Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a Chlamydomonas Insertional Mutant that Disrupts Flagellar Central Pair Microtubule-associated Structures

Two alleles at a new locus, central pair–associated complex 1 (CPC1), were selected in a screen for Chlamydomonas flagellar motility mutations. These mutations disrupt structures associated with central pair microtubules and reduce flagellar beat frequency, but do not prevent changes in flagellar activity associated with either photophobic responses or phototactic accumulation of live cells. Comparison of cpc1 and pf6 axonemes shows that cpc1 affects a row of projections along C1 microtubules distinct from those missing in pf6, and a row of thin fibers that form an arc between the two central pair microtubules. Electron microscopic images of the central pair in axonemes from radial spoke–defective strains reveal previously undescribed central pair structures, including projections extending laterally toward radial spoke heads, and a diagonal link between the C2 microtubule and the cpc1 projection. By SDS-PAGE, cpc1 axonemes show reductions of 350-, 265-, and 79-kD proteins. When extracted from wild-type axonemes, these three proteins cosediment on sucrose gradients with three other central pair proteins (135, 125, and 56 kD) in a 16S complex. Characterization of cpc1 provides new insights into the structure and biochemistry of the central pair apparatus, and into its function as a regulator of dynein-based motility.
Microfocusing source and multilayer-based beam generator for Mo Kα radiation

Two-dimensional multilayer optics have been widely used for enhancing and monochromatizing x-ray beams for various diffraction applications. However, when they are applied to Mo Kα radiation, the performance suffers from the fact that multilayer optics can use only a very small portion of the source. This is because the rocking curve of a multilayer becomes narrower at higher energy. Comparing to the optics for the Cu Kα radiation, the throughput of the optics for Mo Kα depends heavily on how small the source is. Based on the theoretical ray-tracing study, we have designed, fabricated and tested a system combining a microfocusing x-ray source and a side-by-side multilayer optic. Initial test results agree well with the theoretical expectation. The flux gain for a sample smaller than 100 micrometers is about 9 fold compared to a system composing of 2 kW sealed tube and graphite monochromator. The resolution of a diffractometer can also be improved by configuring the optical path. This paper will discuss the system design, detailed comparison between this system and a sealed tube-graphite monochromator based system, and possible applications such as small molecule diffraction system. A theoretical comparison to a rotating anode based system will also be discussed.
An Alternative Model of the Lower Extremity during Locomotion

An alternative to the Iterative Newton-Euler or linked segment model was developed to compute lower extremity joint moments using the mechanics of the double pendulum. The double pendulum model equations were applied to both the swing and stance phases of locomotion. Both the Iterative Newton-Euler and double pendulum models computed virtually identical joint moment data over the entire stride cycle. The double pendulum equations, however, also included terms for other mechanical factors acting on limb segments, namely hip acceleration and segment angular velocities and accelerations Thus, the exact manners in which the lower extremity segments interacted with each other could be quantified throughout the gait cycle. The linear acceleration of the hip and the angular acceleration of the thigh played comparable roles to muscular actions during both swing and stance.
Development of Microbubble Contrast Agents with Biochemical Recognition and Tunable Acoustic Response

