligible patients with a median age of 38.5 (17‐49) years, 36 (75%) received allo‐HSCT at a median of 108 days after CR1. The median follow‐up was 1726 days. The primary end‐point, 3‐year disease‐free survival (DFS) based on an intent to treat analysis, was 43.8% (95% confidence interval [CI], 30%‐57%), suggesting the efficacy of this treatment because the lower limit of the 95% CI exceeded the threshold response rate of 20%. The 3‐year overall survival, post‐transplant DFS, and non‐relapse mortality rates were 54.2% (95% CI, 39%‐67%), 58.3% (95% CI, 41%‐72%), and 25.0% (95% CI, 12%‐40%), respectively. The median ITD allelic ratio (AR) was 0.344 (0.006‐4.099). Neither FLT3‐ITD AR nor cooccurring genetic alterations was associated with a poor DFS. This prospective study indicated the efficacy and safety of allo‐HSCT for FLT3‐ITD AML patients in CR1. This study was registered at: www.umin. ac.jp/ctr/ as #UMIN000003433.
On the origin and evolution of major morphological characters

Although the mathematical principles underpinning population‐level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least‐constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained (“burdened”, in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever‐increasing restriction on the scope of evolution, nor does it require drastic events to overcome or “break” it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype‐phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make‐up being of secondary importance. It should prove possible to recast traditional notions of body‐plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.
Evaluation of weaning regimen and seminal plasma biology on reproductive management in cattle

Evaluation of weaning regimen and seminal plasma biology on reproductive management in cattle John F. Odhiambo The goal of any reproductive management system in cattle is to ensure that cows breed at the earliest opportune time and maintain their pregnancy to term. However, delayed resumption of postpartum ovarian cyclic activity in primiparous beef cows and pregnancy losses in dairy cows continue to impede progress in obtaining sound reproductive efficiency in these species. Three studies were designed to test the following hypotheses: 1) Does removal of lactational stress in beef cows by early weaning of calves improve cow energy profile and postpartum reproductive performance? 2) Does artificial insemination (AI) with adjunctive seminal plasma (SP) or transforming growth factor beta-1 (TGF-β1) improve conception rates in lactating dairy and beef cows? 3) Does seminal plasma of dairy bulls differ in expression of proteins that might be used as potential biomarkers of male fertility? In experiment 1, pregnant and lactating beef cows (n = 408) were assigned randomly to wean calves either at 180 d of age (early weaning) or 45 d later (normal weaning). Body energy status was evaluated by periodic measurements of body weight (BW), body condition score (BCS), rib and rump fat. Reproductive performance was determined by calving intervals (CI), intervals from breeding to calving (BCI), retention in herd, and adjusted 205-d weaning weight of the subsequent calf. In experiment 2, lactating beef (n = 1090) and dairy (n = 800) cows received 0.5 mL SP, 40 ng recombinant human TGF-β1, or 0.5 mL bovine serum albumin (BSA) or were left untreated at insemination. Pregnancy was determined by transrectal ultrasonography 35 to 40 d post insemination or from records of calves born in the subsequent calving season. In experiment 3, seminal plasma from high (n = 8) and low (n = 6) fertility bulls at Select Sires Inc. (Plains City, OH) were assayed for TGF-β1 content, and subsequently analyzed by 2-D fluorescence difference gel electrophoresis (2-D DIGE) for presence of potential biomarkers of male fertility. Early weaning and cow age improved (P < 0.001) energy partitioning and production efficiency in beef cows. Rump fat measurements predicted body energy status better than BW or BCS (P < 0.001). Inseminations with SP and/or TGF-β1 numerically increased (P = 0.07) conception rates in beef and dairy cows. Concentrations of TGF-β1 in seminal plasma were numerically greater (P = 0.25) in high fertility dairy bulls than those of low fertility. Expression of fertility associated proteins did not differ (P > 0.05) between high and low fertility bulls. However, their expression patterns were altered by semen processing. In conclusion, reproductive efficiency in primiparous beef cows can be improved by removal of lactational stress during mid to late pregnancy, while in dairy cows inseminations with adjunctive SP and/or incorporation of some seminal plasma proteins into semen during processing might improve conceptions rates after AI.
An indirect role for cyclin B‐Cdc2 in inducing chromosome condensation in Xenopus egg extracts *

