Miracle-dz/UniFAR-FTUs huggingface dataset:
Volta potential phase plate for in-focus phase contrast transmission electron microscopy

Significance Biological electron cryomicroscopy is limited by the radiation sensitivity of the samples and the consequent need to minimize exposure to the beam. This, in turn, results in low-contrast images with a poor signal-to-noise ratio. The current practice to improve phase contrast by defocusing results in contrast transfer functions necessitating image restoration to provide interpretable data. Phase plates enable in-focus phase contrast, but the existing ones, including the thin film Zernike-type phase plate, suffer from severe limitations, such as a short usable life span, fringing artifacts, and problems in using them in automated data acquisition procedures. The Volta phase plate presented here solves those problems and has the potential to become a practical solution for in-focus phase contrast in transmission electron microscopy. We describe a phase plate for transmission electron microscopy taking advantage of a hitherto-unknown phenomenon, namely a beam-induced Volta potential on the surface of a continuous thin film. The Volta potential is negative, indicating that it is not caused by beam-induced electrostatic charging. The film must be heated to ∼200 °C to prevent contamination and enable the Volta potential effect. The phase shift is created “on the fly” by the central diffraction beam eliminating the need for precise phase plate alignment. Images acquired with the Volta phase plate (VPP) show higher contrast and unlike Zernike phase plate images no fringing artifacts. Following installation into the microscope, the VPP has an initial settling time of about a week after which the phase shift behavior becomes stable. The VPP has a long service life and has been used for more than 6 mo without noticeable degradation in performance. The mechanism underlying the VPP is the same as the one responsible for the degradation over time of the performance of thin-film Zernike phase plates, but in the VPP it is used in a constructive way. The exact physics and/or chemistry behind the process causing the Volta potential are not fully understood, but experimental evidence suggests that radiation-induced surface modification combined with a chemical equilibrium between the surface and residual gases in the vacuum play an important role.
Recombination‐deficient mutants of Salmonella typhimurium are avirulent and sensitive to the oxidative burst of macrophages

Mutations in the genes recA and recBC were constructed in the virulent Salmonella typhimurium strain 14028s. Both the recA and recBC mutants were attenuated in mice. The mutants were also sensitive to killing by macrophages in vitro. The recombination mutants were no longer macrophage sensitive in a variant line of J774 macrophage‐like cells that fail to generate superoxide. This suggests that repair of DNA damage by Salmonella is necessary for full virulence in vivo and that the oxidative burst of phagocytes is one source of such DNA damage.
Formulation of Small Size Gold Nanoparticles Stabilized with Novel Polyethylene Glycol ( PEG )-N-Acetyl Cysteine ( NAC ) Conjugate

Background: Gold nano particles demonstrate size-related properties; their photonic and catalytic properties were found to be very attractive for materials applications as well as biomedical/biochemical. Methods to synthesis gold nano-particles were reported in previous studies, however, formation of uniform small gold nano particles and stabilizing these GNPs at protein containing solution is still challenging. Therefore, the main objective of this study is to develop a new simple and reproducible method to synthesize small gold nano particles and to stabilize them at protein containing solutions for possible medical uses such cancer imaging and therapy. Results: We synthesized small gold nano particles with average diameter of ~ 3.5 nm as well we developed and synthesized a PEG–NAC conjugate to stabilize the GNPs at protein containing solutions. Conclusions: Our new method to synthesize GNPs is successful and reproducible, further the new PEG-NAC conjugate that we developed is capable of binding the surface of the gold nano-particles and provides the GNPs enhanced solubility and improved stability particularly at protein containing solutions. Received date: 23/09/2016 Accepted date: 12/10/2016 Published date: 19/10/2016
Conditioned eyeblink learning is formed and stored without cerebellar granule cell transmission