Author(s): Nakatsuka, Matthew Allan Masao | Abstract: Microbubbles, consisting of gas-filled cores encapsulated within phospholipid or polymer shells, are the most widely used ultrasound contrast agents in the world. Because of their acoustic impedance mismatch with surrounding tissues and compressible gaseous interiors, they have high echogenicities that allow for efficient backscatter of ultrasound. They can also generate unique harmonic frequencies when insonated near their resonance frequency, depending on physical microbubble properties such as the stiffness and thickness of the encapsulating shell. Microbubbles are used to detect a number of cardiovascular diseases, but current methodologies lack the ability to detect and distinguish small, rapidly growing abnormalities that do not produce visible blockage or slowing of blood flow. This work describes the development, formulation, and validation of microbubbles with various polymer shell architectures designed to modulate their acoustic ability. We demonstrate that the addition of a thick disulfide crosslinked, poly(acrylic acid) encapsulating shell increases a bubble's resistance to cavitation and changes its resonance frequency. Modification of this shell architecture to use hybridized DNA strands to form crosslinks between the polymer chains allows for tuning of the bubble acoustic response. When the DNA crosslinks are in place, shell stiffness is increased so the bubbles do not oscillate and acoustic signal is muted. Subsequently, when these DNA strands are displaced, partial acoustic activity is restored. By using aptamer sequences with a specific affinity towards the biomolecule thrombin as the DNA crosslinking strand, this acoustic "ON/OFF" behavior can be specifically tailored towards the presence of a specific biomarker, and produces a change in acoustic signal at concentrations of thrombin consistent with acute deep venous thrombosis. Incorporation of the emulsifying agent poly(ethylene glycol) into the encapsulating shell improves microbubble yield and circulation half-life substantially, allowing for the in vivo detection of a blood clot in a rabbit model. The results presented here show a unique marriage of highly specific molecular imaging and sonography that could be tailored towards a wide variety of cardiovascular abnormalities
A Matlab toolbox to analyze slip transfer through grain boundaries

Slip transmission across grain boundaries is an essential micromechanical processes during deformation of polycrystalline materials. Slip transmission processes can be characterized based on the geometrical arrangement of active slip systems in adjacent grains and the value of the critical resolved shear stress acting on the incoming and possible outgoing slip systems. We present a Matlab toolbox which enables quantification of grain boundary slip transfer properties and comparison with experiments. Using a graphical user interface, experimental grain boundary data can be directly exported as input files for crystal plasticity finite element simulation of bicrystal experiments.
Role of ambulatory blood pressure monitoring in patients with acromegaly

Background: Hypertension is associated with increased cardiovascular deaths in patients with acromegaly. Objective: To evaluate the accuracy of blood pressure (BP) by 24-h ambulatory blood pressure monitoring (ABPM) and office BP measurements to represent the real BP status in acromegalic patients and its relationship with acromegalic activity and echocardiogram parameters. Patients and methods: Cohort of 37 patients with acromegaly in a tertiary endocrine outpatient service. Results: Twenty-three percent of the patients were considered hypertensive by ABPM versus 32% by office BP measurements (P = 0.006). BP obtained from the ABPM was associated with growth hormone, insulin-like growth factor type 1 levels and echocardiogram parameters of acromegalic myocardiopathy. Nondipper behavior presented a significant association with the hormonal profile. Conclusion: BP levels assessed by ABPM were associated with acromegalic activity and echocardiogram parameters. ABPM can correctly identify BP levels and their repercussion on acromegalic patients.
UV laser cutting of organic nanofibers

Nanofibers made from organic molecules such as para-hexaphenyl allow guiding of electromagnetic waves. Since they possess nanometric widths and heights but macroscopic lengths they represent the smallest possible optical waveguides. Recently, gain enhancement has been observed, pointing to possible applications as nanolasers. Owing to their self assembly growth mode on mica substrates the nanofibers posses well-defined morphology. In order to implement these aggregates into new optical devices or to enhance feedback and thus build up a resonator structure a defined cutting of the end faces is necessary. This article presents results from the first experimental studies in this direction. Irradiation with UV laser pulses of 193 nm at a fluence of 100 mJ/cm2 removes the fibers completely without damaging the substrate. In addition, the fibers can be cut in any orientation relative to their long axes. The quality of the ablation process in terms of readsorbed debris and steepness of cutting is investigated by atomic force and scanning electron as well as fluorescence microscopy.
Surface modification of poly(dimethylsiloxane) (PDMS) microchannels with DNA capture-probes for potential use in microfluidic DNA analysis systems

