Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyrethroid resistance persists after ten years without usage against Aedes aegypti in governmental campaigns: Lessons from São Paulo State, Brazil

Background Aedes aegypti, vector of dengue, chikungunya and Zika viruses, is found at high densities in tropical urban areas. The dissemination of this vector is partially the consequence of failures in current vector control methods, still mainly relying upon insecticides. In the State of São Paulo (SP), Brazil, public health managers employed pyrethroids against Ae. aegypti adults from 1989 to 2000, when a robust insecticide resistance monitoring system detected resistance to pyrethroids in several Ae. aegypti populations. However, pyrethroids are also the preferred compounds engaged in household applications due to their rapid knockdown effect, lower toxicity to mammals and less irritating smell. Methodology/Principal findings We evaluated pyrethroid resistance in Ae. aegypti populations over the course of a decade, from 2004 to 2015, after interruption of pyrethroid public applications in SP. Qualitative bioassays with papers impregnated with a deltamethrin diagnostic dose (DD) performed with insects from seven SP municipalities and evaluated yearly from 2006 to 2014, detected resistance in most of the cases. Quantitative bioassays were also carried out with four populations in 2011, suggesting a positive correlation between resistance level and survivorship in the DD bioassays. Biochemical tests conducted with seven insect populations in 2006 and 2015, detected increasing metabolic alterations of all major classes of detoxifying enzymes, mostly of mixed function oxidases. Genotyping of the voltage-gated sodium channel (AaNaV, the pyrethroid target-site) with a TaqMan real time PCR based technique was performed from 2004 to 2014 in all seven localities. The two kdr mutations, Val1016Ile and Phe1534Cys, known to be spread throughout Brazil, were always present with a severe decrease of the susceptible allele over time. Conclusions/Significance These results are discussed in the context of public and domestic insecticide use, the necessity of implementation of a strong integrated vector control strategy and the conceptual misunderstanding between 'vector control' and 'chemical control of vectors'.
The Relationship Between Iron Deficiency Anemia and Sensorineural Hearing Loss in the Pediatric and Adolescent Population.

Purpose A correlation between iron deficiency anemia (IDA) and sudden sensorineural hearing loss (SNHL) was described in adults. In this study, we examined if there is a relationship between IDA and hearing loss in the pediatric population. Method This was a retrospective cohort study of data collected from the Informatics for Integrating Biology and the Bedside database from 2011 to 2016. Children and adolescents 4-21 years old seen at Penn State Milton S. Hershey Medical Center, Hershey, PA, were examined for hearing loss and IDA status. Hearing loss was determined by International Classification of Disease-9 and -10 codes, and IDA was determined by both low hemoglobin and serum ferritin levels for age and sex. Results We identified 20,113 patients. Prevalence of hearing loss and IDA was 1.7% and 2.3%, respectively. The prevalence of all hearing loss was 3.0% in the IDA cohort and 1.7% in those without IDA. Children and adolescents with IDA are at increased odds of developing SNHL (adjusted odds ratio: 3.67, 95% CI [1.60-7.30]). Conclusions Children with IDA demonstrate increased likelihood of SNHL. Although correction of IDA in those with hearing loss has yet to be linked to improvements in hearing outcomes, screening for and correcting IDA among pediatric patients will positively affect overall health status. Supplemental Material: https://doi.org/10.23641/asha.5087071.
Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies

A fundamental and important challenge in modern datasets of ever increasing dimensionality is variable selection, which has taken on renewed interest recently due to the growth of biological and medical datasets with complex, non-i.i. d. structures. Naïvely applying classical variable selection methods such as the Lasso to such datasets may lead to a large number of false discoveries. Motivated by genome-wide association studies in genetics, we study the problem of variable selection for datasets arising from multiple subpopulations, when this underlying population structure is unknown to the researcher. We propose a unified framework for sparse variable selection that adaptively corrects for population structure via a low-rank linear mixed model. Most importantly, the proposed method does not require prior knowledge of sample structure in the data and adaptively selects a covariance structure of the correct complexity. Through extensive experiments, we illustrate the effectiveness of this framework over existing methods. Further, we test our method on three different genomic datasets from plants, mice, and human, and discuss the knowledge we discover with our method.
Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

ABSTRACT Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.
Current Status of Long Non-Coding RNAs in Human Breast Cancer

Breast cancer represents a major health burden in Europe and North America, as recently published data report breast cancer as the second leading cause of cancer related death in women worldwide. Breast cancer is regarded as a highly heterogeneous disease in terms of clinical course and biological behavior and can be divided into several molecular subtypes, with different prognosis and treatment responses. The discovery of numerous non-coding RNAs has dramatically changed our understanding of cell biology, especially the pathophysiology of cancer. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts >200 nucleotides in length. Several studies have demonstrated their role as key regulators of gene expression, cell biology and carcinogenesis. Deregulated expression levels of lncRNAs have been observed in various types of cancers including breast cancer. lncRNAs are involved in cancer initiation, progression, and metastases. In this review, we summarize the recent literature to highlight the current status of this class of long non-coding lncRNAs in breast cancer.
Role of N Terminus-Truncated NS1 Proteins of Influenza A Virus in Inhibiting IRF3 Activation