Classical conditioning of the eyeblink reflex is elicited by paired presentation of a conditioned stimulus and an unconditioned stimulus and represents a basic form of cerebellum-dependent motor learning. Purkinje cells and the deep nuclei receive convergent information of conditioned stimulus and unconditioned stimulus through the mossy fiber and climbing fiber projections, respectively. To explore the relative importance of these neural circuits and the underlying mechanism in associative eyeblink learning, we adopted a novel gene-manipulating technique, termed reversible neurotransmission blocking (RNB). In this technology, cerebellar granule cells specifically expressed neurotransmission-blocking tetanus toxin in a doxycycline (DOX)-dependent manner. Extracellular recording of Purkinje cells in awake RNB mice revealed that DOX treatment and withdrawal reversibly turned off and on simple spikes elicited by granule cell inputs, respectively, without interference with complex spikes evoked by climbing fiber inputs. Blockade of granule cell inputs to Purkinje cells abolished eyeblink conditioned responses (CRs) in a DOX-dependent manner. Importantly, when granule cell inputs recovered by removal of DOX, normal CRs were immediately produced in the DOX-treated, CR-negative RNB mice from the beginning of reconditioning. This learning process in RNB mice during DOX treatment was completely abolished by bilateral lesion of the interpositus nucleus before eyeblink conditioning. These results indicate that the convergent information at the interpositus nucleus is critical for acquisition and storage of learning in intimate association with the Purkinje cell circuit for expression of CRs in eyeblink conditioning.
Use of CT to evaluate and compare intranasal features in brachycephalic and normocephalic dogs.

OBJECTIVES To evaluate and compare nasal mucosal contact, septal deviation and caudal aberrant nasal turbinates in brachycephalic and normocephalic dogs using computed tomography. METHODS Dogs without nasal disease and having undergone computed tomography scan of the head (plica alaris to the cribiform plate) were retrospectively selected and divided into brachycephalic and normocephalic groups. Eighteen brachycephalic and 32 normocephalic dogs were included. Anatomic criteria were used to locate predetermined pairs of intranasal structures and nasal mucosal contact was described as present or absent for each site. Septal deviations were identified and measured using angle of septal deviation. Caudal aberrant nasal turbinates were identified and categorised when present. RESULTS Prevalence of nasal mucosal contact was significantly higher in brachycephalic dogs. No significant difference was seen in prevalence or in angle of septal deviation between groups. Prevalence of caudal aberrant nasal turbinates was significantly higher in brachycephalic dogs. CLINICAL SIGNIFICANCE Nasal mucosal contact and caudal aberrant nasal turbinates were significantly more prevalent in brachycephalic dogs than in normocephalic dogs in our study. Computed tomography can be a valuable aid in obtaining data on nasal mucosal contact, caudal aberrant nasal turbinates and septal deviations. Combination of computed tomography with endoscopy and functional airway testing would be useful to further evaluate the correlation between intranasal features and symptoms of brachycephalic airway syndrome.
Cell type-specific and inflammatory-induced expression of haptoglobin gene in lung.

BACKGROUND Haptoglobin (HP) is a hemoglobin-binding protein and a major acute phase reactant. Recently, HP has been shown to possess antioxidant and angiogenic properties. HP is known to be produced mainly in the liver. Expression of HP in specific cells of nonhepatic origin including lung cells has not been studied before. The presence of extracellular plasma proteins in lung epithelial fluid has been assumed to be of blood serum origin. EXPERIMENTAL DESIGN To investigate the expression of the HP gene in lung, the presence of HP mRNA and the production of HP protein in the lung were examined by Northern blot analysis and immunoprecipitation, respectively. Cellular expression of HP during development and inflammation were studied by in situ hybridization with lung tissues derived from different gestational stages from baboons and mice and from mice treated with lipopolysaccharide. RESULTS Northern blot and in situ hybridization analyses established a high level of expression of HP in fetal and adult lung tissues, which were confined to the epithelial lining of the airways in mouse and baboon. After inflammation had been induced in vivo, expression of the HP gene rose fourfold in lung, an increase compatible with that observed in normal mouse liver. However, HP mRNA level was not significantly altered in airway epithelium. Instead, HP expression in alveolar epithelial cells, most likely type 2 cells, was strongly increased. CONCLUSIONS Our data suggest that locally synthesized HP provides a major source of antioxidant and/or antimicrobial activity in the mucus blanket as well as in the alveolar fluid in the lung. The regulation and cell type-specific expression of HP during development and inflammation indicate a protective role for HP in lung and confirm recent reports that HP plays important roles in protecting against infection and in repairing injured tissues.
Robust speaker verification in reverberant conditions using estimated acoustic parameters — A maximum likelihood estimation and training on the fly approach

