Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome‐wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti

ExoS/ChvI two‐component signaling in the nitrogen‐fixing α‐proteobacterium Sinorhizobium meliloti is required for symbiosis and regulates exopolysaccharide production, motility, cell envelope integrity and nutrient utilization in free‐living bacteria. However, identification of many ExoS/ChvI direct transcriptional target genes has remained elusive. Here, we performed chromatin immunoprecipitation followed by microarray analysis (chIP‐chip) to globally identify DNA regions bound by ChvI protein in S. meliloti. We then performed qRT‐PCR with chvI mutant strains to test ChvI‐dependent expression of genes downstream of the ChvI‐bound DNA regions. We identified 64 direct target genes of ChvI, including exoY, rem and chvI itself. We also identified ChvI direct target candidates, like exoR, that are likely controlled by additional regulators. Analysis of upstream sequences from the 64 ChvI direct target genes identified a 15 bp‐long consensus sequence. Using electrophoretic mobility shift assays and transcriptional fusions with exoY, SMb21440, SMc00084, SMc01580, chvI, and ropB1, we demonstrated this consensus sequence is important for ChvI binding to DNA and transcription of ChvI direct target genes. Thus, we have comprehensively identified ChvI regulon genes and a ‘ChvI box’ bound by ChvI. Many ChvI direct target genes may influence the cell envelope, consistent with the critical role of ExoS/ChvI in growth and microbe–host interactions.
The Potential Role of Synanthropic Rodents and Flies in the Transmission of Enterocytozoon bieneusi on a Dairy Cattle farm in China

Enterocytozoon bieneusi causes microsporidiosis, a condition with complex epidemiology involving both direct and indirect transmission routes. To assess the potential role of synanthropic rodents and flies in the transmission of this pathogen, a total of 277 cattle fecal samples, 199 synanthropic rodents, and 50 batches of 20 flies were collected from a cattle farm. These samples were screened for the presence of E. bieneusi by PCR and sequencing of the internal transcribed spacer (ITS) region of the rRNA gene. The positive rates of cattle, synanthropic rodents, and flies were 11.9% (33/277), 4.0% (8/199) and 12.0% (6/50), respectively. Nineteen genotypes were identified, including 11 known genotypes (BEB6, I, COS‐I, EbpC, D, J, CHS5, CHG1 to CHG3 and CHG14) and eight novel genotypes (named CHC9 to CHC16). The dominant genotype detected in the present study, BEB6, was found in all three categories of hosts. Moreover, human pathogenic genotypes D and EbpC were also observed in both synanthropic rodents and flies. These results demonstrate that synanthropic rodents and flies may act as biological disseminator or mechanical vector in the transmission of microsporidiosis to humans. Efforts should be made to minimize threats from these commensal animals to public health.
Biomechanical study of injectable hollow pedicle screws for PMMA augmentation in severely osteoporotic lumbar vertebrae: effect of PMMA distribution and volume on screw stability.

