Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity

SUMMARY Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.
The hypoxia signalling pathway in haematological malignancies

Haematological malignancies are tumours that affect the haematopoietic and the lymphatic systems. Despite the huge efforts to eradicate these tumours, the percentage of patients suffering resistance to therapies and relapse still remains significant. The tumour environment favours drug resistance of cancer cells, and particularly of cancer stem/initiating cells. Hypoxia promotes aggressiveness, metastatic spread and relapse in most of the solid tumours. Furthermore, hypoxia is associated with worse prognosis and resistance to conventional treatments through activation of the hypoxia-inducible factors. Haematological malignancies are not considered solid tumours, and therefore, the role of hypoxia in these diseases was initially presumed to be inconsequential. However, hypoxia is a hallmark of the haematopoietic niche. Here, we will review the current understanding of the role of both hypoxia and hypoxia-inducible factors in different haematological tumours.
Validation of the lung cancer staging system revisions using a large prospective clinical trial database (ACOSOG Z0030).

OBJECTIVES A new revision of the international lung cancer staging system has been recently introduced. The revisions are largely focussed on the T descriptor. We sought to test the validity of this new system on a separate prospectively collected cohort of patients from a recent multicentre trial of early-stage lung cancer. METHODS We reviewed the prospectively collected data from 1012 patients undergoing pulmonary resection for early-stage lung cancer in the ACOSOG Z0030 trial. TNM descriptors and overall staging were assessed using both the sixth and seventh editions of the American Joint Committee on Cancer and the Union Internationale Contre le Cancer (AJCC/UICC) lung cancer staging system. Survival results were analysed according to both staging allocations. RESULTS Using the proposed criteria, the number of patients by stage in the sixth and seventh edition allocations, respectively, were as follows: IA (432, 431); IB (402, 303); IIA (39, 167); IIB (94, 70); IIIA (26, 40); IIIB (19,0); there were no stage IV patients by either version. Overall, 180 (18%) patients had a change in the stage group from the sixth to seventh edition versions with 76 (8%) being downstaged and 104 (10%) being upstaged. In the sixth edition staging system based on pathological stages, median survivals in years were as follows: IA, NA; IB, 7.7; IIA, 4.0; IIB, 3.6; IIIA, 2.6 and IIIB, 2.4. Five-year survivals were: IA, 76.4%; IB, 62.0%; IIA, 47.8%; IIB, 40.4%; IIIA, 31.3% and IIIB, 44.4%. In the new system, median survivals in years were as follows: IA, NA; IB, 8.2; IIA, 4.4; IIB, 3.6 and IIIA, 1.8. Five-year survivals were: IA, 76.9%; IB, 65.0%; IIA, 48.5%; IIB, 42.9% and IIIA, 30.6%. Survival analysis and Kaplan-Meier survival curves showed more monotonic progression, distinction and homogeneity within groups in the seventh edition. CONCLUSIONS This study provides an external validation of the recently revised lung cancer staging system using a large multicentre database. The seventh edition of the AJCC/UICC lung cancer staging system appears to be an improvement over the preceding system.
Combined twist-bend with compact-size and broad bandwidth

A novel combined twist-bend with compact-size and broad bandwidth is proposed in this letter. It provides an interconnection of two waveguides with 90 degrees oriented cross-sections and a perpendicular alignment of their axes. The basic structure consists of a multi-step central waveguide and two transformer sections, which made the twist-bend with compact size and broad bandwidth. For verification purpose, a prototype has been manufactured and measured. Measurements of a WR28 combined twist-bend exhibit a return loss greater than 24 dB and a insertion loss better than 0.1 dB over the full waveguide bandwidth. Also the good agreement has been found between the simulated and measured results.
Upper limb training/assessment program using passive force controllable rehabilitation system

Upper limb rehabilitation training for Hemiplegie patients has been conducted mainly by human therapists. Training methods and conditions depend strongly on their experience because of the wide range of individual differences between patients. The force control and sensing functions of rehabilitation robots are expected to be used for the qualitative assessment of next-generation computational rehabilitation. In this study, we developed a simple exercise machine for upper limbs (SEMUL) using an electro-rheological fluid brake, as a safe brake-type robotic rehabilitation system. We also developed a new upper limb training/assessment program, called “WIPE,” for the SEMUL. Furthermore, we conducted clinical tests on twelve subjects (six each for the SEMUL training and for general training). We adopted the ABA design methodology for the clinical research tests. The motor functions of upper limbs were assessed using five clinical scores: Fugl-Meyer Assessment (FMA), Brunnstrome recovery stage, Simple Test for Evaluating Hand Function (STEF), Stroke Impairment Assessment Set (SIAS), and Motor Activity Log. Improvements of the FMA, STEF, and SIAS in the SEMUL training groups were found to be higher than those in the general training groups.
Osteoporosis Is the Most Important Risk Factor for Odontoid Fractures in the Elderly