Speaker recognition has been developed into a relatively mature state over the past few decades through continuous research and development work. Existing methods typically use the robust features extracted from noise and reverberation free speech signals, and therefore can achieve high recognition accuracy only in idealised conditions. Excessive reverberation as often occurs in many real world applications is known to compromise recognition performance. In this paper, a maximum likelihood estimation algorithm is proposed for blind-estimate reverberation time from speech signals submitted for verification. The estimates are used to choose matched acoustic impulse response or transfer function for the including in the retraining or fine tuning of the pattern recognition model on the fly. The training on the fly approach alleviates the detrimental impact of reverberation on authentication accuracy. Experimental results have shown significant improvement in system performance in terms of reduced equal error rate and detection error trade-off. This paper discusses the rationale, details the algorithm. And discusses the potential and limitations of this new method.
Cessation of Menstruation Improves the Correlation of FPG to Hemoglobin A1c in Caucasian Women

BACKGROUND: Anemia is known to cause spurious hemoglobin A1c (HbA1c) results. The effect of menstruation on HbA1c was tested by correlating it to FPG in non-anemic premenopausal and in menopausal women. METHOD: Non-diabetic, non-obese middle-aged Caucasian women were classified as premenopausal or menopausal. Hemogram, FPG, and A1c results were obtained. RESULTS: Hemoglobin concentrations were lower in the premenopausal group. FPG showed a poor correlation to A1c value overall (r = 0.251, p = 0.001) which was improved by multiplying the A1c % by the total hemoglobin concentration to create an absolute A1c value (r = 0.362, p = 0.000). When the data was sorted by menopause status, the correlation of FPG to Absolute A1c improved (r = 0.463, p = 0.000) in the menopausal women, but remained low (r = 0.283, p = 0.005) in the premenopausal women. CONCLUSIONS: Menstruation may be a significant factor affecting the accuracy of A1c concentrations. ABBREVIATIONS: A1c = hemoglobin A1c; BMI = body mass index; CI = confidence interval, FPG = fasting plasma glucose; HbA1c = hemoglobin A1c; MBG = mean blood glucose; MCV: mean corpuscular volume; NGSP = National Glycohemoglobin Standardization Program; RDW = red blood cell distribution width.
Resuscitation of Vibrio vulnificus from the viable but nonculturable state

Stationary-phase-grown cells of the estuarine bacterium Vibrio vulnificus became nonculturable in nutrient-limited artificial seawater microcosms after 27 days at 5 degrees C. When the nonculturable cells were subjected to temperature upshift by being placed at room temperature, the original bacterial numbers were detectable by plate counts after 3 days, with a corresponding increase in the direct viable counts from 3% to over 80% of the total cell count. No increase in the total cell count was observed during resuscitation, indicating that the plate count increases were not due to growth of a few culturable cells. Chloramphenicol and ampicillin totally inhibited resuscitation of the nonculturable cells when added to samples that had been at room temperature for up to 24 h. After 72 h of resuscitation, the inhibitors had an easily detectable but reduced effect on the resuscitated cells, indicating that protein and peptidoglycan synthesis were still ongoing. Major changes in the morphology of the cells were discovered. Nonculturable cells of V. vulnificus were small cocci (approximately 1.0 micron in diameter). Upon resuscitation, the cells became large rods with a size of mid-log-phase cells (3.0 microns in length). Four days after the cells had become fully resuscitated, the cell size had decreased to approximately 1.5 micron in length and 0.7 micron in width. The cells were able to go through at least two cycles of nonculturability and subsequent resuscitation without changes in the total cell count. This is the first report of resuscitation, without the addition of nutrient, of nonculturable cells, and it is suggested that temperature may be the determining factor in the resuscitation from this survival, or adaptation, state of certain species in estuarine environments.
Smart or stupid depends on who is your counterpart: a cobweb model with heterogeneous expectations

