Miracle-dz/UniFAR-FTUs huggingface dataset:
Microtubule release from the centrosome in migrating cells

In migrating cells, force production relies essentially on a polarized actomyosin system, whereas the spatial regulation of actomyosin contraction and substrate contact turnover involves a complex cooperation between the microtubule (MT) and the actin filament networks (Goode, B.L., D.G. Drubin, and G. Barnes. 2000. Curr. Opin. Cell Biol., 12:63–71). Targeting and capture of MT plus ends at the cell periphery has been described, but whether or not the minus ends of these MTs are anchored at the centrosome is not known. Here, we show that release of short MTs from the centrosome is frequent in migrating cells and that their transport toward the cell periphery is blocked when dynein activity is impaired. We further show that MT release, but not MT nucleation or polymerization dynamics, is abolished by overexpression of the centrosomal MT-anchoring protein ninein. In addition, a dramatic inhibition of cell migration was observed; but, contrary to cells treated by drugs inhibiting MT dynamics, polarized membrane ruffling activity was not affected in ninein overexpressing cells. We thus propose that the balance between MT minus-end capture and release from the centrosome is critical for efficient cell migration.
Detection of Metadata Tampering Through Discrepancy Between Image Content and Metadata Using Multi-task Deep Learning

Image content or metadata editing software availability and ease of use has resulted in a high demand for automatic image tamper detection algorithms. Most previous work has focused on detection of tampered image content, whereas we develop techniques to detect metadata tampering in outdoor images using sun altitude angle and other meteorological information like temperature, humidity and weather, which can be observed in most outdoor image scenes. To train and evaluate our technique, we create a large dataset of outdoor images labeled with sun altitude angle and other meteorological data (AMOS+M2), which to our knowledge, is the largest publicly available dataset of its kind. Using this dataset, we train separate regression models for sun altitude angle, temperature and humidity and a classification model for weather to detect any discrepancy between image content and its metadata. Finally, a joint multi-task network for these four features shows a relative improvement of 15.5% compared to each of them individually. We include a detailed analysis for using these networks to detect various types of modification to location and time information in image metadata.
uFLIP-OC: Understanding Flash I/O Patterns on Open-Channel Solid-State Drives

Solid-State Drives (SSDs) have gained acceptance by providing the same block device abstraction as magnetic hard drives, at the cost of suboptimal resource utilisation and unpredictable performance. Recently, Open-Channel SSDs have emerged as a means to obtain predictably high performance, based on a clean break from the block device abstraction. Open-channel SSDs embed a minimal flash translation layer (FTL) and expose their internals to the host. The Linux open-channel SSD subsystem, LightNVM, lets kernel modules as well as user-space applications control data placement and I/O scheduling. This way, it is the host that is responsible for SSD management. But what kind of performance model should the host rely on to guide the way it manages data placement and I/O scheduling? For addressing this question we have defined uFLIP-OC, a benchmark designed to identify the I/O patterns that are best suited for a given open-channel SSD. Our experiments on a Dragon-Fire Card (DFC) SSD, equipped with the OX controller, illustrate the performance impact of media characteristics and parallelism. We discuss how uFLIP-OC can be used to guide the design of host-based data systems on open-channel SSDs.
Update on tuberculosis biomarkers: From correlates of risk, to correlates of active disease and of cure from disease

Tuberculosis (TB) remains a devastating disease, yet despite its enormous toll on global health, tools to control TB are insufficient and often outdated. TB Biomarkers (TB‐BM) would constitute extremely useful tools to measure infection status and predict outcome of infection, vaccination or therapy. There are several types of TB‐BM: Correlate of Infection; Correlate of TB Disease; Correlate of Increased Risk of Developing Active TB Disease; Correlate of the Curative Response to Therapy; and Correlate of Protection (CoP). Most TB‐BM currently studied are host‐derived BM, and consist of transcriptomic, proteomic, metabolomic, cellular markers or marker combinations (‘signatures’). In particular, vaccine‐inducible CoP are expected to be transformative in developing new TB vaccines as they will de‐risk vaccine research and development (R&D) as well as human testing at an early stage. In addition, CoP could also help minimizing the need for preclinical studies in experimental animals.
In Vivo Analysis of Cajal Body Movement, Separation, and Joining in Live Human Cells