OBJECTIVEThe purpose of this study was to compare stability of injectable hollow pedicle screws with different numbers of holes using different volumes of polymethylmethacrylate (PMMA) in severely osteoporotic lumbar vertebrae and analyze the relationship between screw stability and distribution and volume of PMMA.METHODSForty-eight severely osteoporotic cadaveric lumbar vertebrae were randomly divided into 3 groups-groups A, B, and C (16 vertebrae per group). The screws used in group A had 4 holes (2 pairs of holes, with the second hole of each pair placed 180° further along the thread than the first). The screws used in group B had 6 holes (3 pairs of holes, placed with the same 180° difference in position). Unmodified conventional screws were used in group C. Each group was randomly divided into subgroups 0, 1, 2, and 3, with different volumes of PMMA used in each subgroup. Type A and B pedicle screws were directly inserted into the vertebrae in groups A and B, respectively, and then different volumes of PMMA were injected through the screws into the vertebrae in subgroups 0, 1, 2, and 3. The pilot hole was filled with different volumes of PMMA followed by insertion of screws in groups C0, C1, C2, and C3. Distributions of PMMA were evaluated radiographically, and axial pull-out tests were performed to measure the maximum axial pullout strength (Fmax). RESULTSRadiographic examination revealed that PMMA surrounded the anterior third of the screws in the vertebral bodies (VBs) in groups A1, A2, and A3; the middle third of screws in the junction area of the vertebral body (VB) and pedicle in groups B1, B2, and B3; and the full length of screws evenly in both VB and pedicle in groups C1, C2, and C3. In addition, in groups A3 and B3, PMMA from each of the screws (left and right) was in contact with PMMA from the other screw and the PMMA was closer to the posterior wall and pedicle than in groups A1, A2, B1, and B2. One instance of PMMA leakage was found (in group B3). Two-way analysis of variance revealed that 2 factors-distribution and volume of PMMA-significantly influenced Fmax (p < 0.05) but that they were not significantly correlated (p = 0.078). The Fmax values in groups in which screws were augmented with PMMA were significantly better than those in groups in which no PMMA was used (p < 0.05). CONCLUSIONSPMMA can significantly improve stability of different injectable pedicle screws in severely osteoporotic lumbar vertebrae, and screw stability is significantly correlated with distribution and volume of PMMA. The closer the PMMA is to the pedicle and the greater the quantity of injected PMMA used, the greater the pedicle screw stability is. Injection of 3.0 mL PMMA through screws with 4 holes (2 pair of holes, with the screws in each pair placed on opposite sides of the screw) produces optimal stability in severely osteoporotic lumbar vertebrae.
The effectiveness of a brief intervention to reduce alcohol consumption in pregnancy: a controlled trial

Objectives Alcohol consumption during pregnancy potentially has significant effects on both mother and baby. The aim of the study was to determine the effectiveness of a brief intervention to reduce alcohol consumption during pregnancy. Methods This study was performed at the outpatient antenatal clinics of a large academic maternity teaching hospital in Dublin city centre. Six hundred and fifty-six women who drank alcohol before pregnancy were recruited at their first antenatal clinic visit. Drinking patterns before pregnancy, since becoming pregnant, and in later pregnancy (at ~32 weeks of gestation) were assessed using the Alcohol Use Disorders Identification Test (AUDIT). A controlled study was conducted – participants were allocated to either the brief intervention group (screening and 5 minutes of non-directive discussion of their drinking pattern) or a control group (screening and treatment as usual). Results Before pregnancy, 57% of women consumed five or more units of alcohol per drinking occasion (i.e. binge drinking); during pregnancy, the rate of binge drinking fell to 4.8%. Sixty per cent of women who drank before pregnancy ceased drinking when pregnant, and a further 9% reduced their intake substantially. Four hundred and ninety-nine women were followed up in later pregnancy. The brief intervention did not produce any significant reduction in alcohol consumption above that attributable to pregnancy and comprehensive screening in antenatal care. Larger reductions in alcohol intake during pregnancy were associated with younger age, non-Irish nationality and greater intake of alcohol before first antenatal clinic visit. Conclusion Pregnancy itself produces abstinence and large reductions in alcohol consumption, even among women who drink relatively heavily. Consequently, a universal screening and brief intervention programme is not warranted but screening and targeted interventions could be appropriate such as repeated interventions for those who continue to binge drink. Future research could include evaluating interventions for those women who continue to binge drink during pregnancy and exploring ways of maintaining reductions in alcohol consumption among women who decreased consumption during pregnancy.
Estimation of the infinitesimal generator by square-root approximation

In recent years, for the analysis of molecular processes, the estimation of time-scales and transition rates has become fundamental. Estimating the transition rates between molecular conformations is—from a mathematical point of view—an invariant subspace projection problem. We present a method to project the infinitesimal generator acting on function space to a low-dimensional rate matrix. This projection can be performed in two steps. First, we discretize the conformational space in a Voronoi tessellation, then the transition rates between adjacent cells is approximated by the geometric average of the Boltzmann weights of the Voronoi cells. This method demonstrates that there is a direct relation between the potential energy surface of molecular structures and the transition rates of conformational changes. We will show also that this approximation is correct and converges to the generator of the Smoluchowski equation in the limit of infinitely small Voronoi cells. We present results for a two dimensional diffusion process and alanine dipeptide as a high-dimensional system.
Endotoxin regulates matrix genes increasing reactive oxygen species generation by intercellular communication between palmitate‐treated hepatocyte and stellate cell

