Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic mutational analysis of the amino‐terminal domain of the Listeria monocytogenes ActA protein reveals novel functions in actin‐based motility

The Listeria monocytogenes ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerization and propulsion of the bacterium through the cytoplasm. We have constructed 20 clustered charged‐to‐alanine mutations in the NH2‐terminal domain of ActA and replaced the endogenous actA gene with these molecular variants. These 20 clones were evaluated in several biological assays for phenotypes associated with particular amino acid changes. Additionally, each protein variant was purified and tested for stimulation of the Arp2/3 complex, and a subset was tested for actin monomer binding. These specific mutations refined the two regions involved in Arp2/3 activation and suggest that the actin‐binding sequence of ActA spans 40 amino acids. We also identified a ‘motility rate and cloud‐to‐tail transition’ region in which nine contiguous mutations spanning amino acids 165–260 caused motility rate defects and changed the ratio of intracellular bacteria associated with actin clouds and comet tails without affecting Arp2/3 activation. Several unusual motility phenotypes were associated with amino acid changes in this region, including altered paths through the cytoplasm, discontinuous actin tails in host cells and the tendency to ‘skid’ or dramatically change direction while moving. These unusual phenotypes illustrate the complexity of ActA functions that control the actin‐based motility of L. monocytogenes.
Hierarchical bioimaging and quantification of vasculature in disease models using corrosion casts and microcomputed tomography

A wide range of disorders are associated with alterations of the central and peripheral vascular system. Modified vascular corrosion casting using a newly developed polymer, allows for the first time hierarchical assessment of 3D vessel data in animals down to the level of capillaries. Imaging of large volumes of vasculature at intermediate resolution (16 μm) was performed using a desktop micro-computed tomography system. Subsequently regions of interest were identified for additional high resolution imaging (1.4 μm) at the X-ray Tomographic Microscopy (XTM) station of the Swiss Light Source (SLS). A framework for systematic hierarchical imaging and quantification was developed. Issues addressed included enhanced XTM data acquisition, introduction of local tomography, sample navigation, advanced post processing, and data combination. In addition to visual assessment of qualitative changes, morphometrical and architectural indices were determined using direct 3D morphometry software developed in house. Vessel specific parameters included thickness, surface, connectivity, and vessel length. Reconstructions of cerebral vasculature in mutant mice modeling Alzheimer's disease revealed significant changes in vessel architecture and morphology. In the future, a combination of these techniques may support drug discovery. Additionally, future ultra-high-resolution in vivo systems may even allow non-invasive tracking of temporal alterations in vascular morphology.
Expression of genes belonging to the interacting TLR cascades, NADPH-oxidase and mitochondrial oxidative phosphorylation in septic patients

Background and objectives Sepsis is a complex disease that is characterized by activation and inhibition of different cell signaling pathways according to the disease stage. Here, we evaluated genes involved in the TLR signaling pathway, oxidative phosphorylation and oxidative metabolism, aiming to assess their interactions and resulting cell functions and pathways that are disturbed in septic patients. Materials and methods Blood samples were obtained from 16 patients with sepsis secondary to community acquired pneumonia at admission (D0), and after 7 days (D7, N = 10) of therapy. Samples were also collected from 8 healthy volunteers who were matched according to age and gender. Gene expression of 84 genes was performed by real-time polymerase chain reactions. Their expression was considered up- or down-regulated when the fold change was greater than 1.5 compared to the healthy volunteers. A p-value of ≤ 0.05 was considered significant. Results Twenty-two genes were differently expressed in D0 samples; most of them were down-regulated. When gene expression was analyzed according to the outcomes, higher number of altered genes and a higher intensity in the disturbance was observed in non-survivor than in survivor patients. The canonical pathways altered in D0 samples included interferon and iNOS signaling; the role of JAK1, JAK2 and TYK2 in interferon signaling; mitochondrial dysfunction; and superoxide radical degradation pathways. When analyzed according to outcomes, different pathways were disturbed in surviving and non-surviving patients. Mitochondrial dysfunction, oxidative phosphorylation and superoxide radical degradation pathway were among the most altered in non-surviving patients. Conclusion Our data show changes in the expression of genes belonging to the interacting TLR cascades, NADPH-oxidase and oxidative phosphorylation. Importantly, distinct patterns are clearly observed in surviving and non-surviving patients. Interferon signaling, marked by changes in JAK-STAT modulation, had prominent changes in both survivors and non-survivors, whereas the redox imbalance (iNOS signaling, oxidative phosphorylation and superoxide radical degradation) affecting mitochondrial functions was prominent in non-surviving patients.
An epidemiological investigation of Campylobacter in pig and poultry farms in the Mekong delta of Vietnam