Traumatic odontoid fractures (TOFs) have been described as the most common injury affecting the C‐spine in the elderly. Previous studies have identified degenerative changes and bone loss as important predisposing factors. However, their interaction and respective age‐adjusted impact needs further clarification. We conducted a retrospective analysis of 5303 patients (aged ≥60 years) admitted to a level I trauma center between January 2008 and January 2016 who underwent CT imaging of the C‐spine. Ninety‐two patients with TOF and 80 patients with other cervical spine fractures (OCSF) were identified and a respective 3:1 age‐ and sex‐matched control group without fractures after trauma was built. In all groups, cervical bone mineral density (cBMD) was determined using phantom calibration, and degenerative changes were evaluated in a qualitative manner. In all groups, the severity of degenerative changes of the C‐spine increased with age (all p < 0.05) and was inversely correlated with cBMD (all p < 0.05). cBMD was the only significant predictor of a TOF in a multivariate logistic regression model (adjusted odds ratio [OR] = 3.066, 95% confidence interval [CI] 1.432–6.563 for cervical osteoporosis). An association between odontoid cysts and TOF reached significance only in Anderson and D'Alonzo (A&D) type II TOFs (aOR = 1.383; 95% CI 1.012–1.890). Patients with OCSFs, compared with patients with TOFs, were younger (median 74 versus 83 years) and had a higher cBMD (median 208 mg/mL versus 172 mg/mL). No differences were observable when comparing cBMD and grades of degenerative changes between OCSFs and their control group (all p >0.1). Decreased cBMD is the major predisposing factor for the occurrence of TOF but not for OCSF in the elderly. The severity of odontoid cysts was found to be a cBMD‐independent factor associated with A&D type II TOFs. However, degenerative changes in the odontoid neighboring joints seem to be an epiphenomenon of bone loss and older age but do not independently predispose for TOF. © 2017 American Society for Bone and Mineral Research.
IFITM3 Rs12252-C Variant Increases Potential Risk for Severe Influenza Virus Infection in Chinese Population

Background: Interferon Inducible Transmembrane 3 (IFITM3) is a key factor in interferon pathway and it involves host's immune response against multiple viruses. IFITM3 rs12252-C was associated with severe influenza virus infection in several studies, however whether this association is universal to all types of influenza virus or diverse ethnic populations remain controversial. Method: A case-control genetic association study was performed from September 2013 to April 2014 and September 2014 to April 2015. All samples were tested for influenza using RT-PCR, and genotyped by High Resolution Melting assay. Results: A total of 65 healthy people, 165 mild influenza-like illness (ILI) cases and 315 severe acute respiratory infection (SARI) cases were enrolled in this study. The frequency of CC genotype was much higher in SARI cases with IVI than that in ILI cases with IVI (61.59 vs. 27.16%), leading a 4.67-fold greater risk for severe IVI than other two genotypes. Moreover, the risk of IFITM3 rs12252-C variant for severe IVI was specific for both influenza A and influenza B. Conclusion: IFITM3 rs12252 CC genotype was associated with severity rather than susceptibility of IVI in Chinese population, and this strong effect was observed in all subtypes of seasonal influenza infection.
Evidence that brief stress may induce the acute phase response in rats.

Exposing rats to a single session of inescapable tail shock (IS) reduces corticosteroid binding globulin (CBG) 24 h later (Fleshner et al., Endocrinology 136: 5336-5342, 1995). The present experiments examined whether reductions in CBG are differentially affected by controllable vs. identical uncontrollable tail shock, are mediated by IS-induced glucocorticoid elevation, or reflect IS-induced activation of the acute phase response and whether IS produces fever. The results demonstrate that 1) equivalent reductions in CBG are observed in response to escapable tail shock or yoked IS, 2) IS-induced CBG reduction is not blocked by adrenalectomy in rats that receive basal corticosteroid replacement or by pretreatment with RU-38486, and 3) IS appears to activate the acute phase response, since IS reduces serum levels of an acute-phase negative reactant (CBG), increases serum levels of acute-phase positive reactants (haptoglobin and α1-acid glycoprotein), and increases core body temperature 20-24 h later.
Thermal Properties of Semiconductor Low-Dimensional Structures

In this paper we review our work on thermal and thermoelectric properties of semiconductor low-dimensional structures, e.g. quantum wells and quantum wires, with emphasis on the effects of spatial confinement of acoustic phonons. We particularly concentrate on calculation of the phonon relaxation rates in mass-difference, Umklapp, point defect, and dislocation scattering processes that takes into account confinement of phonon modes. A possibility of device performance enhancement via phonon engineering and thermoelectric applications of low-dimensional structures are also discussed.
The toxicity of different lead salts to Enchytraeus crypticus in relation to bioavailability in soil