Poly(dimethylsiloxane) (PDMS) is an elastomeric material used for microfluidic devices and is especially suited to medical and forensic applications. This is due to its relatively low cost, ease of fabrication, excellent optical transmission characteristics and its ability to support electroosmotic flow, required during electrophoretic separations. These aspects combined with its large range of surface modification chemistries, make PDMS an attractive substrate in microfluidic devices for, in particular, DNA separation. Here, we report the successful wet chemical surface modification of PDMS microchannels using a simple three step method to produce an isothiocyanate-terminated surface. Initially, PDMS was oxygen plasma treated to produce a silanol-terminated surface, this was then reacted with 3-aminopropyltriethoxysilane with subsequent reaction of the now amine-terminated surface with p-phenylenediisothiocyanate. Water contact angle measurements both before and after modification showed a reduction in hydrophobicity from 101o for native PDMS to 94o for the isothiocyante-terminated PDMS. The isothiocyanate-terminated surface was then coupled with an amineterminated single-stranded DNA (ssDNA) oligonucleotide capture probe via a thiourea linkage. Confirmation of capture probe attachment was observed using fluorescent microscopy after hybridization of the capture probes with fluorescently labeled complimentary ssDNA oligonucleotides.
Adaptive PVD Steganography Using Horizontal, Vertical, and Diagonal Edges in Six-Pixel Blocks

The traditional pixel value differencing (PVD) steganographical schemes are easily detected by pixel difference histogram (PDH) analysis. This problem could be addressed by adding two tricks: (i) utilizing horizontal, vertical, and diagonal edges and (ii) using adaptive quantization ranges. This paper presents an adaptive PVD technique using 6-pixel blocks. There are two variants. The proposed adaptive PVD for -pixel blocks is known as variant 1, and the proposed adaptive PVD for -pixel blocks is known as variant 2. For every block in variant 1, the four corner pixels are used to hide data bits using the middle column pixels for detecting the horizontal and diagonal edges. Similarly, for every block in variant 2, the four corner pixels are used to hide data bits using the middle row pixels for detecting the vertical and diagonal edges. The quantization ranges are adaptive and are calculated using the correlation of the two middle column/row pixels with the four corner pixels. The technique performs better as compared to the existing adaptive PVD techniques by possessing higher hiding capacity and lesser distortion. Furthermore, it has been proven that the PDH steganalysis and RS steganalysis cannot detect this proposed technique.
Optogenetically enhanced axon regeneration: motor versus sensory neuron‐specific stimulation

Brief neuronal activation in injured peripheral nerves is both necessary and sufficient to enhance motor axon regeneration, and this effect is specific to the activated motoneurons. It is less clear whether sensory neurons respond in a similar manner to neuronal activation following peripheral axotomy. Further, it is unknown to what extent enhancement of axon regeneration with increased neuronal activity relies on a reflexive interaction within the spinal circuitry. We used mouse genetics and optical tools to evaluate the precision and selectivity of system‐specific neuronal activation to enhance axon regeneration in a mixed nerve. We evaluated sensory and motor axon regeneration in two different mouse models expressing the light‐sensitive cation channel, channelrhodopsin (ChR2). We selectively activated either sensory or motor axons using light stimulation combined with transection and repair of the sciatic nerve. Regardless of genotype, the number of ChR2‐positive neurons whose axons had regenerated successfully was greater following system‐specific optical treatment, with no effect on the number of ChR2‐negative neurons (whether motor or sensory neurons). We conclude that acute system‐specific neuronal activation is sufficient to enhance both motor and sensory axon regeneration. This regeneration‐enhancing effect is likely cell autonomous.
Comparison of the Impact of the Ventilation Ducts on Thermal Properties of the Exterior Walls

Implementation of the ventilation ducts is one of the ways how to reduce the moisture in the vertical masonry structures. Functional ventilation ducts provide air inlet and outlet, which absorb diffusing moisture from the rehabilitated walls in these ducts. This causes the reduction of moisture in the structure. The implementation of the ventilation ducts is associated with the worsening of thermal parameters of the rehabilitated walls. This paper compares three variants of structural solutions of ventilation ducts and their impact on thermal parameters of the rehabilitated structure.
Macrolide therapy is associated with reduced mortality in acute respiratory distress syndrome (ARDS) patients.

