Miracle-dz/UniFAR-FTUs huggingface dataset:
Wendlandia exserta: a pertinent source of antioxidant and antimicrobial agent

Abstract Objective The aim of the present investigation was to assess the antioxidant, antibacterial and antifungal activities of various fractions of Wendlandia exserta (Roxbukan Pansara). Methods The methanolic extract of W. exserta (Roxbukan Pansara) was dissolved in water (distilled) and then partitioned with solvents e.g. n-hexane, CHCl3, EtOAc and n-BuOH consecutively. Antioxidant potential of above mentioned fractions and remaining aqueous fraction was checked by four methods. Antimicrobial activity was examined by four bacteria and four fungi by the disc diffusion method by using a standard, as positive control. Results The aqueous fraction displayed maximum value of diphenyl picryl hydrazyl (DPPH) radical inhibition (85.94%±0.35) with an IC50 value of 415.31±0.26 μg mL−1. The aqueous fraction also displayed the maximum ferric reducing antioxidant power (FRAP) value [64.5±0.15 μg of trolox equivalents (TE)] as well as maximum inhibition of lipid peroxidation (42.32%±0.59) and maximum value of total phenolic contents (87.10±1.10). However, the n-BuOH fraction was found to display the maximum value of total antioxidant activity (0.529±0.76). The fractions also displayed good antimicrobial activity against various microorganisms. Conclusions It was concluded that polar fractions of W. exserta showed good antioxidant and antimicrobial activity, so these might be useful in pharmacological preparations.
Predictions of Protein-Protein Interactions in Schistosoma Mansoni

Background Schistosoma mansoni invasion of the human host involves a variety of cross-species protein-protein interactions. The pathogen expresses a diverse arsenal of proteins that facilitate the breach of physical and biochemical barriers present in skin, evasion of the immune system, and digestion of human hemoglobin, allowing schistosomes to reside in the host for years. However, only a small number of specific interactions between S. mansoni and human proteins have been identified. We present and apply a protocol that generates testable predictions of S. mansoni-human protein interactions. Methods In this study, we first predict S. mansoni-human protein interactions based on similarity to known protein complexes. Putative interactions were then scored and assessed using several contextual filters, including the use of annotation automatically derived from literature using a simple natural language processing methodology. Our method predicted 7 out of the 10 previously known cross-species interactions. Conclusions Several predictions that warrant experimental follow-up were presented and discussed, including interactions involving potential vaccine candidate antigens, protease inhibition, and immune evasion. The application framework provides an integrated methodology for investigation of host-pathogen interactions and an extensive source of orthogonal data for experimental analysis. We have made the predictions available online for community perusal. Author Summary The S. mansoni parasite is the etiological agent of the disease Schistomiasis. However, protein-protein interactions have been experimentally characterized that relate to pathogenesis and establishment of infection. As with many pathogens, the understanding of these interactions is a key component for the development of new vaccines. In this project, we have applied a computational whole-genome comparative approach to aid in the prediction of interactions between S. mansoni and human proteins and to identify important proteins involved in infection. The results of applying this method recapitulate several previously characterized interactions, as well as suggest additional ones as potential therapeutic targets.
A Single Pair of Neurons Defines a Neuropeptide-Dependent Aversive Memory Channel in Drosophila melanogaster

