Miracle-dz/UniFAR-FTUs huggingface dataset:
Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis

Bordetella pertussis is the causative agent of human whooping cough, a highly contagious respiratory disease which despite vaccination programs remains the major cause of infant morbidity and mortality. The requirement of the RNA chaperone Hfq for virulence of B. pertussis suggested that Hfq-dependent small regulatory RNAs are involved in the modulation of gene expression. High-throughput RNA sequencing revealed hundreds of putative noncoding RNAs including the RgtA sRNA. Abundance of RgtA is strongly decreased in the absence of the Hfq protein and its expression is modulated by the activities of the two-component regulatory system BvgAS and another response regulator RisA. Whereas RgtA levels were elevated under modulatory conditions or in the absence of bvg genes, deletion of the risA gene completely abolished RgtA expression. Profiling of the ΔrgtA mutant in the ΔbvgA genetic background identified the BP3831 gene encoding a periplasmic amino acid-binding protein of an ABC transporter as a possible target gene. The results of site-directed mutagenesis and in silico analysis indicate that RgtA base-pairs with the region upstream of the start codon of the BP3831 mRNA and thereby weakens the BP3831 protein production. Furthermore, our data suggest that the function of the BP3831 protein is related to transport of glutamate, an important metabolite in the B. pertussis physiology. We propose that the BvgAS/RisA interplay regulates the expression of RgtA which upon infection, when glutamate might be scarce, attenuates translation of the glutamate transporter and thereby assists in adaptation of the pathogen to other sources of energy.
High-throughput sequencing of murine immunoglobulin heavy chain repertoires using single side unique molecular identifiers on an Ion Torrent PGM

With the advent of high-throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. Advances in sequencing technology enable the IonTorrent Personal Genome Machine (PGM) to cover the full-length of IG mRNA transcripts. Nucleotide insertions and deletions (indels) are the dominant errors of the PGM sequencing platform and can critically influence IG repertoire assessments. Here, we present a PGM-tailored IG repertoire sequencing approach combining error correction through unique molecular identifier (UID) barcoding and indel detection through ImMunoGeneTics (IMGT), the most commonly used sequence alignment database for IG sequences. Using artificially falsified sequences for benchmarking, we found that IMGT's underlying algorithms efficiently detect 98% of the introduced indels. Undetected indels are either located at the end of the sequences or produce masked frameshifts with an insertion and deletion in close proximity. The complementary determining regions 3 (CDR3s) are returned correct for up to 3 insertions or 3 deletions through conservative culling. We further show, that our PGM-tailored unique molecular identifiers result in highly accurate HTS data if combined with the presented processing strategy. In this regard, considering sequences with at least two copies from datasets with UID families of minimum 3 reads result in correct sequences with over 99% confidence. Finally, we show that the protocol can readily be used to generate homogenous datasets for bulk sequencing of murine bone marrow samples. Taken together, this approach will help to establish benchtop-scale sequencing of IG heavy chain transcripts in the field of IG repertoire research.
Fetal mummification in the major domestic species: current perspectives on causes and management

Fetal mummification is an uncommon condition in most domestic species. While most often seen in multiparous and polytocous species like swine, it is also observed in monotocous species when the fetus is retained for a long time. The low prevalence of the condition may help explain the scarcity of information in the literature. To further complicate the study of this phenomenon, the physiological mechanisms that maintain pregnancy vary between species, implying different pathways for the condition. The exact outcome of early fetal mortality is unpredictable, and is influenced by several factors, including the cause of fetal mortality, differences in pregnancy between species, stage of gestation at fetal death, and number of fetuses. Based on our current knowledge of natural fetal mummification events, there are a number of prerequisites for the process of fetal mummification to occur. Examining the circumstances associated with fetal mummification can help scientists better understand the etiology and clinical situation in different species. The objective of this article is to review fetal mummification in the major domestic species: cattle, goats, sheep, horses, swine, dogs, and cats. This paper discusses the clinical situation, the most common and important etiologies, and the treatment approaches for restoring future pregnancy in the female, and where applicable, herd fertility.
Doxorubicin-induced elevated oxidative stress and neurochemical alterations in brain and cognitive decline: protection by MESNA and insights into mechanisms of chemotherapy-induced cognitive impairment (“chemobrain”)