We have studied the cytoplasmic mechanism that induces metaphase chromosome condensation in cell‐free Xenopus egg extracts. To analyze the mechanism responsible for inducing chromosome condensation separately from those responsible for sperm chromatin remodeling and nuclear envelope disassembly, we used Xenopus sperm chromatin that had already been remodeled to nucleosomal chromatin by incubating demembranated sperm with egg extracts added with lysolecithin. We found that inhibition of cyclin B‐Cdc2 with butyrolactone I abolished chromosome condensation of the remodeled sperm chromatin by M‐phase egg extracts, but incubation of the chromatin with active cyclin B‐Cdc2 alone did not induce chromosome condensation, indicating a requirement for cytoplasmic factor(s) in addition to cyclin B‐Cdc2 for the induction of chromosome condensation. We further demonstrated that if the cyclin B‐Cdc2‐dependent phosphorylation state was protected against dephosphorylation by a preincubation of M‐phase extracts with ATP‐γ‐S, chromosome condensation and phosphorylation of chromosomal histone H1 occurred even when extracts were depleted of cyclin B‐Cdc2 activity. The chromosome condensation seen in the absence of cyclin B‐Cdc2 was completely inhibited with another protein kinase inhibitor, 6‐dimethylaminopurine, implying that a protein kinase other than cyclin B‐Cdc2 was involved in the induction of chromosome condensation. These results strongly suggest that a cyclin B‐Cdc2‐dependent protein kinase cascade is involved in inducing chromosome condensation and the phosphorylation of chromosomal histone H1.
Cytotoxicity and oxidative DNA damage induced by microcystin-LR

Objective To compare cytotoxic effects of microcystin-LR(MCLR) on human hepatoma cell lines HT17 and HepG2,and then study the oxidative DNA damages induced by MCLR.Methods Cytotoxicity was measured by MTT assay,and oxidative DNA damages were detected using immunostaining of 8-hydroxydeoxiguanosine(8-OHdG). Results Significant cytotoxic effects in HT17 cells were observed at MCLR concentrations higher than 1 μg/ml.Dose-respond relationship was found between MCLR exposure and cell viability.HT17 cells were more sensitive than HepG2 cells.MCLR even at non-cytotoxic concentration significantly increased the levels of 8-OHdG.Conclusion HT17 cells with the expression of organic anion transporting polypeptides(OATP)1B1 are more sensitive to MCLR.MCLR even at non-cytotoxic dose induces oxidative DNA damages,which may contribute to their genotoxicity during long-term exposure.
Investigating the biological properties of tigecycline

Antibiotic resistance of many bacterial strains to current antibiotic treatment strategies are increasing. Bacterial biofilm related diseases displaying resistance to current antibiotics is an area of intense investigations. Failure to eradicate biofilm forming pathogenic microorganisms, coupled with an exacerbated host immune response results in extensive tissue damage and ultimately chronic inflammation within infected patients. Periodontitis and cystic fibrosis (CF) represent typical forms of chronic inflammatory disease The aim of this study was to evaluate the efficacy of a newly developed glycylcycline, tigecycline, against non-pseudomonal Gram-negative CF pathogens and oral pathogens commonly associated with inflammatory disease of the lung and oral cavity, respectively. Minimum inhibitory concentrations (MICs) of periodontal and pulmonary pathogens in planktonic growth phase and sessile biofilms were determined by serial doubling dilutions with tigecycline. Furthermore, planktonic MICs and sessile MICs exposed to tigecycline and a competitive efflux pump inhibitor MC-207,110 EPI were assessed by XTT assays. In addition the biomasses of sessile biofilms exposed to tigecycline and EPI were determined by crystal violet assay. This investigation demonstrated a significant improvement in the susceptibility of both planktonic and sessile cells to tigecycline following the addition of an EPI, indicating that the EPI enhanced sensitivity to antibiotic treatment of resistant bacterial strains. Furthermore, bacterial biofilm biomass of the CF pathogen Burkholderia cepacia was reduced significantly by co treatments of tigecycline and EPI. Finally, the immunomodulatory properties of tigecycline were evaluated using clinically relevant epithelial cell lines, A549 OKF6-TERT2 and a primary neutrophil cell line. Oral and pulmonary cell lines were co-inoculated with subinhibitory concentration of tigecycline and Escherichia coli derived lipopolysaccharide (LPS). The neutrophil cell line was co-inoculated with (phorbol 12-myristate acetate) PMA and tigecycline. Epithelial IL-6 and IL-8 levels were determined by ELISA and RT-qPCR, demonstrating only marginal down-regulation in some cases of these inflammatory mediators. However, tigecycline at subinhibitory concentrations did reduce the levels of IL-8 and MMP-9 synthesised by neutrophils in a dose dependent manner. In conclusion, tigecycline alone is ineffective at killing and reducing biomass of mature biofilms associated with chronic inflammatory disease of the lungs and oral cavity, however the addition of a competitive efflux pump inhibitor decreased resistance of the bacterial biofilm to tigecycline. This would suggest a possible new chemotherapeutic use to treat patients who suffer from a chronic inflammatory disease. Furthermore, down-regulation of inflammatory mediators by subinhibitory concentration of tigecycline may indicate a potential use in the therapeutic management of both CF and periodontal disease, and other diseases of chronic inflammatory origin.
Analysis of skeletal and cardiac muscle from desmin knock‐out and normal mice by high resolution separation of myosin heavy‐chain isoforms