Previous studies have shown that gut‐derived bacterial endotoxins contribute in the progression of simple steatosis to steatohepatitis, although the mechanism(s) remains inaccurate to date. As hepatic stellate cells (HSC) play a pivotal role in the accumulation of excessive extracellular matrix (ECM), leading to collagen deposition, fibrosis, and perpetuation of inflammatory response, an in vitro model was developed to investigate the crosstalk between HSC and hepatocytes (human hepatoma cell) pretreated with palmitate. Bacterial lipopolysaccharide (LPS) stimulated HSC with phosphorylation of the p38 mitogen‐activated protein kinase/NF‐κB pathway, while several important pro‐inflammatory cytokines were upregulated in the presence of hepatocyte–HSC. Concurrently, fibrosis‐related genes were regulated by palmitate and the inflammatory effect of endotoxin where cells were more exposed or sensitive to reactive oxygen species (ROS). This interaction was accompanied by increased expression of the mitochondrial master regulator, proliferator‐activated receptor gamma coactivator alpha, and a cytoprotective effect of the agent N‐acetylcysteine suppressing ROS production, transforming growth factor‐β1, and tissue inhibitor of metalloproteinase‐1. In summary, our results demonstrate that pro‐inflammatory mediators LPS‐induced promote ECM rearrangement in hepatic cells transcriptionally committed to the regulation of genes encoding enzymes for fatty acid metabolism in light of differences that might require an alternative therapeutic approach targeting ROS regulation.
Towards Efficient Visual Guidance in Limited Field-of-View Head-Mounted Displays

Understanding, navigating, and performing goal-oriented actions in Mixed Reality (MR) environments is a challenging task and requires adequate information conveyance about the location of all virtual objects in a scene. Current Head-Mounted Displays (HMDs) have a limited field-of-view where augmented objects may be displayed. Furthermore, complex MR environments may be comprised of a large number of objects which can be distributed in the extended surrounding space of the user. This paper presents two novel techniques for visually guiding the attention of users towards out-of-view objects in HMD-based MR: the 3D Radar and the Mirror Ball. We evaluate our approaches against existing techniques during three different object collection scenarios, which simulate real-world exploratory and goal-oriented visual search tasks. To better understand how the different visualizations guide the attention of users, we analyzed the head rotation data for all techniques and introduce a novel method to evaluate and classify head rotation trajectories. Our findings provide supporting evidence that the type of visual guidance technique impacts the way users search for virtual objects in MR.
Emerging Multiport Electrical Machines and Systems - Part II

THE Special Section on “Emerging Multiport Electrical Machines and Systems” presents recent advances and challenges in the field of emerging electrical machines and systems with multiple electrical and/or mechanical ports, ranging from new machine/converter/system topologies to design and optimization methods, advanced control strategies, performance evaluation, and explorations for up-and-coming applications. Part II of this Special Section (Part I was published in the November 2018 issue of the IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS) includes 18 papers, from a total of 34 accepted papers, as grouped in Table I. Their main contributions are examined below to help readers have a quick aerial-view of the hottest research topics and state-of-the-art solutions in this fast-growing research area. In [item 1) in the Appendix], a cage-assisted magnetic barrier rotor, i.e., the hybrid rotor, for the conventional brushless doubly fed induction machine (BDFIM) is designed and analyzed with the general airgap field modulation theory in an attempt to enhance the torque capability of the machine. Experimental results are provided to show the superiority of the proposed rotor design and analysis method. [Item 2) in the Appendix] develops a new multiobjective design approach to size and optimize a flux-modulated double-rotor flux-switching permanent magnet (PM) machine with multiple driving modes considered. The electromagnetic characteristics of the optimized machine are investigated in detail. Experimental tests on a prototype are carried out to check the effectiveness of the developed design approach. [Item 3) in the Appendix] investigates a novel dual-winding fault-tolerant motor drive system with a redundant bridge arm for aerospace applications. The novel fault-tolerant motor drive system is suitable for aircrafts with a single power supply as it reduces the drive cost, the number of independent power sources, and the power switch count. A novel fault-tolerant control strategy is also introduced and experimentally validated, showing the strong fault-tolerant capability of the motor drive system in case of one-phase and multiphase winding faults. In [item 4) in the Appendix], a flux-modulated double-rotor machine for series-parallel hybrid electric vehicles (HEVs) is proposed. Boundary operating conditions are discussed. Power flows in various operating modes are examined and corresponding power equations are deduced. An HEV system based on the proposed flux-modulated double-rotor machine is simulated with an United States Environmetal Protection Agency driving cycle to test the availability of various operating modes. The
Changes in the fat body and oocysts during starvation and vitellogenesis in a mosquito, Aedes aegypti (L.)