The present study aimed to assess the bioavailability and toxicity of lead nitrate and lead chloride to Enchytraeus crypticus in a natural standard soil. Worms were exposed to Pb‐spiked soil for 21 d, and survival and reproduction were related to total, 0.01 M CaCl2‐extractable, and porewater Pb concentrations in the soil and internal concentrations in the surviving animals. The Pb availability for Pb(NO3)2 and PbCl2 was similar, as confirmed by Langmuir and Freundlich isotherms. The Pb concentrations in surviving worms increased with increasing Pb concentrations in the soil and did not differ for the 2 Pb salts. Lead was toxic to E. crypticus at median lethal concentrations (LC50s) of 543 and 779 mg Pb/kg dry soil and median effect concentrations (EC50s) of 189 and 134 mg Pb/kg dry soil, for Pb(NO3)2 and PbCl2, respectively. Mortality of E. crypticus was related to internal Pb concentrations in the worms rather than to total or available Pb concentrations in the soil, whereas reproduction toxicity was better explained from Pb concentrations in 0.01 M CaCl2 extracts or porewater of the test soil than from total Pb concentrations in the soil or Pb concentrations in the worms. Overall, the bioavailability and toxicity of Pb(NO3)2 and PbCl2 to E. crypticus in LUFA 2.2 soil did not differ. Environ Toxicol Chem 2017;36:2083–2091. © 2017 SETAC
DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy

Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments. The microscopic method used to analyze aerobiological samples and the inconspicuous fungal characters do not allow a in depth taxonomical identification. Here, we present a first assessment of fungal diversity from airborne samples using a DNA metabarcoding analysis. The nuclear ITS2 region was selected as barcode to catch fungal diversity in mixed airborne samples gathered during two weeks in four sites of North-Eastern and Central Italy. We assessed the taxonomic composition and diversity within and among the sampled sites and compared the molecular data with those obtained by traditional microscopy. The molecular analyses provide a tenfold more comprehensive determination of the taxa than the traditional morphological inspections. Our results prove that the metabarcoding analysis is a promising approach to increases quality and sensitivity of the aerobiological monitoring. The laboratory and bioinformatic workflow implemented here is now suitable for routine, high-throughput, regional analyses of airborne fungi.
Long term outcome in children of sex chromosome abnormalities

An unduly pessimistic description of what it means to have an extra X or Y chromosome is frequently given to the parents of an affected fetus or child by geneticists and paediatricians because the source of their information has been biased towards abnormality. In 1967 the Medical Research Council set up a cytogenetic survey of consecutive newborn infants to establish the incidence of the various chromosome abnormalities. The long term follow up of children with sex chromosome abnormalities ascertained in the survey, which screened 34 380 newborns in Edinburgh between 1967 and 1979, has enabled a more balanced prognosis to be reached. Most boys with the karyotypes 47,XXY and 47,XYY and girls with 47,XXX are never diagnosed. While that may suggest that the conditions are of no importance to the affected individuals, I will show using the following results that this is not the case. Based on the incidence at birth obtained from cytogenetic surveys of around 200 000 infants from the UK, Denmark, Canada, the USA, and Japan, an XXY karyotype was found in 1.3 per 1000 male infants, while XYY and XXX occurred with a frequency of 1 per 1000 male or female infants, respectively.1 Using these incidence figures Abramsky and Chapelle2 found that 10% of expected cases of XXY boys were identified at amniocentesis, a further 26% were diagnosed in childhood or adult life on account of hypogonadism, gynaecomastia, infertility, or developmental delay, leaving 64% undiagnosed. Among XYY boys, where there is no advanced paternal age effect, 85% were calculated to be undiagnosed either before or after birth. Abramsky and Chapelle did not include XXX females, but an estimate can be made from the maternal age distribution of 57 affected newborns where 26% were born to mothers over the age of 35 years. It is reasonable to …
The international consortium on the Ehlers–Danlos syndromes

Since 1998, two developments have led to concerns that the EDS nosology needs to be substantially revised. The first development was the clinical and molecular characterization of several new EDS variants, which substantially broadened the molecular basis underlying EDS. The second was the growing concern, in the absence of genetic diagnosis, that the hypermobile type of EDS had an expanded phenotype, may be genetically heterogeneous, and that the diagnostic criteria currently in use were inadequate. Furthermore, there is a dire need for the development of guidelines for management for each type of EDS to allow both the specialist and the generalist to care for affected individuals and their families. We have been meeting together as an international consortium over the past 2 years to establish these new criteria and management and care guidelines © 2017 Wiley Periodicals, Inc.
High Rates of Actin Filament Turnover in Budding Yeast and Roles for Actin in Establishment and Maintenance of Cell Polarity Revealed Using the Actin Inhibitor Latrunculin-A