Abstract We investigate the dynamics of a cobweb model with heterogeneous expectations, generalizing the famous model of Brock and Hommes (Brock, W. A., and C. H. Hommes. 1997. “A Rational Route to Randomness.” Econometrica 65 (5): 1059–1095) by adding a new predictor – periodical expectation – which predicts that the price will revert to its level two periods previously. We show that under the periodical expectation, when the agents are homogeneous, they will always make wrong predictions, whereas when the agents are heterogeneous, they may be either smart or stupid depending on their counterparts’ types. Moreover, in the cobweb framework, the periodical predictor may be a destabilizer in some cases, but a stabilizer in other cases. We also find that in the cobweb model with rational, naive and periodical expectations, under certain refined conditions, the rational predictor may be endogenously dominated by naive and periodical predictors.
Automated Preemptive Hardware Isolation of High-Risk Computing Applications

In the face of anticipated persistent cyber attacks it may be desirable to preemptively isolate critical computing applications in hardware. We describe an investigation into providing preemptive hardware isolation by automating the transformation of binaries targeted for general-purpose processors (GPPs) into circuitizable finite state machine with datapath (FSMD) descriptions that are impervious to many vulnerabilities associated with GPPs. These generated FSMDs contain no program memory and do not require access to external data memory, so conventional exploits predicated upon memory manipulation are eviscerated. We show how such descriptions can be used to increase the security and resilience of highrisk applications that would otherwise be deployed as software hosted on a GPP, and discuss situations where this may be desirable. We describe a prototype tool that transforms binaries targeted for the Intel 8051 into circuitizable custom FSMDs, and discuss how the prototype transforms common programmatic constructs in ways that often mitigate and sometimes negate the vulnerabilities contained within the original binaries. The Intel 8051 was chosen for this initial investigation because it is often used in modern USB controllers, and is representative of a class of GPPs that are ubiquitous in embedded systems. We show how interrupt-driven binaries are transformed by the prototype, and discuss techniques used to increase the computational density and decrease interrupt servicing latencies of FSMDs derived from interrupt-driven binaries. Our findings indicate that the prototype is capable of automatically generating circuitizable custom machine descriptions that significantly reduce the likelihood of compromise by conventional remote-origin attacks.
Detection of nine microorganisms from the initial carious root lesions using a TaqMan-based real-time PCR.

OBJECTIVE The purpose of this study was to quantify nine selected cariogenic bacteria in plaque from sound root surfaces and initial carious root lesions using TaqMan PCR and to analyse a putative dependence on the kind of initial periodontal treatment. MATERIAL AND METHODS Fifty-four subjects with generalized chronic periodontitis were randomly allocated to one of the following initial periodontal therapies: full-mouth disinfection, full-mouth scaling and root planing or scaling and root planing within 7 days. Plaque samples were taken before and after periodontal treatment and analysed by TaqMan PCR. RESULTS The quantity of the cariogenic bacteria Actinomyces spp. , Streptococcus mutans, Streptococcus sobrinus, Lactobacilllus spp. , Rothia dentocariosa, Parvimonas micra, Propionibacterium acnes and Neisseria mucosa were significantly higher, while the quantity of Veillonella parvula was significantly lower on initial carious lesions than on the sound surfaces both before and after periodontal therapy. No significant differences could be found in any of the tested bacteria except P. micra on initial carious lesions and sound surfaces for both examinations between the groups. CONCLUSION All the nine species analysed were found to be present in initial carious root lesions as well as sound root surfaces but in different quantities, independent of the different periodontal therapies.
Methodological Challenges in Studies Comparing Prehospital Advanced Life Support with Basic Life Support