Background Macrolides have been associated with favorable immunological effects in various inflammatory disease states. We investigated the association between macrolide therapy and mortality in patients with the acute respiratory distress syndrome (ARDS). Methods This was an unplanned secondary analysis of patients with ARDS within a large prospective observational study of critically ill patients in the intensive care units (ICUs) of two university-affiliated hospitals in the Netherlands. The exposure of interest was low-dose macrolide use prescribed for another reason than infection; we excluded patients who received high-dose macrolides for an infection. The primary endpoint was 30-day mortality. The association between macrolide therapy and mortality was determined in the whole cohort, as well as in a propensity score matched cohort; the association was compared between pulmonary versus non-pulmonary ARDS, and between two biological phenotypes based on plasma levels of 20 biomarkers. Results In total, 873 patients with ARDS were analyzed, of whom 158 patients (18%) received macrolide therapy during stay in ICU for a median duration of 3 (interquartile range, 1-4) days. Erythromycin was the most frequent prescribed macrolide (97%). Macrolide therapy was associated with reduced 30-day mortality in the whole cohort [22.8% vs. 31.6%; crude odds ratio (OR), 0.64 (interquartile range, 0.43-0.96), P=0.03]. The association in the propensity score matched cohort remained significant [22.8% vs. 32.9%; OR, 0.62 (interquartile range, 0.39-0.96), P=0.03]. Propensity matched associations with mortality were different in patients with non-pulmonary ARDS vs. pulmonary ARDS and also varied by biological phenotype. Conclusions These data together show that low-dose macrolide therapy prescribed for another reason than infection is associated with decreased mortality in patients with ARDS.
Random Survival Forest in practice: a method for modelling complex metabolomics data in time to event analysis.

BACKGROUND The application of metabolomics in prospective cohort studies is statistically challenging. Given the importance of appropriate statistical methods for selection of disease-associated metabolites in highly correlated complex data, we combined random survival forest (RSF) with an automated backward elimination procedure that addresses such issues. METHODS Our RSF approach was illustrated with data from the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam study, with concentrations of 127 serum metabolites as exposure variables and time to development of type 2 diabetes mellitus (T2D) as outcome variable. Out of this data set, Cox regression with a stepwise selection method was recently published. Replication of methodical comparison (RSF and Cox regression) was conducted in two independent cohorts. Finally, the R-code for implementing the metabolite selection procedure into the RSF-syntax is provided. RESULTS The application of the RSF approach in EPIC-Potsdam resulted in the identification of 16 incident T2D-associated metabolites which slightly improved prediction of T2D when used in addition to traditional T2D risk factors and also when used together with classical biomarkers. The identified metabolites partly agreed with previous findings using Cox regression, though RSF selected a higher number of highly correlated metabolites. CONCLUSIONS The RSF method appeared to be a promising approach for identification of disease-associated variables in complex data with time to event as outcome. The demonstrated RSF approach provides comparable findings as the generally used Cox regression, but also addresses the problem of multicollinearity and is suitable for high-dimensional data.
Error Recovery in the Time-Triggered Paradigm with FTT-CAN

Data networks are naturally prone to interferences that can corrupt messages, leading to performance degradation or even to critical failure of the corresponding distributed system. To improve resilience of critical systems, time-triggered networks are frequently used, based on communication schedules defined at design-time. These networks offer prompt error detection, but slow error recovery that can only be compensated with bandwidth overprovisioning. On the contrary, the Flexible Time-Triggered (FTT) paradigm uses online traffic scheduling, which enables a compromise between error detection and recovery that can achieve timely recovery with a fraction of the needed bandwidth. This article presents a new method to recover transmission errors in a time-triggered Controller Area Network (CAN) network, based on the Flexible Time-Triggered paradigm, namely FTT-CAN. The method is based on using a server (traffic shaper) to regulate the retransmission of corrupted or omitted messages. We show how to design the server to simultaneously: (1) meet a predefined reliability goal, when considering worst case error recovery scenarios bounded probabilistically by a Poisson process that models the fault arrival rate; and, (2) limit the direct and indirect interference in the message set, preserving overall system schedulability. Extensive simulations with multiple scenarios, based on practical and randomly generated systems, show a reduction of two orders of magnitude in the average bandwidth taken by the proposed error recovery mechanism, when compared with traditional approaches available in the literature based on adding extra pre-defined transmission slots.
Prestroke treatment with beta-blockers for hypertension is not associated with severity and poor outcome in patients with ischemic stroke: data from a national stroke registry