Parallel information processing in distinct channels is a common functional principle of nervous systems to facilitate rapid and precise extraction of specific features. A hallmark of such parallel processing is that the originally acquired information is initially segregated into individual processing channels that are tuned to extract distinct features of the input before re-converging them to guide appropriate responses. Parallel processing also applies to aversive olfactory memories in Drosophila where the metabolically costly and more enduring memory channel is sensitive to cold anesthesia (ASM) whereas the parallel anesthesia resistant memory channel (ARM) is only transient. The molecular basis and functional significance of this segregation of aversive olfactory memories in parallel channels is currently unclear. Here, we show that an aversive unconditioned stimulus (US) used in classical olfactory conditioning experiments is responsible for synaptic activity-driven neuronal nuclear calcium transients in distinct areas of the fly brain. These areas include the fly's association center, the mushroom bodies (MBs), as well as the fly's master regulator of its neuropeptidergic system, the pars intercerebralis (PI). Blockade of nuclear calcium signaling allowed us to functionally and morphologically separate the role of cAMP, a classical signaling pathway in learning and memory, and nuclear calcium signaling in the establishment of consolidated long-term memories (LTM) (Weislogel et al., 2013). In addition, we show that the US activates the fly’s widespread neuropeptidergic system and, in particular, the PI which results in multiple local signaling events or even systemic responses. Furthermore, we show that the acquisition and formation of all ASM phases requires additional release of mature neuropeptides from a single pair of dorsal paired medial (DPM) neurons. DPM neurons form a recurrent network with mushroom body neurons that has been shown to be involved in the formation of serotonin-dependent ARM, consolidation of memory and linking these consolidation processes to sleep. Our results reveal that DPMs define a qualitatively distinct parallel memory channel that strictly depends on mature neuropeptides and that is, within the first hours after training, behaviorally additive to the neuropeptide-independent ARM channel. Afterwards, in its subsequent consolidated phase, the ASM channel becomes exclusive towards the ARM channel. Thus, we propose that DPM neurons are capable of gating the simultaneous formation of two parallel memory channels by means of using two distinct signaling systems. Finally, given that neuropeptide signaling appears to be more widely involved in the processing of the US, it could represent a general mean of defining parallel processing channels.
Antibacterial activity of methanol extracts from selected seaweed of south east coast of India

Seaweeds offer a rich source of bioactive molecules; the present study was carried out to the antimicrobial activity of Methanol extract of three species of marine macroalgae were screened for their antimicrobial potency against seven pathogenic bacterial strains. Three seaweeds Ulva lactuca, Sargassum wightii and Gracilaria edulis were collected from four different stations (Station 1 (Chinnamuttom), Station 2 (Mandapam), Station 3 (Rameshwaram) and Station 4 (Thondi) of South East coast of India. Their antibacterial activity was evaluated. The methanolic extracts of U. lactuca showed high activity against Salmonella typhii (10±1.4) in station I. S. wightii inhibited Streptococcus faecalis ( 6.5± 0.7) the most in station III and G. edulis showed a maximum zone of inhibition against Streptococcus faecalis (8± 0.6) in station III. Among these three species U. lactuca significantly showed maximum antimicrobial activity than the other species (P<0.05). Results of the present study confirmed the potential use of seaweed extracts as a source of antibacterial compounds.
Pathogenesis of Bartonella Henselae in the Domestic Cat: Use of a PCR-based Assay for the Detection and Differentiation of B. Henselae Genotype I and Genotype II in Chronically Infected Cats.

Bartonella henselae is a zoonotic agent in which the domestic cat serves as the natural reservoir, and humans acquire potentially serious infections associated with this microorganism. The purpose o f this research is to contribute to the understanding of the pathogenesis of B. henselae in the domestic cat using a molecular approach. Using sequence differences in a portion of thel6S rRNA gene between B. henselae genotype I, and B. henselae genotype II, a nested polymerase chain reaction (nPCR) was designed and used to investigate various phases of feline bartonellosis. The nPCR detected 3.2 organisms per milliliter of blood which is below the detection limits of standard bacterial culture. Bartonella henselae LSU 16 genotype II, Bartonella henselae Baby genotype II, Bartonella henselae 87-66 genotype I, and Bartonella henselae Houston-1 genotype I were used in this study to infect cats. The PCR assay detected Bartonella DNA in 40 blood samples that were culture negative. The bacteremia as determined by PCR lasted for a period of 1 to 9 weeks longer than determined by culture methods in 10 of the 16 cats. An episode of relapsing bacteremia occurred in two cats during the infection. Of the twenty-three cats examined, Bartonella DNA was detected in various tissues from 10 of the 23 cats. The spleen of nine o f the 10 cats was positive for Bartonella DNA. The other tissues in which Bartonella DNA was detected included bone marrow, lymph node, kidney, lung, liver, brain, and heart valve. Histopathological lesions associated with nonspecific antigenic stimulation were seen in the cats but organisms could not be visualized in tissue. RNA expression analysis using the RT-PCR assay with primers specific for the 16S rRNA and the citrate synthase gene (gitA) of Bartonella detected no Bartonella RNA
Occurrence of Cowpea mild mottle virus in Common Bean and Associated Weeds in Northeastern Brazil