ABSTRACT The NS1 protein encoded by influenza A virus antagonizes the interferon response through various mechanisms, including blocking cellular mRNA maturation by binding the cellular CPSF30 3′ end processing factor and/or suppressing the activation of interferon regulatory factor 3 (IRF3). In the present study, we identified two truncated NS1 proteins that are translated from internal AUGs at positions 235 and 241 of the NS1 open reading frame. We analyzed the cellular localization and function of the N-truncated NS1 proteins encoded by two influenza A virus strains, Udorn/72/H3N2 (Ud) and Puerto Rico/8/34/H1N1 (PR8). The NS1 protein of PR8, but not Ud, inhibits the activation of IRF3, whereas the NS1 protein of Ud, but not PR8, binds CPSF30. The truncated PR8 NS1 proteins are localized in the cytoplasm, whereas the full-length PR8 NS1 protein is localized in the nucleus. The infection of cells with a PR8 virus expressing an NS1 protein containing mutations of the two in-frame AUGs results in both the absence of truncated NS1 proteins and the reduced inhibition of activation of IRF3 and beta interferon (IFN-β) transcription. The expression of the truncated PR8 NS1 protein by itself enhances the inhibition of the activation of IRF3 and IFN-β transcription in Ud virus-infected cells. These results demonstrate that truncated PR8 NS1 proteins contribute to the inhibition of activation of this innate immune response. In contrast, the N-truncated NS1 proteins of the Ud strain, like the full-length NS1 protein, are localized in the nucleus, and mutation of the two in-frame AUGs has no effect on the activation of IRF3 and IFN-β transcription. IMPORTANCE Influenza A virus causes pandemics and annual epidemics in the human population. The viral NS1 protein plays a critical role in suppressing type I interferon expression. In the present study, we identified two novel truncated NS1 proteins that are translated from the second and third in-frame AUG codons in the NS1 open reading frame. The N-terminally truncated NS1 encoded by the H1N1 PR8 strain of influenza virus that suppresses IRF3 activation is localized primarily in the cytoplasm. We demonstrate that this truncated NS1 protein by itself enhances this suppression, demonstrating that some strains of influenza A virus express truncated forms of the NS1 protein that function in the inhibition of cytoplasmic antiviral events.
One-round Walks in Linear Congestion Games

Which is the approximation ratio of the solutions achieved after a oneround walk starting from the empty strategy profile in linear congestion games for the social function defined as the sum of the players' costs? The exact answer has been given only for the cases of unweighted players with unrestricted sets of strategies and weighted players with singleton strategies on identical resources. In this note, we survey results, techniques and open problems from this research topic.
Harnessing the power of communities: career networking strategies for bioscience PhD students and postdoctoral researchers

With an ever more competitive global labour market, coupled with an ever-increasing population of PhD-qualified graduates, the ability to communicate effectively and build strategic connections with others can be advantageous in the job-search process. Whether in pursuit of a tenure-track or non-academic position, many postdoctoral researchers and PhD students will benefit from networking as early as possible to enhance their career prospects. Sometimes viewed cynically as 'using people' or dismissed as 'the old boy network,' the ability to make meaningful connections and build relationships can be more valuable than other job-related skills in order to gain entry to, and progress within, many professions. This mini-review highlights the positive influence of networking and how bioscience PhD students and postdoctoral researchers can harness the power of communities to achieve career success. It is argued that those who make connections and promote personal patronage through networking can gain an advantage over their contemporaries. A summary of key theories and research studies that underpin the practice of networking provides credence to these assertions, which are further substantiated with examples pertinent to the academic community. Although primarily focussed on the biosciences, much of the content is applicable to other scientists at a similar career stage.
Genome and Plasmid Analysis of blaIMP-4-Carrying Citrobacter freundii B38