Chemotherapy-induced cognitive impairment (CICI) is now widely recognized as a real and too common complication of cancer chemotherapy experienced by an ever-growing number of cancer survivors. Previously, we reported that doxorubicin (Dox), a prototypical reactive oxygen species (ROS)-producing anti-cancer drug, results in oxidation of plasma proteins, including apolipoprotein A-I (ApoA-I) leading to tumor necrosis factor-alpha (TNF-α)-mediated oxidative stress in plasma and brain. We also reported that co-administration of the antioxidant drug, 2-mercaptoethane sulfonate sodium (MESNA), prevents Dox-induced protein oxidation and subsequent TNF-α elevation in plasma. In this study, we measured oxidative stress in both brain and plasma of Dox-treated mice both with and without MESNA. MESNA ameliorated Dox-induced oxidative protein damage in plasma, confirming our prior studies, and in a new finding led to decreased oxidative stress in brain. This study also provides further functional and biochemical evidence of the mechanisms of CICI. Using novel object recognition (NOR), we demonstrated the Dox administration resulted in memory deficits, an effect that was rescued by MESNA. Using hydrogen magnetic resonance imaging spectroscopy (H1-MRS) techniques, we demonstrated that Dox administration led to a dramatic decrease in choline-containing compounds assessed by (Cho)/creatine ratios in the hippocampus in mice. To better elucidate a potential mechanism for this MRS observation, we tested the activities of the phospholipase enzymes known to act on phosphatidylcholine (PtdCho), a key component of phospholipid membranes and a source of choline for the neurotransmitter, acetylcholine (ACh). The activities of both phosphatidylcholine-specific phospholipase C (PC-PLC) and phospholipase D were severely diminished following Dox administration. The activity of PC-PLC was preserved when MESNA was co-administered with Dox; however, PLD activity was not protected. This study is the first to demonstrate the protective effects of MESNA on Dox-related protein oxidation, cognitive decline, phosphocholine (PCho) levels, and PC-PLC activity in brain and suggests novel potential therapeutic targets and strategies to mitigate CICI.
A novel in vitro assay reveals SNARE topology and the role of Ykt6 in autophagosome fusion with vacuoles

Autophagy is a catabolic pathway that delivers intracellular material to the mammalian lysosomes or the yeast and plant vacuoles. The final step in this process is the fusion of autophagosomes with vacuoles, which requires SNARE proteins, the homotypic vacuole fusion and protein sorting tethering complex, the RAB7-like Ypt7 GTPase, and its guanine nucleotide exchange factor, Mon1-Ccz1. Where these different components are located and function during fusion, however, remains to be fully understood. Here, we present a novel in vitro assay to monitor fusion of intact and functional autophagosomes with vacuoles. This process requires ATP, physiological temperature, and the entire fusion machinery to tether and fuse autophagosomes with vacuoles. Importantly, we uncover Ykt6 as the autophagosomal SNARE. Our assay and findings thus provide the tools to dissect autophagosome completion and fusion in a test tube.
Phytochemical analysis, antimicrobial and antioxidant activities of different parts of Pleocaulus sessilis (Nees) Bremek (Acanthaceae)