Cowpea mild mottle virus (CPMMV - Carlavirus, Betaflexiviridae) is a positive single-stranded RNA virus transmitted by the whitefly Bemisia tabaci. Common bean is a staple food in Brazil, and virus-associated diseases can cause important crop losses. The first report of CPMMV in Brazil was in common bean (Phaseolus vulgaris L.) in the states of Sao Paulo and Parana, causing angular yellow mosaic. More recently, CPMMV has re-emerged and was frequently found infecting beans in Goias State and Distrito Federal, located in central Brazil. However, in the northeastern region, CPMMV infection in common bean plants has not been reported.
TNF-α induces reactivation of human cytomegalovirus independently of myeloid cell differentiation following post-transcriptional establishment of latency

We used the Kasumi-3 model to study HCMV latency and reactivation in myeloid progenitor cells. Kasumi-3 cells were infected with HCMV strain TB40/Ewt-GFP, flow sorted for GFP+ cells, and cultured for various times to monitor establishment of latency, as judged by repression of viral gene expression (RNA/DNA ratio) and loss of virus production. We found that, in the vast majority of cells, latency was established post-transcriptionally in the GFP+ infected cells: transcription was initially turned on, and then turned off. We also found that some of the GFP-cells were infected, suggesting that latency might be established in these cells at the outset of infection. We were not able to test this hypothesis because some GFP-cells expressed lytic genes, and thus, it was not possible to separate them from GFP-quiescent cells. In addition, we found that the pattern of expression of lytic genes that have been associated with latency, including UL138, US28, and RNA2.7, was the same as that of other lytic genes, indicating that there was no preferential expression of these genes once latency is established. We confirmed previous studies showing that TNF-α induced reactivation of infectious virus, and by analyzing expression of the progenitor cell marker CD34 as well as myeloid cell differentiation markers in IE+ cells after treatment with TNF-α, we showed that TNF-α induced transcriptional reactivation of IE gene expression independently of differentiation. TNF-α-mediated reactivation in Kasumi-3 cells was correlated with activation of NF-κB, KAP-1 and ATM. IMPORTANCE HCMV is an important human pathogen that establishes lifelong latent infection in myeloid progenitor cells, and reactivates frequently to cause significant disease in immunocompromised people. Our observation that viral gene expression is first turned on, and then turned off to establish latency suggests that there is a host defense, which may be myeloid-specific, responsible for transcriptional silencing of viral gene expression. Our observation that TNF-α induces reactivation independently of differentiation provides insight into molecular mechanisms that control reactivation.
Lordosis Angle and Indirect Foraminal Decompression Following Interspinous Process Fixation with an Expandable Device A Cadaveric Radiographic Analysis

Interspinous process (ISP) fixation devices are used in spinal constructs to allow for stabilization of the spinal segment and indirect decompression of the neural elements. A lordotic, expandable ISP implant may allow for better decompression than traditional non-lordotic ISP devices, given its ability to maximize spinous process distraction while maintaining optimal spinal alignment. The purpose of this study is to compare lordosis and indirect neuroforaminal decompression between a ratcheting ISP (ISP R), a static barrel ISP (ISP B), and AERIAL (Globus Medical, Inc., Audubon, PA, USA), an expandable ISP device (ISP EXP), used in conjunction with a lateral lumbar interbody fusion spacer (LS) and lateral plate (LP) construct. Five L3-L4 spinal segments were instrumented with each ISP device in a randomized order. Micro-chromatography (microCT) scans were taken of each construct and the following parameters were analyzed: lordosis angle, anterior disc height, posterior disc height, interspinous process distance, neuroforaminal area, and neuroforaminal height. No significant change in lordosis was found for any treatment group (p>0.05). All three ISP constructs provided trending (0.05≤p<0.10) or significant (p<0.05) increases in neuroforaminal decompression parameters relative to the injured condition. While no significant differences were seen between the three ISP groups in the decompression parameters tested, the ISP EXP group showed the largest increase in foraminal height and area in comparison to ISP R and ISP B, while maintaining lordosis angle. Although statistical differences were not seen, the AERIAL expandable ISP device, when used in conjunction with a lateral spacer and lateral plate, achieved improvements in neuroforaminal height and area while maintaining the lordosis angle in the lumbar spine. An expandable ISP device such as AERIAL offers the added benefits of optimization to individual patient anatomy with minimum insertion height, which may improve surgeon workflow and by avoiding impaction, may reduce spinous process fracture risk in comparison to traditional ISP devices.
Understanding the in vivo functions of Holliday junction resolvase Yen1

