Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonality and weather dependance of Acinetobacter baumannii complex bloodstream infections in different climates in Brazil

Recent studies report seasonality in healthcare-associated infections, especially those caused by Acinetobacter baumannii complex. We conducted an ecologic study aimed at analyzing the impact of seasons, weather parameters and climate control on the incidence and carbapenem-resistance in A. baumannii complex bloodstream infections (ABBSI) in hospitals from regions with different climates in Brazil. We studied monthly incidence rates (years 2006–2015) of ABBSI from hospitals in cities from different macro-regions in Brazil: Fortaleza (Ceará State, Northeast region), Goiânia (Goiás State, Middle-west) and Botucatu (São Paulo State, Southeast). Box-Jenkins models were fitted to assess seasonality, and the impact of weather parameters was analyzed in Poisson Regression models. Separate analyses were performed for carbapenem-resistant versus carbapenem-susceptible isolates, as well as for infections occurring in climate-controlled intensive care units (ICUs) versus non-climate-controlled wards. Seasonality was identified for ABSSI ICUs in the Hospitals from Botucatu and Goiânia. In the Botucatu hospital, where there was overall seasonality for both resistance groups, as well as for wards without climate control. In that hospital, the overall incidence was associated with higher temperature (incidence rate ratio for each Celsius degree, 1.05; 95% Confidence Interval, 1.01–1.09; P = 0.006). Weather parameters were not associated with ABBSI in the hospitals from Goiânia and Fortaleza. In conclusion, seasonality was found in the hospitals with higher ABBSI incidence and located in regions with greater thermal amplitude. Strict temperature control may be a tool for prevention of A. baumanii infections in healthcare settings.
Strain PCC 6803 tRNAGlu Gene Provides tRNA for Protein and Chlorophyll Biosynthesis

In the cyanobacterium Synechocystis sp. strain PCC 6803 (Synechocystis 6803) 8-aminolevulinic acid (ALA), the sole precursor for the synthesis of the porphyrin rings of heme and chlorophyll, is formed from glutamate activated by acylation to tRNAGlu (G. P. O'Neill, D. M. Peterson, A. Schon, M. W. Chen, and D. Soll, J. Bacteriol. 170:3810-3816, 1988; S. Rieble and S. I. Beale, J. Biol. Chem. 263:8864-8871, 1988). We report here that Synechocystis 6803 possesses a single tRNAGlU gene which was transcribed as monomeric precursor tRNA and matured into the two tRNAGI, species. They differed in the extent of modification of the first anticodon base, 5-methylaminomethyl-2-thiouridine (O'Neill et al., 1988). The two tRNA species had equivalent capacities to stimulate the tRNA-dependent formation of ALA in Synechocystis 6803 and to provide glutamate for protein biosynthesis in an Escherichia coli-derived translation system. These results are in support of a dual role of tRNAGIU. The levels of tRNAGIU were examined by Northern (RNA) blot analysis of cellular RNA and by aminoacylation assays in cultures of Synechocystis 6803 in which the amount of chlorophyll synthesized was modulated over a 10-fold range by various illumination regimens or by the addition of inhibitors of chlorophyll and ALA biosynthesis. In these cultures, the level of tRNAGlU was always a constant fraction of the total tRNA population, suggesting that tRNAGI" and chlorophyll levels are regulated independently. In addition, the tRNAGI, was always fully aminoacylated in vivo.
Clonal Groups and from Escherichia coli 07:K1

The 0-specific lipopolysaccharide side chains of Escherichia coli 07 and Shigella boydii type 12 possess similar but not identical chemical structures. We investigated the genetic relatedness between the 0-specific side chain genes in members of these two species. Examination of outer membrane protein and lipopolysaccharide (LPS) banding patterns demonstrated that five strains which had been identified as S. boydii type 12 fell into two clonal groups, SBl and SB2. Hybridizations with 07-specific radiolabeled probes derived from the chromosomal DNA of an E. coli 07 strain detected identical fragments among the three SBl strains of S. boydii type 12 and the two E. coli 07 reference isolates. The two other S. boydii type 12 strains, which belonged to the SB2 clone, did not show homologies with the 07 probe under high-stringency conditions of hybridization. The homology between the 07 and type 12 LPS gene regions from the SBl strains was further confirmed by the construction of 0-specific side chain-deficient mutations in these strains by homologous recombination of
Two 3-Glycanase Genes Are Clustered in Bacillus polymyxa: Molecular Cloning, Expression, and Sequence Analysis of Genes