When Aedes aegypti females first emerge as adults, their oocytes possess no yolk. The abdominal fat body cells contain large quantities of lipid, protein, and glycogen, and possess many free ribosomes, but have very little rough endoplasmic reticulum (RER). When the females are starved for four days, their oocytes form fine lipid and protein yolk endogenously, the latter being located mainly around the nucleus. The adipocytes in these fasted mosquitoes have greatly reduced amounts of lipid, protein and glycogen and contain many cytolysosomes. Seven hours after 4‐day‐starved females had fed on blood, their oocytes begin filling with exogenous protein yolk at the oolemma, and lipid arises endogenously throughout the ooplasm. At this hour, the fat cells have synthesized more RER than is seen in unfed controls. Twenty‐four hours post blood meal, the follicle cells have secreted discrete endochorionic plaques onto the oolemma. At this period, the adipocytes are densely filled with RER, and show for the first time many Golgi bodies and protein inclusions. They have noticeably less glycogen than at seven hours. Within 48 hours after mosquitoes have fed on blood, the endochorion forms a continuous layer around the steadily enlarging egg which is synthesizing additional protein and lipid yolk. Concurrently, the adipocytes show a greatly increased amount of glycogen and a significant reduction of RER. By the sixtieth hour after the blood meal, the follicle cells are attenuated, and the fat cells have less RER and more glycogen than at 48 hours. The nurse cells steadily decrease in size during vitellogenesis and release material onto the micropyle.
Distinct Inflammatory Changes of the Pancreas of Slowly Progressive Insulin-dependent (Type 1) Diabetes

Objective The aim of this study was to identify the distinct pathological changes on the endocrine and exocrine pancreas of slowly progressive insulin-dependent diabetes mellitus (SPIDDM) or latent autoimmune diabetes in adults. Methods The pancreases from 12 islet autoantibody–positive SPIDDM patients and 19 age-matched subjects with no diabetes were examined histologically for islet inflammation/insulitis, expressions of cytokines, and enterovirus VP1 protein, exocrine pancreatic inflammation, pancreatic ductal changes, major histocompatibility complex class I hyperexpression, and amylin-positive amyloid in the islets. Results Insulitis dominant for CD8+ T-cells and CD68+ macrophages was observed in all SPIDDM cases irrespective of duration of diabetes and weight of residual beta cells. Major histocompatibility complex class I hyperexpression on residual beta cells was observed in SPIDDM. All SPIDDM exocrine pancreases showed extensive inflammation, dilated pancreatic ducts, and periductal fibrosis. As many as 75% (9/12) of pancreases had pancreatic intraepithelial neoplasia, which is assumed to be associated with ductal obstruction/narrowing and exocrine pancreatic inflammation, in SPIDDM. Amylin-positive amyloid deposition was not detected in SPIDDM. Conclusions Persistent insulitis with preserved beta cells and major histocompatibility complex class I hyperexpression and exocrine pancreatic inflammation with pancreatic intraepithelial neoplasia are distinct histological features of SPIDDM pancreas.
Molecular and Cellular Response to Experimental Anisakis pegreffii (Nematoda, Anisakidae) Third-Stage Larval Infection in Rats