Elaborate replication fork recovery pathways support the duplication of the genome under replication stress. Nucleases and helicases take center stage in these pathways, but our understanding of the molecular underpinnings remains incomplete. The Holliday junction resolving nucleases Mus81-Mms4 (human MUS81-EME1) and Yen1 (GEN1) act redundantly to remove replication-associated homologous recombination repair intermediates, safeguarding chromosome segregation. They are cell cycle regulated, so that Mus81-Mms4/MUS81-EME1 activity peaks first, making it the major resolvase in yeast and human. Yen1/GEN1 subsequently provides a catchall activity for the resolution of recombinational joint molecules that escape the attention of Mus81-Mms4. In this work, we used budding yeast as a model to explore whether additional, Mus81-independent functions of Yen1 exist, potentially outside the context of canonical Holliday junction resolution. To this end, we investigated the reported genetic interactome of YEN1. We disproved a purported genetic interaction between YEN1 and PBY1, linking wrongly assigned PBY1 interactions to MUS81-MMS4 instead. More significantly, addressing a synthetic sick interaction between YEN1 and the conserved nuclease-helicase DNA2, we identify a first unique function of Yen1 in targeting replication, as opposed to recombination, intermediates. Furthermore, we uncover a novel role for the elusive Dna2 helicase activity in the recovery of stalled replication intermediates. Our findings provide new insight into the replication stress response in eukaryotes.
Development and validation of a triplex qPCR assay to detect efflux pump-mediated antibiotic resistance in Burkholderia pseudomallei

Burkholderia pseudomallei, the causative agent of the deadly tropical disease melioidosis, is intrinsically resistant to many antibiotics, leaving few effective treatment options. Trimethoprim-sulfamethoxazole (SXT), meropenem (MEM) and doxycycline (DOX) are valuable antibiotics for melioidosis treatment due to inherently low or no primary resistance. Although considered rare, upregulation of one or more resistance-nodulation-division (RND) efflux pumps is now known to lead to acquired resistance towards these drugs in B. pseudomallei. Here, we developed a triplex quantitative PCR assay to detect upregulation of the three clinically relevant RND efflux systems: AmrAB-OprA, BpeB-OprB and BpeEF-OprC. The triplex assay was tested on seven clinically-derived B. pseudomallei isogenic pairs, where the latter strain of each pair had altered regulator activity and exhibited reduced susceptibility to SXT, MEM or DOX. The triplex assay accurately detected efflux pump upregulation between isogenic pairs, which corresponded with decreased antibiotic susceptibility. We further verified assay performance on eight laboratory-generated B. pseudomallei mutants encoding efflux pump regulator mutations. Targeting antibiotic resistance in B. pseudomallei using molecular genotyping provides clinicians with a rapid tool to identify potential treatment failure in near real-time, enabling informed alteration of treatment during an infection and improved patient outcomes. IMPORTANCE The melioidosis bacterium Burkholderia pseudomallei is intrinsically resistant to many antibiotics, limiting treatment options to a handful of drugs including meropenem, doxycycline and trimethoprim-sulfamethoxazole. Although rare, there have now been several documented melioidosis cases where resistance to these antibiotics has developed during an infection, leading to treatment failure and increased mortality rates. Interestingly, all strains resistant to these drugs exhibit increased efflux pump expression, representing a shared molecular signature that can be exploited for rapid diagnostic purposes. Here, we developed and validated a single-tube real-time qPCR assay to detect clinically relevant efflux pump upregulation in B. pseudomallei, an important first step towards high-level resistance. This triplex assay offers a drastically reduced turn-around-time compared to current methodology, enabling earlier detection of resistance emergence. Implementation of this new diagnostic will aid clinicians in the selection of appropriate therapy, thereby minimizing resistance development and treatment failure for this high-mortality disease.
Earnings Mobility and Measurement Error: A Pseudo‐Panel Approach