Cajal bodies (also known as coiled bodies) are subnuclear organelles that contain specific nuclear antigens, including splicing small nuclear ribonucleoproteins (snRNPs) and a subset of nucleolar proteins. Cajal bodies are localized in the nucleoplasm and are often found at the nucleolar periphery. We have constructed a stable HeLa cell line, HeLaGFP-coilin, that expresses the Cajal body marker protein, p80 coilin, fused to the green fluorescent protein (GFP-coilin). The localization pattern and biochemical properties of the GFP-coilin fusion protein are identical to the endogenous p80 coilin. Time-lapse recordings on 63 nuclei of HeLaGFP-coilin cells showed that all Cajal bodies move within the nucleoplasm. Movements included translocations through the nucleoplasm, joining of bodies to form larger structures, and separation of smaller bodies from larger Cajal bodies. Also, we observed Cajal bodies moving to and from nucleoli. The data suggest that there may be at least two classes of Cajal bodies that differ in their size, antigen composition, and dynamic behavior. The smaller size class shows more frequent and faster rates of movement, up to 0.9 μm/min. The GFP-coilin protein is dynamically associated with Cajal bodies as shown by changes in their fluorescence intensity over time. This study reveals an unexpectedly high level of movement and interactions of nuclear bodies in human cells and suggests that these movements may be driven, at least in part, by regulated mechanisms.
Supercritical Fluid–Liquid–Solid (SFLS) Synthesis of Si and Ge Nanowires Seeded by Colloidal Metal Nanocrystals

Semiconductor nanowires, 5 to 20 nm in diameter and micrometers in length, appear to be promising candidates for a variety of new technologies, including computing, memory, and sensor applications. Suitable for these applications, silicon (Si) and germanium (Ge) nanowires ranging from 4 to 30 nm in diameter and micrometers in length can be produced in high temperature supercritical fluids by thermally degrading organosilane or organogermane precursors in the presence of organic‐monolayer‐protected gold nanocrystals. Although gas phase vapor–liquid–solid (VLS) methods can be used to produce a variety of different nanowire materials, high temperature supercritical fluids provide wire size control through nanocrystal size selection prior to synthesis, and high product yields due to the high precursor solubility.
Structural Fillsfor Large wood Objects: Contrasting and Complementary Approaches

AbstractThe most up-to-date publication on the full range of aesthetic compensation materials for wood remains R. Barclay and D.W Grattan's paper in the ICOM Committee for Conservation preprints, “A silicone rubber/microballoon mixture for gap-filling in wooden objects” (1988). Because of the wide range of materials covered in that paper, the issue of structural compensation was not treated in great depth. This article will focus on philosophy, materials, and techniques used today by wood conservators when structural (weight-bearing and shear-resisting) compensation is required. Aesthetic fill material is not necessarily dependent upon specific compatibility with the substrate material, so the range of choice of materials can be quite broad. However, since material and strength compatibilities are critical to a structural fill, those applied to wood objects fall within a fairly small range. Literature on the subject is limited, and practices among wood conservators are relatively uniform: wood fills, ther.
Immunocytochemistry and Fluorescence in Situ Hybridization in HER-2/neu Status in Cell Block Preparations

OBJECTIVE Recent studies have validated the use of cytologic materials to determine HER-2/neu status. Good concordance has been shown between results obtained by immunocytochemistry (ICC), immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) on cytologic and surgical specimens. However, the utility of cytologic cell block material in determining HER-2/neu status has not been reported and is the subject of this study. STUDY DESIGN HER-2/neu status was determined in 25 cases of primary or metastatic breast carcinoma by IHC and FISH. All cases were formalin-fixed, paraffin-embedded (FPPE) cell block preparations. ICC was performed using monoclonal antibodies TAB250 (Zymed) and CB11 (Novacastra Laboratories). FISH analysis was performed using the PathVysion HER-2 probe kit (Vysis, Inc.). Results of ICC and FISH were compared in each case. RESULTS Of 25 cases studied, 17 showed no protein overexpression or amplification. Five cases showed protein overexpression and amplification. The remaining 3 cases showed 2+ staining intensity by ICC in 10, 20, and 50% of carcinoma cells, respectively, and all demonstrated lack of amplification. CONCLUSION Immunocytochemistry performed on FFPE cell block material is a reliable method for determining HER-2/neu status in cytologic specimens. We recommend routine preparation of FFPE cell block material in instances of suspected primary of metastatic breast carcinoma.
Inhibition of the Ras/Raf/extracellular signal-regulated kinase 1/2 signaling pathway by compounds of natural origin for possible treatment of spinal cord injury: An in silico approach