Two genes, xynD and gluB, encoding a xylanase and an endo-4-(1,3)-(1,4)-glucanase (lichenase) from Bacillus polymyxa have been cloned and expressed in Escherichia coli and Bacillus subtilis. A sequenced DNA fragment of 4,466 bp contains both genes, which are separated by 155 bp. The xynD and gluB genes encode proteins of 67.8 kDa (XYND) and 27 kDa (GLUB). Two peptides with molecular masses of 62 and 53 kDa appear in cell extracts of E. coli and culture supernatants of B. subtWis clones containing the xynD gene. Both peptides show xylanase activity in zymogram analysis. The XYND enzyme also shows Ot-L-arabinofuranosidase activity. The XYND peptide and the xylanase XYNZ from Clostridium thermocellum (0. Grepinet, M. C. Chebrou, and P. Beguin, J. Bacteriol. 170:4582-4588, 1988) show 64% homology in a stretch of about 280 amino acids.
Helicobacterpylori by Allelic Exchange

Isogenic urease-negative mutants of Helicobacter pylori were constructed by allelic replacement. A region of cloned H. pylori DNA containing the structural urease genes (ureA and ureB) was disrupted by insertion of a mini-Tn3-Km transposon. Electrotransformation of H. pylori cells with kanamycin-ureB-disrupted derivative plasmids resulted in isolation of kanamycin-resistant H. pylori transformants. Competence for electrotransformation appeared to be restricted to certain wild-type H. pyloyi isolates; only 1 isolate (of 10 tested) was consistently transformed. Two of the kanamycin-resistant H. pylori transformants were further studied and shown to be urease negative. Southern hybridization analyses demonstrated that the urease-negative mutants had been constructed by allelic exchange involving simultaneous replacement of the ureB gene with the kanamycin-ureB-disrupted copy and loss of the vector. Immunoblot studies ofwhole-cell extracts of the isogenic ureB mutants with anti-H. pyloni sera indicated the absence of a polypeptide with an apparent molecular mass of 61 kDa; thus, the mutants no longer synthesized the UreB product. Generation of stable, genetically engineered urease mutants ofH. pylori will be useful for addressing the role of urease in the pathogenesis ofH. pylori infection.
Schistosoma mansoni Protect Rats

Schistosoma mansoni adult worm 28-kilodalton (kDa) proteins were separated on polyacrylamide slab gels, recovered by electrophoretic elution, and used to immunize Fischer rats. After the second or third inijection, inguinal lymph node T lymphocytes were propagated in vitro for 4 weeks in the presence of syngeneic antigen-presenting cells and adult worm antigens in medium containing interleukin-2. After this period of culture, 99% of the cells expressed the W3/13+ surface phenotype and 93% of the cells expressed the W3/25+ surface phenotype. These cells were then tested for their in vivo functional activity after transfer to Fischer rats that had been either infected with S. mansoni cercariae or immunized with the 28-kDa purified protein. In each case, an increase of S. mansoni-specific antibodies was observed. Whereas anti-28-kDa antibodies were only detectable at day 40 postinfection in controls iu'ected with normal T lymphocytes, they appeared as early as day 13 postinfection when the animals received 28-kDa protein-specific T lymphocytes. This led to an effective protection of infected rats (45 to 85%) which correlated with the increase in S. mansoni-specific antibodies. These results therefore demonstrate that the 28-kDa protein possesses epitopes capable of activating helper T cells, which confer a strong protective immunity by enhancing the production of cytotoxic antibodies. The stimulation of the 28-kDa-specific T cells with recombinant proteins suggests that the major epitopes are located toward the carboxylic end of the molecule.
H202 and Gamma Radiation