ABSTRACT Sequencing of the blaIMP-4-carrying C. freundii B38 using the PacBio SMRT technique revealed that the genome contained a chromosome of 5,134,500 bp and three plasmids, pOZ172 (127,005 bp), pOZ181 (277,592 bp), and pOZ182 (18,467 bp). Plasmid pOZ172 was identified as IncFIIY, like pP10164-NDM and pNDM-EcGN174. It carries a class 1 integron with four cassettes (blaIMP-4-qacG2-aacA4-aphA15) and a complete hybrid tni module (tniR-tniQ-tniB-tniA). The recombination of tniR from Tn402 (identical) with tniQBA from Tn5053 (99%) occurred within the res site of Tn402/5053. The Tn402/5053-like integron, named Tn6017, was inserted into Tn1722 at the res II site. The replication, partitioning, and transfer systems of pOZ181 were similar to those of IncHI2 plasmids (e.g., R478) and contained a sul1-type class 1 integron with the cassette array orf-dfrA1-orf-gcu37-aadA5 linked to an upstream Tn1696 tnpA-tnpR and to a downstream 3′ conserved sequence (3′-CS) and ISCR1. A Tn2 transposon encoding a blaTEM-1 β-lactamase was identified on pOZ182. Other interesting resistance determinants encoded on the B38 chromosome included multidrug resistance (MDR) efflux pumps, an AmpC β-lactamase, and resistances to Cu, Ag, As, and Zn. This is the first report of a complete tni module linked to a blaIMP-4-carrying class 1 integron, which, together with other recently reported non-sul1 integrons, represents the emergence of a distinct evolutionary lineage of class 1 integrons lacking a 3′-CS (qacEΔ1-sul1). The unique cassette array, complete tni module of Tn6017, and incompatibility group of pOZ172 suggest a blaIMP-4 evolutionary pathway in C. freundii B38 different from that for other blaIMP-4 genes found in Gram-negative bacteria in the Western Pacific region.
AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy

To develop a fast and automated volume‐of‐interest (VOI) prescription pipeline (AutoVOI) for single‐voxel MRS that removes the need for manual VOI placement, allows flexible VOI planning in any brain region, and enables high inter‐ and intra‐subject consistency of VOI prescription.
A Low-Rank Approximation-Based Transductive Support Tensor Machine for Semisupervised Classification

In the fields of machine learning, pattern recognition, image processing, and computer vision, the data are usually represented by the tensors. For the semisupervised tensor classification, the existing transductive support tensor machine (TSTM) needs to resort to iterative technique, which is very time-consuming. In order to overcome this shortcoming, in this paper, we extend the concave-convex procedure-based transductive support vector machine (CCCP-TSVM) to the tensor patterns and propose a low-rank approximation-based TSTM, in which the tensor rank-one decomposition is used to compute the inner product of the tensors. Theoretically, concave-convex procedure-based TSTM (CCCP-TSTM) is an extension of the linear CCCP-TSVM to tensor patterns. When the input patterns are vectors, CCCP-TSTM degenerates into the linear CCCP-TSVM. A set of experiments is conducted on 23 semisupervised classification tasks, which are generated from seven second-order face data sets, three third-order gait data sets, and two third-order image data sets, to illustrate the performance of the CCCP-TSTM. The results show that compared with CCCP-TSVM and TSTM, CCCP-TSTM provides significant performance gain in terms of test accuracy and training speed.
The Structure and Properties Formation of the NiTi Shape Memory Rods after Hot Rotary Forging

Shape memory effects, the course and characteristic temperatures of phase transitions and mechanical properties and surface properties of NiTi alloys strongly depend on the chemical composition, the production process used and the plastic working and thermomechanical treatment as well as surface treatment. The test alloy was obtained by vacuum metallurgy by melting the components in a graphite crucible and casting into a graphite ingot mould. In order to obtain the rods in the process of hot plastic working, hot forging was applied using a smith hammer and rotary hot forging on a swaging machine. The resulting rods were subjected to an appropriate heat treatment and thermo mechanical treatment to obtain, at room temperature, a parent phase structure B2.The paper presents the results of the research of NiTi rods after hot rotary forging. The phase composition of the samples of the tested alloy after different heat treatments were determined by X-ray powder diffraction technique. It was found that at room temperature, depending upon the processing the samples had a structure parent phase with a small amount of martensite. The courses of phase transitions and the changes of the temperature characteristic were determined on the basis of the recorded DSC curves. It was found that the test rate after aging in the temperature range of 400-500 °C transitions take place involving the rhombohedral R phase. The temperature ranges of shape recovery of samples after various heat treatments were determined by recording the recovery of the shape during heating, in tests performed according to the standard ASTM 2082-06.
Self-assembly of Fine Particles Applied to the Production of Antireflective Surfaces

We introduce a new fabrication process for antireflective structured surfaces. A 4-inch silicon wafer was dipped in a suspension of 300-㎚-diameter silica particles dispersed in a toluene solution. When the wafer was drawn out of the suspension, a hexagonally packed monolayer structure of particles self-assembled on almost the complete wafer surface. Due to the simple process, this could be applied to micro- and nano-patterning. The self-assembled silica particles worked as a mask for the subsequent reactive ion etching. An array of nanometer-sized pits could be fabricated since the regions that correspond to the small gaps between particles were selectively etched off. As etching progressed, the pits became deeper and combined with neighboring pits due to side-etching to produce an array of cone-like structures. We investigated the effect of etching conditions on antireflection properties, and the optimum shape was a nano-cone with height and spacing of 500 ㎚ and 300 ㎚, respectively. This nano-structured surface was prepared on a 30 × 10-㎚ area. The reflectivity of the surface was reduced 97% for wavelengths in the range 400-700 ㎚.
Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates

ABSTRACT Epigenome-wide DNA methylation association studies have identified highly replicable genomic loci sensitive to maternal smoking during gestation. The role of inter-individual genetic variation in influencing DNA methylation, leading to the possibility of confounding or bias of such associations, has not been assessed. We investigated whether the DNA methylation levels at the top 10 CpG sites previously associated with exposure to maternal smoking during gestation were associated with individual genetic variation at the genome-wide level. Genome-wide association tests between DNA methylation at the top 10 candidate CpG and genome-wide SNPs were performed in 736 case and control participants of the California Childhood Leukemia Study. Three of the strongest maternal-smoking sensitive CpG sites in newborns were significantly associated with SNPs located proximal to each gene: cg18146737 in the GFI1 gene with rs141819830 (P = 8.2×10−44), cg05575921 in the AHRR gene with rs148405299 (P = 5.3×10−10), and cg12803068 in the MYO1G gene with rs61087368 (P = 1.3×10−18). For the GFI1 CpG cg18146737, the underlying genetic variation at rs141819830 confounded the association between maternal smoking and DNA methylation in our data (the regression coefficient changed from −0.02 [P = 0.139] to −0.03 [P = 0.015] after including the genotype). Our results suggest that further studies using DNA methylation at cg18146737, cg05575921, or cg12803068 that aim to assess exposure to maternal smoking during gestation should include genotype at the corresponding SNP. New methods are required for adequate and routine inclusion of genotypic influence on DNA methylation in epigenome-wide association studies to control for potential confounding.
Toward an Integrated Understanding of Retrograde Control of Photosynthesis.

SIGNIFICANCE Photosynthesis takes place in the chloroplast of eukaryotes, which occupies a large portion of the photosynthetic cell. The chloroplast function and integrity depend on intensive material and signal exchange between all genetic compartments and conditionally secure efficient photosynthesis and high fitness. Recent Advances: During the last two decades, the concept of mutual control of plastid performance by extraplastidic anterograde signals acting on the chloroplast and the feedback from the chloroplast to the extraplastidic space by retrograde signals has been profoundly revised and expanded. It has become clear that a complex set of diverse signals is released from the chloroplast and exceeds the historically proposed small number of information signals. Thus, it is also recognized that redox compounds and reactive oxygen species play a decisive role in retrograde signaling. CRITICAL ISSUES The diversity of processes controlled or modulated by the retrograde network covers all molecular levels, including RNA fate and translation, and also includes subcellular heterogeneity, indirect gating of other organelles' metabolism, and specific signaling routes and pathways, previously not considered. All these processes must be integrated for optimal adjustment of the chloroplast processes. Thus, evidence is presented suggesting that retrograde signaling affects translation, stress granule, and processing body (P-body) dynamics. FUTURE DIRECTIONS Redundancy of signal transduction elements, parallelisms of pathways, and conditionally alternative mechanisms generate a robust network and system that only tentatively can be assessed by use of single-site mutants.
Characterization of SlyA in Shigella flexneri Identifies a Novel Role in Virulence

ABSTRACT The SlyA transcriptional regulator has important roles in the virulence and pathogenesis of several members of the Enterobacteriaceae family, including Salmonella enterica serovar Typhimurium and Escherichia coli. Despite the identification of the slyA gene in Shigella flexneri nearly 2 decades ago, as well as the significant conservation of SlyA among enteric bacteria, the role of SlyA in Shigella remains unknown. The genes regulated by SlyA in closely related organisms often are absent from or mutated in S. flexneri, and consequently many described SlyA-dependent phenotypes are not present. By characterizing the expression of slyA and determining its ultimate effect in this highly virulent organism, we postulated that novel SlyA-regulated virulence phenotypes would be identified. In this study, we report the first analysis of SlyA in Shigella and show that (i) the slyA gene is transcribed and ultimately translated into protein, (ii) slyA promoter activity is maximal during stationary phase and is negatively autoregulated and positively regulated by the PhoP response regulator, (iii) the exogenous expression of slyA rescues transcription and virulence-associated deficiencies during virulence-repressed conditions, and (iv) the absence of slyA significantly decreases acid resistance, demonstrating a novel and important role in Shigella virulence. Cumulatively, our study illustrates unexpected parallels between the less conserved S. flexneri and S. Typhimurium slyA promoters as well as a unique role for SlyA in Shigella virulence that has not been described previously in any closely related organism.