Spinal cord injury (SCI) is a severe disease associated with permanent neurological deficit. Recent studies in the treatment of SCI have demonstrated that the Ras/Raf/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway serves an important role in the disease etiology, and that upregulation of this signaling pathway is associated with the development of SCI. In the present study, inhibition of Ras protein was employed in order to downregulate the Ras/Raf/ERK1/2 signaling pathway using compounds of natural origin from the Interbioscreen natural compound database. To the best of our knowledge, this is the first study using a chemical-computational approach in order to identify novel small molecule inhibitors for Ras. A database of ~50,000 compounds was selected for virtual screening, setting a free energy binding bias of −7 kcal/mol to limit the number of compounds. The subset of compounds generated by virtual screening was further limited by subjecting these to the Lipinski's rule of five parameters. A total of five shortlisted compounds were subjected to molecular docking simulation. The compounds were docked into the GTP binding site of Ras, and the inhibition of this site was examined as a promising strategy for the downregulation of Ras/Raf/ERK1/2 signaling pathway. The compounds bound to the GTP binding site through hydrogen bonds and hydrophobic interactions. The identified lead compound was then subjected to molecular dynamics simulation, and the results revealed that GLY60 in the GTP binding site of Ras protein was the optimal binding site during a 100 nsec run.
Performance evaluation on ad-hoc network of IEEE802.11 with considering multi-rate and per-flow scheduling in relay nodes

This paper evaluates throughput characteristics of a multi-hop network, where a relay node itself has own traffic as well as relays transit traffic. In addition, it also has an individual per-flow scheduling such as weighted round-robin scheme to send transit and own data farther. The best route is determined in terms of various QoS criteria such as total throughput and relay node throughput. Novelty of this paper is that the best route is determined by considering both multi-transmission rate property, performance anomaly as well-known in IEEE802.11 wireless LAN and the scheduling scheme. Evaluation results show interesting characteristics of the network.
Regionalization of Care for Obstetric Hemorrhage and Its Effect on Maternal Mortality

OBJECTIVE: To examine factors that influence the morbidity and mortality of peripartum hysterectomy and analyze the effect of hospital volume on maternal mortality. METHODS: We examined women who underwent peripartum hysterectomy at the time of cesarean delivery in a quality and resource utilization database. Procedure-associated intraoperative, perioperative, and postoperative medical complications, length of stay, intensive care unit use, and maternal mortality were analyzed. Hospitals were stratified into tertiles based on procedure volume and complications and compared using adjusted generalized estimating equations. Results are reported as odds ratios. RESULTS: Maternal mortality among the 2,209 women who underwent peripartum hysterectomy was 1.2%. After adjusting for other clinical and demographic factors, perioperative mortality was 71% (odds ratio 0.29, 95% confidence interval 0.10–0.88) lower in women who underwent operation at high-volume hospitals compared with those treated at low-volume facilities. Hospital volume had no effect on the rates of intraoperative injuries, medical complications, length of stay, or transfusion. In contrast, compared with women treated at low-volume centers, patients who underwent operation at high-volume hospitals had a lower incidence of perioperative surgical complications (odds ratio 0.66, 95% confidence interval 0.47–0.93) and a lower rate of intensive care unit usage (odds ratio 0.53, 95% confidence interval 0.34–0.83). CONCLUSION: Peripartum hysterectomy is associated with substantial morbidity and mortality. Maternal mortality is lower when the procedure is performed in high-volume hospital settings. LEVEL OF EVIDENCE: II
A study of wear on MEMS contact morphologies