The tripeptide glutathione (L-y-glutamyl-L-cysteinylglycine) (GSH) is the predominant low-molecular-weight thiol in many organisms and has been proposed to protect cells from oxidative damage such as that formed by H202 and ionizing radiations (19). Escherichia coli deficient in GSH because of mutations in the gshA gene was found previously (3) to exhibit normal resistance to X irradiation in the presence of oxygen. Other workers reported (21) that E. coli gsh mutants lacked the protective effect of hypoxia during -y irradiation. At least one of the mutants employed previously contains a second mutation that affects its sensitivity to H202 (10), probably because it was mutagenized with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG; 3). To avoid this problem, we isolated transposon insertions in the gshA gene. Strains bearing a gshA::TnlO allele exhibit the expected hypersensitivities to thiol-specific reagents but are not at all defective in their resistance to oxidative damage, including y rays. The E. coli K-12 strains used were as follows: W3110 (gsh+) and NK5991 (W3110 srlD::TnlO) supplied by N. Kleckner; AB1157 (gsh') and BS53 (AB1157 gsh) from B. Sedgwick (24); TJ5 (AB1157 gshB) supplied by J. Fuchs; and KL164 (nalB14) from the Coli Genetic Stock Center (5). Strain W3110 was mutagenized by the lambda hop procedure (26) with a derivative of TnlO (element 9 of Way et al. [26], hereafter called TnlOkm) that confers kanamycin resistance (Kan9. Colonies were collected from kanamycin (50 ,ug/ml) selection plates and stored at -50°C in 25% glycerol. Thawed cells were centrifuged and suspended in M medium (M9 salts [20] with 0.1 mM CaCl2, 1.0 mM MgSO4, 1 llg of thiamine hydrochloride per ml, 0.025% Casamino Acids, and 0.1% glucose) and enriched for gshA mutants essentially by the procedure of Sedgwick and Robins (24) by using one 45-min and two 10-min treatments with 50 ,ug of MNNG per ml. Most (70%) of the isolates obtained in this way showed substantially increased resistance to MNNG when tested individually. Of the three randomly selected MNNGresistant isolates examined, all contained drastically diminished acid-soluble thiols (17). A putative gshA::TnJOkm mutation was transduced from one of these isolates (JTG1) into AB1157 by using bacteriophage P1 (20) and selection for Kanr. One Kanr transductant (JTG10) was selected at random for further study; the mutation it bears was designated gshA20: :TnlOkm. Cellular levels of reduced thiols are given in Table 1. These were quantitated by treating extracts (14) of thawed
Puerarin Attenuates Complete Freund’s Adjuvant-Induced Trigeminal Neuralgia and Inflammation in a Mouse Model via Sirt1-Mediated TGF-β1/Smad3 Inhibition

Background Puerarin, an active compound of radix puerariae, is a major compound used in Chinese herbal medicines and it has been well known for its pharmacological effects, including antioxidant, anti‑inflammatory, neuroprotective and cardioprotective properties. The aim of the present study was to determine the role of puerarin (Pue) in complete Freund’s adjuvant (CFA)-induced trigeminal neuralgia (TN) and the effects of this compound on Sirt1 activity and on the progression of CFA-induced TN. Methods Mice were injected with CFA on the unilateral face to induce TN. A cell model of inflammation-associated TN was established by interleukin-1β (IL-1β; 10 ng/mL) and tumor necrosis factor-α (TNF-α; 50 ng/mL) stimulation of neurons. Reverse transcription-quantitative PCR and Western blot analyses were performed to analyze mRNA and protein expression levels in trigeminal ganglion and nerve cells. Terminal-deoxynucleotidyl transferase mediated nick end labeling (TUNEL) staining was used to determine nerve cell apoptosis following IL-1β/TNF-α or Pue treatment. Results Pue is a conceivable Sirtuin1 (Sirt1) activator used for the prevention of trigeminal nerve injury that attenuates CFA-induced TN and inflammatory cytokine-evoked overactivation of neuronal inflammation and apoptosis. Treatment of mice with inflammatory cytokines induced upregulation of cleaved caspase-3 protein expression, which was neutralized by Pue supplementation. Both in vivo and in vitro experiments led to the conclusion that Pue modulated Sirt1 activation and repressed transforming growth factor-β1 (TGF-β1) protein expression and drosophila mothers against decapentaplegic homolog3 (Smad3) phosphorylation in order to exert neuroprotection. Conclusion The findings suggested that Pue functioned as a potential Sirt1 activator to improve neuroinflammation-induced TN and neuronal apoptosis via the suppression of TGF-β1/Smad3 activity. The pharmacological activity of Pue provides a new perspective for the effective prevention and treatment of TN.
Crystallographic characterization of rare-earth cyanotriphenylborate complexes and the cyanoborates [NCBPh3]1−, [NCBPh2Me]1−, and [NCBPh2(μ-O)BPh2]1−