Background: Anisakiasis is a zoonotic disease caused by accidental ingestion of live Anisakis spp. third-stage larvae present in raw or undercooked seafood. Symptoms of this emerging infectious disease include mild-to-severe abdominal pain, nausea, and diarrhea. Some patients experience significant allergic reactions. Aims: In order to better understand the onset of anisakiasis, we aimed to: (i) histopathologically describe severe inflammatory/hemorrhagic infection site lesions in Sprague-Dawley rats experimentally infected with Anisakis pegreffii larvae; and (ii) qualitatively and quantitatively characterize the transcriptomes of affected tissues using RNA-Seq. Methodology: The experiment was performed on 35 male rats, sacrificed at 5 time points (6, 10, 18, 24, and 32 h post-infection). Gastric intubation was performed with 10 A. pegreffii larvae (N = 5 infected rats per time point) or 1.5 ml of saline (external control N = 2 rats). 16 pools, seven for muscle tissues and nine for stomach tissues, were created to obtain robust samples for estimation of gene expression changes depicting common signatures of affected versus unaffected tissues. Illumina NextSeq 500 was used for paired-end sequencing, while edgeR was used for count data and differential expression analyses. Results: In total, there were 1372 (855 up and 517 down) differentially expressed (DE) genes in the Anisakis-infected rat stomach tissues, and 1633 (1230 up and 403 down) DE genes in the muscle tissues. Elicited strong local proinflammatory reaction seems to favor the activation of the interleukin 17 signaling pathway and the development of the T helper 17-type response. The number of DE ribosomal genes in the Anisakis-infected stomach tissue suggests that A. pegreffii larvae might induce ribosomal stress in the early infection stage. However, the downstream pathways and post-infection responses require further study. Histopathology revealed severe inflammatory/hemorrhagic lesions caused by Anisakis infection in the rat stomach and muscle tissues in the first 32 h. The lesion sites showed infiltration by polymorphonuclear leukocytes (predominantly neutrophils and occasional eosinophils), and to a lesser extent, macrophages. Conclusion: Understanding the cellular and molecular mechanisms underlying host responses to Anisakis infection is important to elucidate many aspects of the onset of anisakiasis, a disease of growing public health concern.
Leaf economics spectrum in rice: leaf anatomical, biochemical, and physiological trait trade-offs

Abstract The leaf economics spectrum (LES) is an ecophysiological concept describing the trade-offs of leaf structural and physiological traits, and has been widely investigated on multiple scales. However, the effects of the breeding process on the LES in crops, as well as the mechanisms of the trait trade-offs underlying the LES, have not been thoroughly elucidated to date. In this study, a dataset that included leaf anatomical, biochemical, and functional traits was constructed to evaluate the trait covariations and trade-offs in domesticated species, namely rice (Oryza species). The slopes and intercepts of the major bivariate correlations of the leaf traits in rice were significantly different from the global LES dataset (Glopnet), which is based on multiple non-crop species in natural ecosystems, although the general patterns were similar. The photosynthetic traits responded differently to leaf structural and biochemical changes, and mesophyll conductance was the most sensitive to leaf nitrogen (N) status. A further analysis revealed that the relative limitation of mesophyll conductance declined with leaf N content; however, the limitation of the biochemistry increased relative to leaf N content. These findings indicate that breeding selection and high-resource agricultural environments lead crops to deviate from the leaf trait covariation in wild species, and future breeding to increase the photosynthesis of rice should primarily focus on improvement of the efficiency of photosynthetic enzymes.
Intrauterine growth restriction associated with paternal isodisomy of chromosome 5: a clinical report and literature survey

Abstract Background: Uniparental disomy (UPD) is a condition where both the chromosomes are inherited from the same parent. The consequences of UPD can be ranging from normal to congenital anomaly depending on the parental origin and chromosome involved. Case characteristics: Here, we describe a case of 2-year-old male with central hypotonia, torticollis, and delayed motor skills born to a nonconsanguineous healthy parent. The proband was prenatally detected with paternal isodisomy 5 and birth was induced at 38 weeks of gestation due to intrauterine growth restriction. There was also confined placental mosaicism along with the isodisomy. Results: No major phenotypic correlation observed. This is the first case of paternal isodisomy 5 with phenotypically normal child. Conclusions: The present case supports the reports that genes on chromosome 5 are nonimprinted. The implications of abnormal genetic findings on genetic counseling are discussed.