SUMMARY Campylobacter are zoonotic pathogens commonly associated with gastroenteritis. To assess the relevance of Campylobacter in Vietnam, an economically transitioning country in SE Asia, we conducted a survey of 343 pig and poultry farms in the Mekong delta, a region characterized by mixed species farming with limited biosecurity. The animal-level prevalence of Campylobacter was 31·9%, 23·9% and 53·7% for chickens, ducks and pigs, respectively. C. jejuni was predominant in all three host species, with the highest prevalence in pigs in high-density production areas. Campylobacter isolates demonstrated high levels of antimicrobial resistance (21% and 100% resistance against ciprofloxacin and erythromycin, respectively). Multilocus sequence type genotyping showed a high level of genetic diversity within C. jejuni, and predicted C. coli inter-species transmission. We suggest that on-going intensification of animal production systems, limited biosecurity, and increased urbanization in Vietnam is likely to result in Campylobacter becoming an increasingly significant cause of human diarrhoeal infections in coming years.
Multilayered ceramic composites – a review

With the aim of improving the toughness of ceramic materials, laminated composites have been successfully developed since Clegg et al. (1990) inserted weak interfaces using very thin graphite layers between silicon carbide sheets and obtained a composite that exhibited non-catastrophic fracture characteristics. The weak interface must allow the crack to deviate either by deflection or delamination; in other words, the interface must exhibit a fracture resistance that is lower than that of the matrix layer. In parallel, ceramic laminated composites with strong interfaces were developed in which the residual tensile and compressive stresses appeared in alternate layers during cooling after sintering. These composites are prepared by stacking ceramic sheets produced by lamination or tape casting or by the sequential formation of layers by slip casting, centrifugation or electrophoretic deposition. The techniques may be combined to obtain a composite with the most adequate configuration. This work presents a review about the obtainment of multilayered ceramic composites as a toughening mechanism of ceramic plates.
Non-Small Cell Lung Cancer beyond Biomarkers: The Evolving Landscape of Clinical Trial Design

The approval of EGFR and ALK directed tyrosine kinase inhibitors materialized the concept of tailoring therapy on the basis of specific biomarkers for treating patients with NSCLC. Research for other biologics, although demonstrating clinical benefit, has been less successful so far for producing biomarkers that predict response. Blocking angiogenesis is the prototype for the agents that belong in the latter group that target specific molecules, yet they are currently approved for relatively unselected groups of patients. In order to meet the goal of personalizing care in the various settings of NSCLC, a wealth of biologics and compounds are currently being tested in clinical trials in different phases of clinical development. In a subset of the relevant studies, a biomarker perspective is appreciated. This review summarizes the clinical rationale of the major ongoing phase II and III NSCLC studies that employ targeting specific molecules with novel agents, as well as innovative strategies, and includes a comparative discussion of the different designs.
Magnitude and Factors Associated with Appropriate Complementary Feeding among Mothers Having Children 6-23 Months-of-Age in Northern Ethiopia; A Community-Based Cross-Sectional Study

Background- Adequate and appropriate complementary feeding during 6-23 months-of-age, is fundamental to the development of each child’s full human potential. Ethiopian national survey reports showed the minimum acceptable diet was 4.2% in same region. But in most cases only timely initiation is considered as the only indicator of complementary feeding. The aim of this study was to assess the prevalence of appropriate complementary feeding practices and associated factors among mothers having 6 - 23 months of age children in Northern Ethiopia. Methods- A community-based cross-sectional study design was conducted among 428 mothers who had children with 6-23 months of age in Northern Ethiopia. Simple random sampling was used to select the required number of sample. Pretest was done among 22 respondents out of the study area. A face-to-face interview was used to collect data using structured questionnaire. Data were entered with EPI info version 3.5. 1 and cleaning and analysis was done by using SPSS version 16. Frequencies distribution, binary and multiple logistic regressions were done. OR with 95% confidence interval was computed to measure the strength of association. Results – The response rate was 98.6%. In this study only 10.75% (95% CI = 8.07, 13.95) children aged 6-23 months received appropriate complementary feeding. Child’s age (AOR=4.21), education level of mother (AOR=3.84), and postnatal care follow up (AOR=2.80) were found to be independent predictor of timely initiation of complementary feeding. Conclusion and recommendations – one out of ten mothers fed complementary foods appropriately to their children aged 6-23 months which was very low. Mothers who are illiterate and completed only primary school need more attention. All mothers must be encouraged to make postnatal care follow up.
The persistance of drug resistant Escherichia coli strains in the majority faecal flora of calves