We report that the actin assembly inhibitor latrunculin-A (LAT-A) causes complete disruption of the yeast actin cytoskeleton within 2–5 min, suggesting that although yeast are nonmotile, their actin filaments undergo rapid cycles of assembly and disassembly in vivo. Differences in the LAT-A sensitivities of strains carrying mutations in components of the actin cytoskeleton suggest that tropomyosin, fimbrin, capping protein, Sla2p, and Srv2p act to increase actin cytoskeleton stability, while End3p and Sla1p act to decrease stability. Identification of three LAT-A resistant actin mutants demonstrated that in vivo effects of LAT-A are due specifically to impairment of actin function and implicated a region on the three-dimensional actin structure as the LAT-A binding site. LAT-A was used to determine which of 19 different proteins implicated in cell polarity development require actin to achieve polarized localization. Results show that at least two molecular pathways, one actindependent and the other actin-independent, underlie polarity development. The actin-dependent pathway localizes secretory vesicles and a putative vesicle docking complex to sites of cell surface growth, providing an explanation for the dependence of polarized cell surface growth on actin function. Unexpectedly, several proteins that function with actin during cell polarity development, including an unconventional myosin (Myo2p), calmodulin, and an actin-interacting protein (Bud6/Aip3p), achieved polarized localization by an actin-independent pathway, revealing interdependence among cell polarity pathways. Finally, transient actin depolymerization caused many cells to abandon one bud site or mating projection and to initiate growth at a second site. Thus, actin filaments are also required for maintenance of an axis of cell polarity.
Histological validation of myocardial microstructure obtained from diffusion tensor magnetic resonance imaging.

Diffusion tensor magnetic resonance imaging (MRI) is a possible new means of elucidating the anatomic structure of the myocardium. It enjoys several advantages over traditional histological approaches, including the ability to rapidly measure fiber organization in isolated, perfused, arrested hearts, thereby avoiding fixation and sectioning of artifacts. However, quantitative validation of this MRI method has been lacking. Here, fiber orientations estimated in the same locations in the same heart using both diffusion tensor MRI and histology are compared in a total of two perfused rabbit hearts. Fiber orientations were statistically similar for both methods and differed on average by 12° at any single location. This is similar to the 10° uncertainty in fiber orientation achieved with histology. In addition, imaging studies performed in a total of seven hearts support a level of organization beyond the myofiber, the recently described laminar organization of the ventricular myocardium.
The Effect of Assortative Mating on the Coexistence of a Hybridogenetic Waterfrog and Its Sexual Host

In central Europe, the hybridogenetic waterfrog Rana esculenta, a hybrid between Rana ridibunda and Rana lessonae, lives in sympatry with one of its parental species, the poolfrog Rana lessonae. As R. esculenta has to backcross constantly with R. lessonae in order to produce viable offspring, this coexistence is obligatory for R. esculenta. Since R. esculenta has a higher primary fitness than R. lessonae, a mechanism is required that prevents the hybrid from driving the parental species, and hence itself, to extinction. Here, we present an analytical model and a computer simulation that investigate whether assortative mating can operate as a such a control mechanism. Our results show that assortative mating is very effective in regulating coexistence in such a hybrid‐host system. This is particularly true when choice is affected by the proportion of the two male types in the population. Furthermore, we could show that even if the species composition in a mixed hybrid‐host population may be largely influenced by differences in life‐history parameters, assortative mating still plays a very important role by stabilizing coexistence. Thus, mating behavior turns out to be more important for the populations dynamics of hybridogenetic waterfrog systems than previously assumed.
Zika virus epidemiology in Bolivia: A seroprevalence study in volunteer blood donors

Background Zika virus (ZIKV), was widely reported in Latin America and has been associated with neuropathologies, as microcephaly, but only few seroprevalence studies have been published to date. Our objective was to determine the seroprevalence amongst Bolivian blood donors and estimate the future potential circulation of the virus. Methodology A ZIKV seroprevalence study was conducted between December 2016 and April 2017 in 814 asymptomatic Bolivian volunteer blood donors residing in various eco-environments corresponding to contrasting entomological activities. It was based on detection of IgG to ZIKV using NS1 ELISA screening, followed by a seroneutralisation test in case of positive or equivocal ELISA result. Conclusions/Significance Analysis revealed that ZIKV circulation occurred in tropical areas (Beni: 39%; Santa Cruz de la Sierra: 21.5%) but not in highlands (~0% in Cochabamba, La Paz, Tarija). It was modulated by Aedes aegypti activity and the virus spread was not limited by previous immunity to dengue. Cases were geo-localised in a wide range of urban areas in Santa Cruz and Trinidad. No differences in seroprevalence related to gender or age-groups could be identified. It is concluded that ZIKV has been intensely circulating in the Beni region and has still a significant potential for propagating in the area of Santa Cruz.