The degree of mobility in incomes is often seen as an important measure of the equality of opportunity in a society and of the flexibility and freedom of its labor market. However, estimation of mobility using panel data is biased by the presence of measurement error and nonrandom attrition from the panel. This study shows that dynamic pseudo‐panel methods can be used to consistently estimate measures of absolute and conditional mobility when genuine panels are not available and in the presence of nonclassical measurement errors. These methods are applied to data on earnings from a Mexican quarterly rotating panel. Absolute mobility in earnings is found to be very low in Mexico, suggesting that the high level of inequality found in the cross‐section will persist over time. However, the study finds conditional mobility to be high, so that households are able to recover quickly from earnings shocks. These findings suggest a role for policies that address underlying inequalities in earnings opportunities.
The palatability of undyed carrot surface-coated with repellents, or dyed blue or green to a terrestrial macroinvertebrate

ABSTRACT Birds are at risk of being poisoned during pest control operations not only through eating toxic baits, but potentially by preying on invertebrates that have, themselves, consumed the toxic baits. Blue baits coated with anthraquinone and/or mint-scented repellents are avoided by some bird species compared with green baits coated with cinnamon oil; however, data on invertebrate avoidance patterns have not been explored. In our first experiment, we measured consumption rates in a large invertebrate, the Auckland tree wētā (Hemideina thoracica) for carrot that had been surface-coated with three repellent formulations: anthraquinone (0.8 g kg−1) (a secondary repellent); anthraquinone (0.8 g kg−1) and pennyroyal oil (a mint-scented product which acts as a primary repellent) (0.5 g kg−1); and cinnamon oil (0.15 g kg−1) (a primary repellent), over 4 days. In a second experiment, we tested whether tree wētā preferred carrot dyed either blue or green over 2 days. Tree wētā ate similar quantities of carrot from all three of the repellent formulations tested, but consumption of all three formulations was significantly lower than the control from the third day of the experiment. Tree wētā ate less blue-dyed carrot than green-dyed carrot on both days of the second experiment, but differences were not significant (day 1, P= 0.057; day 2, P = 0.145). Our findings complement the results of previous studies on some bird species. Together they show the potential of surface-coating baits with anthraquinone and/or mint oil and dyeing them blue in pest control operations to reduce non-target avian by-kill, while not increasing the risk of secondary poisoning of insectivorous species. Our results also indicate that cinnamon oil can be used not only as a toxin mask but also as a repellent to wētā.
Plant growth promoters on growth and yield of summer cherry tomato line (JP-27)

An experiment was accomplished in the Horticulture Farm of Department of Horticulture, Sher-eBangla Agricultural University to evaluate the influence of different plant growth promoters on growth and yield of JP-27 summer cherry tomato line. Four different growth promoters including control viz. F0= Control (Water), F1= Flora (Nitrobenzene 20% w/w) @ 2.5ml/L, F2= 4-CPA @ 2.5 ml/L and F3= GA3 @ 200ppm was used in this experiment arranged in a Randomized Completely Blocked Design (RCBD) with three replications. Maximum plant height, no. of leaves, no. of branches, days to first flower, no. of flowers, no. of fruits, fruit length, single fruit weight, yield/plant and yield/ha (194.5 cm, 28.7, 12.7, 18.0, 48.3, 34.7, 19.9 mm, 20.4 gm, 458.7 gm and 19.0 ton respectively) were found in F3 treatment and maximum fruit diameter (40.7 mm) were found in F2 whereas the minimum (179.7 cm, 13.1, 5.7, 27.3, 36.3, 22.3, 13.5 mm, 33.0 mm, 10.6 gm, 287.9 gm and 13.2 ton respectively) were observed in F0. Thus application of plant growth promoters for improving overall performance of cherry tomato produced in summer can be recommended.