The investigation of the coordination chemistry of rare-earth metal complexes with cyanide ligands led to the isolation and crystallographic characterization of the Ln III cyanotriphenylborate complexes, LnCl2(THF)4(NCBPh3) (Ln = Dy, Y) as well as the cyanoborates [NEt4][B3(μ-O)3(C6H5)4], [NEt4][NCBPh2(μ-O)BPh2], [K(crypt)]2[B3(μ-O)3(C6H5)4][NCBPh2Me]. The [NCBPh2(μ-O)BPh2]1− and (NCBPh2Me)1− anions have not been structurally characterized previously.
Superconducting nanowire single-photon sensing of cerebral blood flow

Abstract. Significance: The ability of diffuse correlation spectroscopy (DCS) to measure cerebral blood flow (CBF) in humans is hindered by the low signal-to-noise ratio (SNR) of the method. This limits the high acquisition rates needed to resolve dynamic flow changes and to optimally filter out large pulsatile oscillations and prevents the use of large source-detector separations (≥3 cm), which are needed to achieve adequate brain sensitivity in most adult subjects. Aim: To substantially improve SNR, we have built a DCS device that operates at 1064 nm and uses superconducting nanowire single-photon detectors (SNSPD). Approach: We compared the performances of the SNSPD-DCS in humans with respect to a typical DCS system operating at 850 nm and using silicon single-photon avalanche diode detectors. Results: At a 25-mm separation, we detected 13 ± 6 times more photons and achieved an SNR gain of 16 ± 8 on the forehead of 11 subjects using the SNSPD-DCS as compared to typical DCS. At this separation, the SNSPD-DCS is able to detect a clean pulsatile flow signal at 20 Hz in all subjects. With the SNSPD-DCS, we also performed measurements at 35 mm, showing a lower scalp sensitivity of 31 ± 6 % with respect to the 48 ± 8 % scalp sensitivity at 25 mm for both the 850 and 1064 nm systems. Furthermore, we demonstrated blood flow responses to breath holding and hyperventilation tasks. Conclusions: While current commercial SNSPDs are expensive, bulky, and loud, they may allow for more robust measures of non-invasive cerebral perfusion in an intensive care setting.
Special Section on Drug Delivery Technologies — Minireview Therapeutic Opportunities in Neuroblastoma Using Nanotechnology

Neuroblastoma (NB) is the most common extracranial solid tumor preferentially occurring in preschoolers. Its character-istic aggressiveness and heterogeneous clinical behavior are especially visible in relapsed or refractory cases and hamper therapeutic success. Although the introduction of novel anti- tumor agents, such as dinutuximab, isotretinoin, irinotecan, or I-131- metaiodobenzylguanidine, has increased survival rates, the situation in high-risk NB remains dismal. Moreover, treatment is particularly aggressive in these patients, leading to short- and long-term toxicities. The extensive research performed using nanotechnology in recent decades has prompted its application as a therapeutic alternative to overcome some of the common limitations of conventional chemotherapy. Nev- ertheless, the therapeutic role of nanomedicine in pediatric tumors like NB is not fully elucidated, and to date, only albumin- bound paclitaxel nanoparticles have reached clinic stages. In this review, we summarize the current therapeutic strategies for NB with special attention to the use of nanomedicine. We also highlight the preclinical studies on passive and active target- ing nanodelivery of therapeutics in experimental NB models.
Expression of tdTomato and luciferase in a murine lung cancer alters the growth and immune microenvironment of the tumor

Imaging techniques based on fluorescence and bioluminescence have been important tools in visualizing tumor progression and studying the effect of drugs and immunotherapies on tumor immune microenvironment in animal models of cancer. However, transgenic expression of foreign proteins may induce immune responses in immunocompetent syngeneic tumor transplant models and augment the efficacy of experimental drugs. In this study, we show that the growth rate of Lewis lung carcinoma (LL/2) tumors was reduced after transduction of tdTomato and luciferase (tdTomato/Luc) compared to the parental cell line. tdTomato/Luc expression by LL/2 cells altered the tumor microenvironment by increasing tumor-infiltrating lymphocytes (TILs) while inhibiting tumor-induced myeloid-derived suppressor cells (MDSCs). Interestingly, tdTomato/Luc expression did not alter the response of LL/2 tumors to anti-PD-1 and anti-CTLA-4 antibodies. These results suggest that the use of tdTomato/Luc-transduced cancer cells to conduct studies in immune competent mice may lead to cell-extrinsic tdTomato/Luc-induced alterations in tumor growth and tumor immune microenvironment that need to be taken into consideration when evaluating the efficacy of anti-cancer drugs and vaccines in immunocompetent animal models.
Multi-target pig tracking algorithm based on joint probability data association and particle filter