Aim: This study aims to investigate antimicrobial and antioxidant activity of leaf, stem, and inflorescence of Pleocaulus sessilis (Nees) Bremek belonging to Acanthaceae. Materials and Methods: The leaves, inflorescences, and stems were separated, dried under shade, powdered, and extracted using methanol by maceration process. Preliminary phytochemical analysis was carried out by standard phytochemical tests. Antibacterial and antifungal activity was carried out by agar well diffusion and poisoned food technique, respectively. Antioxidant activity was evaluated by 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, 2,2-azinobis 3-ethylbenzothiazoline 6-sulfonate (ABTS) radical scavenging and ferric reducing assays. Folin-Ciocalteu reagent method was employed to estimate the total phenolic content of extracts. Results and Discussion: Flavonoids, saponins, steroids, and phenols were present in all three extracts. Extracts were inhibitory to all test bacteria with maximum activity against Klebsiella pneumoniae. Overall, inflorescence extract exhibited high inhibition of test bacteria when compared to other extracts. Extracts were effective in reducing mycelial growth of test fungi. Leaf extract was more effective against test fungi followed by inflorescence and stem extracts. All extracts exhibited dose-dependent radical scavenging and ferric reducing activity. Leaf extract exhibited marked antioxidant activity when compared to other two extracts. The leaf extract scavenged DPPH and ABTS radicals with an inhibitory concentration value of 27.16 μg/ml and 9.16 μg/ml, respectively. Total phenolic content was high in leaf extract (112.13 mg gallic acid equivalents [GAE]/g) followed by inflorescence (85.65 mg GAE/g) and stem (42.42 mg GAE/g) extracts. Conclusion: The plant can be used to treat diseases caused by pathogenic bacteria, prevention, and control of phytopathogens and oxidative damage caused by free radicals. Further studies are to be carried out to isolate and characterize active principles from the plant and to determine their biological activities.
A novel camera calibration method for fish-eye lenses using line features

In this paper, a novel method for the fish-eye lens calibration is presented. The method required only a 2D calibration plane containing straight lines i.e., checker board pattern without a priori knowing the poses of camera with respect to the calibration plane. The image of a line obtained from fish-eye lenses is a conic section. The proposed calibration method uses raw edges, which are pixels of the image line segments, in stead of using curves obtained from fitting conic to image edges. Using raw edges is more flexible and reliable than using conic section because the result from conic fitting can be unstable. The camera model used in this work is radially symmetric model i.e., bivariate non-linear function. However, this approach can use other single view point camera models. The geometric constraint used for calibrating the camera is based on the coincidence between point and line on calibration plane. The performance of the proposed calibration algorithm was assessed using simulated and real data.
Building a foundation: Land-use history and dendrochronology reveal temporal dynamics of a Tsuga canadensis (Pinaceae) forest

Abstract We used historical documents, stand mapping, and new methods of dendrochronological analysis to reconstruct 250 y of land-use history of the Simes Tract in Petersham, MA. These data were then used to interpret the origin of the current forest's stand structure within the experimental plots of the Harvard Forest Hemlock Removal Experiment within the Simes Tract, an experiment that examines the effects of the ongoing decline of Tsuga canadensis on forest ecology. Data from tree cores revealed that the trees in the experimental plots were < 150 y old. These trees have established continually since the 1870s, with recruitment pulses following successive episodes of land division and re-aggregation, logging, irruptions of nonnative insects and pathogens, two moderate droughts, and the 1938 “Great Hurricane”. Our new method of dendrochronological analysis used generalized additive models and focused on year-to-year dynamics to highlight associations between fine-scale changes in tree growth, and both episodic (pulse) and longer-term environmental and biotic drivers. Tsuga canadensis, hypothesized to be a foundation species in this system, achieved its current dominance at the Simes Tract by responding rapidly, both positively and uniformly across age classes, in the 1920s to three concomitant environmental changes that had occurred in the preceding two decades: loss of Castanea dentata to the chestnut blight; selective logging; and a ∼ 7 y drought. In contrast, Betula lenta, Quercus rubra, Acer rubrum, and Pinus strobus have declined in importance since the early 1900s in stands otherwise dominated by T. canadensis. Acer rubrum and P. strobus were selectively harvested or severely damaged by the 1938 hurricane, the peak of B. lenta establishment followed the 1938 hurricane, and Q. rubra growth was impacted by the severe 1981 gypsy moth outbreak. Together, the data illustrate the contingent nature of the establishment dynamics of a foundation species in a New England forest and suggest a more nuanced approach to the role of T. canadensis as a foundation species.
Implementation of Laminate Theory Into Strain Rate Dependent Micromechanics Analysis of Polymer Matrix Composites