Abstract Determining the most appropriate level of care for patients in the prehospital setting during medical emergencies is essential. A large body of literature suggests that, compared with Basic Life Support (BLS) care, Advanced Life Support (ALS) care is not associated with increased patient survival or decreased mortality. The purpose of this special report is to synthesize the literature to identify common study design and analytic challenges in research studies that examine the effect of ALS, compared to BLS, on patient outcomes. The challenges discussed in this report include: (1) choice of outcome measure; (2) logistic regression modeling of common outcomes; (3) baseline differences between study groups (confounding); (4) inappropriate statistical adjustment; and (5) inclusion of patients who are no longer at risk for the outcome. These challenges may affect the results of studies, and thus, conclusions of studies regarding the effect of level of prehospital care on patient outcomes should require cautious interpretation. Specific alternatives for avoiding these challenges are presented. LiT, JonesCMC, ShahMN, CushmanJT, JuskoTA. Methodological challenges in studies comparing prehospital Advanced Life Support with Basic Life Support. Prehosp Disaster Med. 2017;32(4):444–450.
Kazakhstan’s evolving regional economic policy: assessing strategies of post-socialist development

ABSTRACT Core foci of economic geographic research are spatial inequality and policies to mitigate it. The variables considered in creating such policy evolve over time and attend to changing political, social, economic, ecological, and geopolitical circumstances and ideals. As a former Soviet republic with considerable hydrocarbon resources and substantial executive power, Kazakhstan has periodically reconsidered its regional economic policies. This study analyzes Kazakhstani government documents to track evolving strategies of development and utilizes econometric analysis to assess their effect on disparity across the state’s regions. Such research should prove useful in comparison with other cases of the post-Soviet realm and developing states more generally.
Reovirus FAST Protein Transmembrane Domains Function in a Modular, Primary Sequence-Independent Manner To Mediate Cell-Cell Membrane Fusion

ABSTRACT The FAST proteins are a unique family of virus-encoded cell-cell membrane fusion proteins. In the absence of a cleavable N-terminal signal peptide, a single-pass transmembrane domain (TMD) functions as a reverse signal-anchor to direct the FAST proteins into the plasma membrane in an Nexo/Ccyt topology. There is little information available on the role of the FAST protein TMD in the cell-cell membrane fusion reaction. We show that in the absence of conservation in the length or primary amino acid sequence, the p14 TMD can be functionally exchanged with the TMDs of the p10 and p15 FAST proteins. This is not the case for chimeric p14 proteins containing the TMDs of two different enveloped viral fusion proteins or a cellular membrane protein; such chimeric proteins were defective for both pore formation and syncytiogenesis. TMD structural features that are conserved within members of the FAST protein family presumably play direct roles in the fusion reaction. Molecular modeling suggests that the funnel-shaped architecture of the FAST protein TMDs may represent such a conserved structural and functional motif. Interestingly, although heterologous TMDs exert diverse influences on the trafficking of the p14 FAST protein, these TMDs are capable of functioning as reverse signal-anchor sequences to direct p14 into lipid rafts in the correct membrane topology. The FAST protein TMDs are therefore not primary determinants of type III protein topology, but they do play a direct, sequence-independent role in the membrane fusion reaction.
Evaluation of high fidelity patient simulator in assessment of performance of anaesthetists.

BACKGROUND There is increasing emphasis on performance-based assessment of clinical competence. The High Fidelity Patient Simulator (HPS) may be useful for assessment of clinical practice in anaesthesia, but needs formal evaluation of validity, reliability, feasibility and effect on learning. We set out to assess the reliability of a global rating scale for scoring simulator performance in crisis management. METHODS Using a global rating scale, three judges independently rated videotapes of anaesthetists in simulated crises in the operating theatre. Five anaesthetists then independently rated subsets of these videotapes. RESULTS There was good agreement between raters for medical management, behavioural attributes and overall performance. Agreement was high for both the initial judges and the five additional raters. CONCLUSIONS Using a global scale to assess simulator performance, we found good inter-rater reliability for scoring performance in a crisis. We estimate that two judges should provide a reliable assessment. High fidelity simulation should be studied further for assessing clinical performance.