In order to evaluate the health status of pigs in time, monitor accurately the disease dynamics of live pigs, and reduce the morbidity and mortality of pigs in the existing large-scale farming model, pig detection and tracking technology based on machine vision are used to monitor the behavior of pigs. However, it is challenging to efficiently detect and track pigs with noise caused by occlusion and interaction between targets. In view of the actual breeding conditions of pigs and the limitations of existing behavior monitoring technology of an individual pig, this study proposed a method that used color feature, target centroid and the minimum circumscribed rectangle length-width ratio as the features to build a multi-target tracking algorithm, which based on joint probability data association and particle filter. Experimental results show the proposed algorithm can quickly and accurately track pigs in the video, and it is able to cope with partial occlusions and recover the tracks after temporary loss. Keywords: joint probability data association, pig tracking, particle filter, centroid DOI: 10.25165/j.ijabe. 20211404.6105 Citation: Sun L Q, Li Y Y. Multi-target pig tracking algorithm based on joint probability data association and particle filter. Int J Agric & Biol Eng, 2021; 14(4): 199–207.
Morphological and phylogenetic evidence for two new species of Russula subg. Heterophyllidia from Guangdong Province of China

Abstract Two new species of Russulasubg.Heterophyllidia from Guangdong Province of China were described and illustrated based on morphological characters, and their identity supported by molecular phylogeny. R.luofuensis is morphologically characterized by a grayish yellow to brownish orange pileus center with a purplish gray to grayish magenta margin, a surface that is cracked and broken into small golden-brown patches, subglobose to broadly ellipsoid basidiospores with warts fused in short or long chains and a suprapellis composed of hyphal extremities with inflated, ellipsoid or globose cells and attenuated terminal cell. R.subbubalina is distinguished by the blanched almond to dark salmon pileus that is cracked with age, subglobose to broadly ellipsoid basidiospores with wart fused in short or long chains and frequently connected by line connections, a suprapellis with hyphal ends composed of inflated or ellipsoid cells and attenuated terminal cell, and pileocystidia that are mainly clavate and sometimes with round or ellipsoid appendage. The phylogenetic analyses based on ITS-nrLSU-mtSSU-TEF1 dataset were performed using maximum likelihood and Bayesian analysis. In terms of morphological features and molecular data, the former species belongs to subsect. Virescentinae, whereas the latter comes under subsect. Heterophyllinae.
Quantifying the effect of Wakefield et al. (1998) on skepticism about MMR vaccine safety in the U.S.

Background Efforts to trace the rise of childhood vaccine safety concerns in the US often suggest Andrew Wakefield and colleagues’ retracted 1998 Lancet study (AW98)–which alleged that the MMR vaccine can cause children to develop autism–as a primary cause of US vaccine skepticism. However, a lack of public opinion data on MMR safety collected before/after AW98’s publication obscures whether anecdotal accounts are indicative of a potentially-causal effect. Methods We address this problem using a regression discontinuity framework to study change in monthly MMR injury claims (N = 74,850; from 1990–2019) from the Vaccine Adverse Events Reporting System (VAERS) to proxy concern about vaccine safety. Additionally, we suggest a potential mechanism for the effect of AW98 on vaccine skepticism, via automated sentiment analyses of MMR-related news stories (N = 674; from 1996–2000) in major television and newspaper outlets. Results AW98 led to an immediate increase of about 70 MMR injury claims cases per month, averaging across six estimation strategies (meta-analytic effect = 70.44 [52.19, 88.75], p < 0.01). Preliminary evidence suggests that the volume of negative media attention to MMR increased in the weeks following AW98’s publication, across four estimation strategies (meta-analytic effect = 9.59% [3.66, 15.51], p < 0.01). Conclusions Vaccine skepticism increased following the publication of AW98, which was potentially made possible by increased negative media coverage of MMR. Significance Childhood vaccine skepticism presents an important challenge to widespread vaccine uptake, and undermines support for pro-vaccine health policies. In addition to advancing our understanding of the previously-obscured origins of US vaccine skepticism, our work cautions that high-profile media attention to inaccurate scientific studies can undermine public confidence in vaccines. We conclude by offering several recommendations that researchers and health communicators might consider to detect and address future threats to vaccine confidence.