A research program is in progress to develop strain rate dependent deformation and failure models for the analysis of polymer matrix composites subject to impact loads. Previously, strain rate dependent inelastic constitutive equations developed to model the polymer matrix were implemented into a mechanics of materials based micromechanics method. In the current work, the computation of the effective inelastic strain in the micromechanics model was modified to fully incorporate the Poisson effect. The micromechanics equations were also combined with classical laminate theory to enable the analysis of symmetric multilayered laminates subject to in-plane loading. A quasi-incremental trapezoidal integration method was implemented to integrate the constitutive equations within the laminate theory. Verification studies were conducted using an AS4/PEEK composite using a variety of laminate configurations and strain rates. The predicted results compared well with experimentally obtained values.
The Biterm Author Topic in the Sentences Model for E-Mail Analysis

E-mails, which vary in length, are a special form of text. The difference in the lengths of e-mails increases the difficulty of text analysis. To better analyze e-mail, our models must analyze not only long emails but also short e-mails. Unlike normal documents, short texts have some unique characteristics, such as data sparsity and ambiguity problems, making it difficult to obtain useful information from them. However, long text and short text cannot be analyzed in the same manner. Therefore, we have to analyze the characteristics of both. We present the Biterm Author Topic in the Sentences Model (BATS) model; it can discover relevant topics of corpus and accurately capture the relationship between the topics and authors of e-mails. The Author Topic (AT) model learns from a single word in a document, while the BATS is modeled on word co-occurrence in the entire corpus. We assume that all words in a single sentence are generated from the same topic. Accordingly, our method uses only word co-occurrence patterns at the sentence level, rather than the document or corpus level. Experiments on the Enron data set indicate that our proposed method achieves better performance on e-mails than the baseline methods. What’s more, our method analyzes long texts effectively and solves the data sparsity problems of short texts. key words: e-mail analysis, author topic, BATS model, sentence
Phytoplankton pigment specific growth and losses due to microzooplankton grazing in a northern Gulf of Mexico estuary during winter/fall

Microzooplankton dilution grazing experiments were carried out on 6 dates, over a 3 month period at 2 locations in the Bay of St. Louis, MS (BSL) to determine phytoplankton pigment specific growth rates under natural (μ0) and replete (μn) nutrient conditions and microzooplankton grazing. We hypothesized that diatoms would be the largest portion of the phytoplankton composition due to the winter/fall season and that these organisms would have the highest growth/grazing rates. We suspected that river flow from the Jourdan River would adversely affect growth and grazing rates of all phytoplankton classes. Growth rates of 5 phytoplankton accessory pigments (peridinin, fucoxanthin, alloxanthin, zeaxanthin, chlorophyll b) were identified. Intrinsic growth rates (μ0) were often zero or negative (range: —0.46 to 0.56/d) at the location nearest the Jourdan River, particularly for alloxanthin (e.g., cryptophytes) and peridinin (e.g., dinoflagellates). Significant grazing of chlorophyll a was observed on 3 of 6 dates while grazing on marker pigments was variable. The phytoplankton community appeared nutrient limited during all but one experiment (μ0<μn). Intrinsic growth and grazing rates were correlated (p < 0.05, Spearman Rank Order correlation). Peridinin and alloxanthin—based growth and grazing rates were positively correlated with salinity, suggesting a river influence on these 2 phytoplankton pigment classes. We conclude that in the BSL microzooplankton preferentially grazed on the phytoplankton class which had the highest intrinsic growth rate. We show that this is greatly affected by riverine input into the estuary and nutrient limitation.
Population genetics of insecticide resistance in the mosquito Culex pipiens