Summary Two groups of calves, one of three and the other of two animals, were purchased in markets and reared initially on a commercial veal unit for 1 month and 4 months respectively. They were then moved to the Veterinary School, Langford, and kept for a further 6 and 4 months respectively. The animals were sampled weekly and a continual turnover in the strains forming the majority Escherichia coli faecal flora was demonstrated for all calves. Antibacterial-drug resistance, as measured by an Antibiotic Resistance Index (ARI), increased after arrival on the veal unit and persisted at high levels during the whole of their stay. After moving to Langford the ARI fell. Initially there was a reduction in the average number of resistance determinants per resistant strain and then, after a delay of up to 8 weeks, by an increase in the proportion of isolates that were fully sensitive. The source of the sensitive strains was not ascertained, although their appearance was not associated specifically with either weaning or turning out to pasture.
A Two-Phase Innate Host Response to Alphavirus Infection Identified by mRNP-Tagging In Vivo

A concept fundamental to viral pathogenesis is that infection induces specific changes within the host cell, within specific tissues, or within the entire animal. These changes are reflected in a cascade of altered transcription patterns evident during infection. However, elucidation of this cascade in vivo has been limited by a general inability to distinguish changes occurring in the minority of infected cells from those in surrounding uninfected cells. To circumvent this inherent limitation of traditional gene expression profiling methods, an innovative mRNP-tagging technique was implemented to isolate host mRNA specifically from infected cells in vitro as well as in vivo following Venezuelan equine encephalitis virus (VEE) infection. This technique facilitated a direct characterization of the host defense response specifically within the first cells infected with VEE, while simultaneous total RNA analysis assessed the collective response of both the infected and uninfected cells. The result was a unique, multifaceted profile of the early response to VEE infection in primary dendritic cells, as well as in the draining lymph node, the initially targeted tissue in the mouse model. A dynamic environment of complex interactions was revealed, and suggested a two-step innate response in which activation of a subset of host genes in infected cells subsequently leads to activation of the surrounding uninfected cells. Our findings suggest that the application of viral mRNP-tagging systems, as introduced here, will facilitate a much more detailed understanding of the highly coordinated host response to infectious agents.
A Vertex Operator Approach for Form Factors of Belavin's (Z=nZ)-Symmetric Model and Its Application ?

A vertex operator approach for form factors of Belavin's (Z=nZ)-symmetric model is constructed on the basis of bosonization of vertex operators in the A (1) 1 model and vertex-face transformation. As simple application for n = 2, we obtain expressions for 2m-point form factors related to the z and x operators in the eight-vertex model.
Association Between Lower-Extremity Function and Arterial Compliance in Older Adults

The purpose was to identify the association between lower-extremity function and arterial compliance in older men and women. Participants included 46 healthy men (n = 18) and women (n = 28) 60 years of age or older. Lower-extremity functional performance was assessed by the summary performance score (SPS) that includes tests of 5 timed repeated chair rises, standing balance, and 4-meter walking velocity. Arterial compliance and arterial pressure were analyzed through pulsewave analysis. Small arterial compliance (3.74 ± 2.14; mean ± SD) was related (r = 0.34, P = .028) to SPS (11.09 ± 1.19) after adjusting for body surface area, hyperlipidemia, and hypertension. Systolic blood pressure (138 ± 14) also was related to SPS (r = −0.314, P = .040). These results suggest diminished lower-extremity function is associated with decreased small arterial compliance and elevated arterial pressure in older men and women.
Myocardial blood flow and coronary reserve in chronically anemic fetal lambs.