Background: Beta-blockers are not recommended as the initial therapy for hypertension. Reports on associations between use of beta-blockers and stroke severity are inconclusive. We assessed associations between prestroke use of beta-blockers and stroke severity, poststroke disability and death in a large group of hypertensive patients hospitalized with acute ischemic stroke. Methods: All 3915 patients with ischemic stroke, treated prestroke for hypertension and registered in the National Acute Stroke ISraeli, were included. Treatment for hypertension was classified by medication type (beta-blockers, diuretics, calcium antagonists and renin–angiotensin system blockers). Odds ratios for stroke severity by the National Institutes of Health Stroke Scale score, disability or death at discharge (modified Rankin Score ≥2) and 1-month mortality were calculated for patients treated vs. nontreated with beta-blockers, adjusted for admission SBP and additional risk factors. Results: Use of beta-blockers was reported for 2043 (52%) participants. Mean (SD) admission SBP was lower in patients treated than nontreated with beta-blockers [156.7 (28.4) vs. 159.9 (27.8) mmHg; P = 0.0005]. Patients on combination therapy including beta-blockers used more antihypertensive medications than patients on combination therapy not including beta-blockers [mean (SD) = 2.63 (0.70) vs. mean (SD) = 2.17 (0.40); P < 0.0001]. Adjusted odds ratios (95% confidence intervals) for outcomes for beta-blocker users compared with nonusers were 1.09 (0.90–1.32) for severe stroke, 0.87 (0.73–1.03) for disability or death at discharge and 0.99 (0.74–1.31) for 1-month mortality. Findings were similar for patients on monotherapy. Conclusion: Prestroke use of beta-blockers in hypertensive patients with acute ischemic stroke was not associated with stroke severity, functional outcome or death.
Zebrafish vasa RNA but Not Its Protein Is a Component of the Germ Plasm and Segregates Asymmetrically before Germline Specification

Work in different organisms revealed that the vasa gene product is essential for germline specification. Here, we describe the asymmetric segregation of zebrafish vasa RNA, which distinguishes germ cell precursors from somatic cells in cleavage stage embryos. At the late blastula (sphere) stage, vasa mRNA segregation changes from asymmetric to symmetric, a process that precedes primordial germ cell proliferation and perinuclear localization of Vasa protein. Analysis of hybrid fish between Danio rerio and Danio feegradei demonstrates that zygotic vasa transcription is initiated shortly after the loss of unequal vasa mRNA segregation. Blocking DNA replication indicates that the change in vasa RNA segregation is dependent on a maternal program. Asymmetric segregation is impaired in embryos mutant for the maternal effect gene nebel. Furthermore, ultrastructural analysis of vasa RNA particles reveals that vasa RNA, but not Vasa protein, localizes to a subcellular structure that resembles nuage, a germ plasm organelle. The structure is initially associated with the actin cortex, and subsequent aggregation is inhibited by actin depolymerization. Later, the structure is found in close proximity of microtubules. We previously showed that its translocation to the distal furrows is microtubule dependent. We propose that vasa RNA but not Vasa protein is a component of the zebrafish germ plasm. Triggered by maternal signals, the pattern of germ plasm segregation changes, which results in the expression of primordial germ cell–specific genes such as vasa and, consequently, in germline fate commitment.