Thirty years of control of the mosquito Culex pipiens using organophosphate insecticides (OP) has selected for OP-resistance alleles on a world-wide scale. As reviewed here, studies at the levels of gene and population allow identification of the main forces driving this process of adaptation. Three loci are involved in OP-resistance in C. pipiens. For two of these, adaptive mutations were found to be rare events, such that the ubiquitous distribution of certain resistance alleles could only be explained as deriving from a single origin by mutation followed by extensive migration. Population structure analyses confirmed that long-distance migration is frequent. Thus, different resistance alleles could accumulate and compete within populations soon after their origin by mutation. The different selection pressures acting on these alleles, i.e. their selective advantage in the presence of OP and their disadvantage (resistance cost) in absence of OP, were also analysed. Substantial differences in resistance cost among alleles present within the Mediterranean area were discovered. Long-term surveys of Mediterranean populations confirmed the pivotal importance of resistance cost in shaping the evolution of this adaptive polymorphism. Some hypotheses on the functional links between the nature of the initial mutation events and the subsequent evolution of polymorphism are discussed.
Uma Análise Interdisciplinar da Relação entre Gestão da Informação e do Conhecimento e a Pesquisa Qualitativa em Educação

Este artigo de cunho exploratorio e descritivo tem por objetivo relacionar, por meio de revisao de literatura, gestao do conhecimento, processos interdisciplinares em pesquisa qualitativa e gestao da informacao em organizacoes educacionais. A gestao do conhecimento e a pesquisa em educacao sao areas que envolvem uma perspectiva interdisciplinar. No percurso de pesquisa em Gestao do Conhecimento Educacional e Gestao da Informacao e possivel promover relacoes a partir de um olhar focado na gestao dos saberes. Neste sentido, pesquisar qualitativamente a relacao entre contextos empresariais e educacionais implica necessariamente pesquisar sobre comunicacao, intervencao, gestao de pessoas e avaliacao.
Quantifying Dry Rubber Content in Latex Solution Using an Ultrasonic Pulse

Abstract The quality of latex solution harvested from a para rubber tree is determined by the amount of dry rubber content (DRC). In this work, we propose the use of an ultrasonic pulse for quantifying the DRC in latex solution. Fresh latex solutions are acquired locally from different regions in the south of Thailand. The DRC of the solutions is evaluated for calibration purposes by the standard technique as recommended in ISO126:2005. Along with the calibration experiment, the ultrasonic pulse experiment is performed on the same set of the solutions in cylindrical tubes of different lengths. The ultrasonic pulse transverse longitudinally through the tubes which are fully contained with the latex solutions. Ultrasonic speeds and spatial attenuations for different dry rubber contents can then be obtained. Our results reveal that the ultrasonic speed and spatial attenuation are linearly proportional to the amount of dry rubber content in latex solution. Using the empirical relationship between the spatial attenuation and the DRC, we can predict the DRC with the accuracy comparable to that of the microwave-drying technique. Given the size of the tube, our setup is relatively small and can be portable
Optimization of forest age-dependent light-use efficiency and its implications on climate-vegetation interactions in china

Abstract. Forest’s net primary productivity (NPP) is a key index in studying interactions of climate and vegetation, and accurate prediction of NPP is essential to understand the forests’ response to climate change. The magnitude and trends of forest NPP not only depend on climate factors (e.g., temperature and precipitation), but also on the succession stages (i.e., forest stand age). Although forest stand age plays a significant role on NPP, it is usually ignored by remote sensing-based models. In this study, we used remote sensing data and meteorological data to estimate forest NPP in China based on CASA model, and then employed field observations to inversely estimate the parameter of maximum light-use efficiency (emax) of forests in different stand ages. We further developed functions to describe the relationship between maximum light-use efficiency (emax) and forest stand age, and estimated forest age-dependent NPP based on these functions. The results showed that emax has changed according to forest types and the forest stand age. For deciduous broadleaf forest, the average emax of young, middle-aged and mature forest are 0.68, 0.65 and 0.60 gC MJ-1. For evergreen broadleaf forest, the average emax of young, middle-aged and mature forests are 1.05, 1.01 and 0.99 gC MJ-1. For evergreen needleleaf forest, the average emax of young, middle-aged and mature forests are 0.72, 0.57 and 0.52 gC MJ-1.The NPP of young and middle-aged forests were underestimated based on a constant emax. Young forests and middle-aged forests had higher emax, and they were more sensitive to trends and fluctuations of climate change, so they led to greater annual fluctuations of NPP. These findings confirm the importance of considering forest stand age to the estimation of NPP and they are significant to study the response of forests to climate change.