Summary— In this study, using a modified electrophoretic technique, we have defined in the mouse the myosin heavy‐chain composition of both newborn and adult skeletal and cardiac muscles. Using this high resolution technique it was possible to detect modifications in the myosin heavy‐chain expression in both cardiac and skeletal muscles of desmin knock‐out mice.
Transient reactivation of CSF in parthenogenetic one‐cell mouse embryos

During meiosis, the cytostatic factor (CSF) activity stabilizes the activity of the M‐phase promoting factor (MPF) in metaphase II arrested vertebrate oocytes. Upon oocyte activation, the inactivation of both MPF and CSF enables the entry into the first embryonic mitotic cell cycle. Using a biological assay based on cell‐fusion (hybrid between a parthenogenetically activated egg entering the first mitotic division and an activated oocyte), we observed that in activated mouse oocytes a first drop in CSF activity is detectable as early as 20 min post‐activation. This suggests that CSF is inactivated upon MPF inactivation. However, CSF activity increases again to reach a maximum 60 min post‐activation and gradually disappears during the following 40 min. Thus, in activated mouse oocytes (undergoing the transition to interphase) CSF activity fluctuates before definitive inactivation. We found that hybrids arrested in M‐phase, thus containing CSF activity after oocyte activation, have activated forms of MAP kinases while hybrids in interphase have inactive forms of these enzymes. We postulate that CSF inactivation in mouse oocytes proceeds in two steps. The initial inactivation of CSF, required for MPF inactivation, is transient and does not require MAP kinase inactivation. The final inactivation of CSF, required for normal embryonic cell cycle progression, is dependent upon the inactivation of MAP kinases.
The Xenopus laevis centrosome aurora/lpl1‐related kinase

The cDNA encoding the protein kinase pEg2 was originally cloned through a differential screening performed during the early development of Xenopus laevis. pEg2 orthologues were found in various organisms and were classified in a new family of oncogenic mitotic protein kinases named ‘aurora/Ipl1‐related kinases’ after the Drosophila melanogaster gene aurora and the Saccharomyces cerevisiae gene Ipl1. The catalytic activity of pEg2 is necessary for the mitotic microtubule spindle formation in Xenopus laevis egg extracts. The addition of a dominant negative form of pEg2 to in vitro spindle assembly assays leads to monopolar spindles generated by a defect of centrosome separation. In Xenopus cultured cells, pEg2 was confined around the pericentriolar material once centrosomes were duplicated. The centrosome localization does not depend on the presence of microtubules. However, in vitro, the protein binds to taxol‐stabilized microtubules independently of its kinase activity. During mitosis the location of the protein changes, in metaphase the kinase localizes on the microtubules at the poles of the mitotic spindle whereas it is not present on astral microtubules. This localization persists until the segregation of the chromosomes is completed. The presence of the kinase on the spindle may reveal another yet unknown function.
A parsimonious model for locomotor in virtual agents based on dynamical coupling with the environment

In the domain of virtual agents modeling, computationalist approaches tend to predominate. The lack of plausibility of the rules in nature provides models with a low capacity to generalize and a very limited insight into behavioral phenomena. An alternative view is that behavior could emerge as a whole from the basic principles of non‐linear dynamics that underlie such behavior in the environment. This paper presents a dynamic agent endowed with a sensing device, a controller and actuators to interact with the environment. The control architecture is based on ordinary differential equations with the function of modulating the stimulus signals to action signals under a sensory‐motor flow. The parameter values are defined in an evolutionary process depending on the task to be performed. A series of experiments are presented to illustrate certain qualities of our model such as the adaptability to change, a highly intuitive and flexible design methodology, and a high degree of individual autonomy, among others. We think this kind of modeling is useful in the animation world for modeling flocks, crowds, and swarms as a valid alternative to other less parsimonious techniques.
Autonomous activation of histone H1 kinase, cortical activity and microtubule organization in one‐ and two‐cell mouse embryos

The activation of M‐phase promoting factor (MPF) in one‐cell mouse embryo is independent from the nucleus. Other autonomous phenomena include the cortical activity observed at the end of the first cell cycle and the reorganization of the microtubule network. Here, we observed that the autonomous control of MPF activation is present also in two‐cell mouse embryos (H1 kinase activity being higher in the first than in the second cell cycle). Moreover, the disappearance of the cortical activity in anucleated halves is observed when MPF activation takes place. The rounding up of the cytoplast and the mitotic reorganization of the microtubule network correlates with the maximum activity of H1 kinase in anucleated halves from one‐cell embryos. In anucleated halves of two‐cell stage blastomeres neither the cortical activity nor the microtubule reorganization were observed. The degree of activation of histone H1 kinase, and, as a consequence, the cortical activity and the microtubule reorganization, does not depend on the distribution of cyclin B. Finally, the level of cyclin B synthesis is similar in anucleated and nucleated halves derived from both one‐and two‐cell embryos.