Chronic fetal anemia produces large compensatory increases in coronary blood flow in the near-term fetal lamb. To determine if increased coronary flow in anemic fetuses is associated with decreased coronary flow reserve or, alternatively, an increase in coronary conductance, we measured maximal coronary artery conductance during adenosine infusion before and during anemia. Isovolemic hemorrhage over 7 days reduced hematocrit from 30.6 ± 2.7 to 15.8 ± 2.4% ( P < 0.02) and the oxygen content from 7.3 ± 1.4 to 2.6 ± 0.4 ml/dl ( P < 0.001). Coronary blood flow increased from control (202 ± 60) to 664 ± 208 ml ⋅ min-1 ⋅ 100 g-1 with adenosine to 726 ± 169 ml ⋅ min-1 ⋅ 100 g-1 during anemia and to 1,162 ± 250 ml ⋅ min-1 ⋅ 100 g-1 (left ventricle) during anemia with adenosine infusion (all P< 0.001). Coronary conductance, determined during maximal vasodilation, was 18.2 ± 7.7 before and 32.8 ± 11.9 ml ⋅ min-1 ⋅ 100 g-1 ⋅ mmHg-1during anemia ( P < 0.001). Coronary reserve, the difference between resting and maximal myocardial blood flow interpolated at 40 mmHg, was unchanged in control and anemic fetuses (368 ± 142 and 372 ± 201 ml/min). Because hematocrit affects viscosity, anemic fetuses were transfused with blood to acutely increase the hematocrit back to control, and conductance was remeasured. Coronary blood flow decreased 57.3 ± 18.9% but was still 42.6 ± 18.9% greater than control. We conclude that in chronically anemic fetal sheep coronary conductance is increased and coronary reserve is maintained, and this is attributed in part to angiogenesis as well as changes in viscosity.
Clinicopathological Features Associated With the Prognosis of Patients With Adrenal Cortical Carcinoma

AbstractAdrenocortical carcinoma (ACC) is a rare tumor with a poor prognosis. Identification of clinicopathological features and molecular prognostic markers is important for the treatment of ACC. The aim of this study was to evaluate the clinical and histopathological features of ACC for prognostic prediction.This retrospective cohort study included 86 patients pathologically confirmed with ACC in a single center. Ki-67 index was evaluated by immunohistochemical staining of paraffin-embedded samples.The median age of the 86 (46 male and 40 female) patients with ACC was 49 years old (range 21–78), and the mean primary tumor size was 12.2 ± 5.2 cm. ACCs were incidentally found in 29 patients (34%). Three patients (3%) had bilateral ACC, and 59 patients (69%) had distant metastasis (37 synchronous and 22 metachronous). Twenty-four patients (28%) had symptoms from hormone excess or mass effects, and 25 patients (29%) had nonspecific symptoms. The 5-year survival rate for ACC was 28%. Sixty patients underwent surgical treatment, including 37 patients with an R0 resection. Tumor size, Ki-67 index, stage, and resection status were independently associated with overall survival by multivariate analysis. In patients with R0 resection, recurrence was significantly associated with larger tumor size and functional tumor.Tumor size, Ki-67 index, stage, and resection status are important prognostic indicators of survival in ACC patients.
Dynamic reorganization of photosynthetic supercomplexes during environmental acclimation of photosynthesis

Plants and algae have acquired the ability to acclimate to ever-changing environments in order to survive. During photosynthesis, light energy is converted by several membrane protein supercomplexes into electrochemical energy, which is eventually used to assimilate CO2. The efficiency of photosynthesis is modulated by many environmental factors such as quality and quantity of light, temperature, drought, and CO2 concentration, among others. Accumulating evidence indicates that photosynthetic supercomplexes undergo supramolecular reorganization within a short time frame during acclimation to an environmental change. This reorganization includes state transitions that balance the excitation of photosystem I and II by shuttling peripheral antenna proteins between the two, thermal energy dissipation that occurs at energy-quenching sites within the light-harvesting antenna generated for negative feedback when excess light is absorbed, and cyclic electron flow that is facilitated between photosystem I and the cytochrome bf complex when cells demand more ATP and/or need to activate energy dissipation. This review will highlight the recent findings regarding these environmental acclimation events in model organisms with particular attention to the unicellular green alga C. reinhardtii and with reference to the vascular plant A. thaliana, which offers a glimpse into the dynamic behavior of photosynthetic machineries in nature.
AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin

Loss of epithelial polarity impacts organ development and function; it is also oncogenic. AMPK, a key sensor of metabolic stress stabilizes cell-cell junctions and maintains epithelial polarity; its activation by Metformin protects the epithelial barrier against stress and suppresses tumorigenesis. How AMPK protects the epithelium remains unknown. Here, we identify GIV/Girdin as a novel effector of AMPK, whose phosphorylation at a single site is both necessary and sufficient for strengthening mammalian epithelial tight junctions and preserving cell polarity and barrier function in the face of energetic stress. Expression of an oncogenic mutant of GIV (cataloged in TCGA) that cannot be phosphorylated by AMPK increased anchorage-independent growth of tumor cells and helped these cells to evade the tumor-suppressive action of Metformin. This work defines a fundamental homeostatic mechanism by which the AMPK-GIV axis reinforces cell junctions against stress-induced collapse and also provides mechanistic insight into the tumor-suppressive action of Metformin. DOI: http://dx.doi. org/10.7554/eLife.20795. 001