The fabrication of many micro electro mechanical systems (MEMS) is mainly based on silicon and its compounds and, for moving structures such as micromotors, tribological behaviour plays a key role in the performance. In this paper the wear of MEMS-compatible materials has been investigated for a range of contact areas and contact forces typical of MEMS. Special test specimens incorporating a range of micromachined micro structures on their top surfaces have been fabricated in order to simulate those conditions. These single crystal silicon (SCS) micro structures were coated with a range of materials used in MEMS; diamond-like carbon (DLC), silicon nitride (Si3N4), silicon dioxide (SiO2), and doped and undoped polysilicon. A specimen-on-disc arrangement (a development of the macroscopic pin-on-disc) was used for the wear experiments and dead weight loading was applied using micro loads specially calibrated for this purpose. The results show that the wear rates of DLC and SCS sliding on DLC decrease with increasing sliding distance whereas Si3N4 and SiO2 showed approximately linear wear behaviour. The effect of contact morphology and contact pressure was investigated for doped polysilicon sliding on DLC and for doped and undoped polysilicon sliding on Si3N4. The results can be attributed to the differing mechanical and chemical properties of the materials leading to wear mechanisms ranging from asperity fracture to asperity deformation.
The impact of the 2005 International Society of Urological Pathology consensus guidelines on Gleason grading – a matched‐pair analysis

To investigate whether the International Society of Urological Pathology (ISUP) 2005 revision of the Gleason grading system has influenced the risk of biochemical recurrence (BCR) after radical prostatectomy (RP), as the new guideline implies that some prostate cancers previously graded as Gleason score 6 (3 + 3) are now considered as 7 (3 + 4).
Modulation Design for Wireless Information and Power Transfer with Nonlinear Energy Harvester Modeling

Far-field wireless power transfer (WPT) and simultaneous wireless information and power transfer (SWIPT) have become increasingly important in radio frequency (RF) and communication communities recently. The problem of modulation design for SWIPT has however been scarcely addressed. In this paper, a modulation scheme based on asymmetric phase-shift keying (PSK) is considered, which improves the SWIPT rate-energy tradeoff region significantly. The nonlinear rectifier model, which accurately models the energy harvester, is adopted for evaluating the output direct current (DC) power at the receiver. The harvested DC power is maximized under an average power constraint at the transmitter and a constraint on the rate of information transmitted via a multi-carrier signal over a flat fading channel. As a consequence of the rectifier nonlinearity, this work highlights that asymmetric PSK modulation provides benefits over conventional symmetric PSK modulation in SWIPT and opens the door to systematic modulation design tailored for SWIPT.
Scalable SQL and NoSQL data stores

In this paper, we examine a number of SQL and socalled "NoSQL" data stores designed to scale simple OLTP-style application loads over many servers. Originally motivated by Web 2.0 applications, these systems are designed to scale to thousands or millions of users doing updates as well as reads, in contrast to traditional DBMSs and data warehouses. We contrast the new systems on their data model, consistency mechanisms, storage mechanisms, durability guarantees, availability, query support, and other dimensions. These systems typically sacrifice some of these dimensions, e.g. database-wide transaction consistency, in order to achieve others, e.g. higher availability and scalability.
Non-invasive whole-body plethysmograph for assessment and prediction of radiation-induced lung injury using simultaneously acquired nitric oxide and lung volume measurements

Radiation-induced lung injury (RILI) is a prevalent side effect in patients who undergo thoracic irradiation as part of their cancer treatment. Preclinical studies play a major role in understanding disease onset under controlled experimental conditions. The aim of this work is to develop a single-chambered optimized, non-invasive, whole-body plethysmograph prototype for unrestrained small animal lung volume measurements for preclinical RILI studies. The system is also designed to simultaneously obtain nitric oxide (NO) measurements of the expired breath. The device prototype was tested using computer simulations, phantom studies and in vivo measurements in experimental animal models of RILI. The system was found to improve resemblance to true breathing signal characteristics as measured by improved skewness (21.83%) and kurtosis (51.94%) in addition to increased overall signal sensitivity (3.61%) of the acquired breath signal, when compared to matching control data. NO concentration data was combined with breath measurements in order to predict early RILI onset. The system was evaluated using serial weekly measurements in hemi-thorax irradiated rats (n = 8) yielding a classification performance of 50.0%, 62.5%, 87.5% using lung volume only, NO only, and combined measurements of both, respectively. Our results indicate that improved performance could be achieved when measurements of lung volume are combined with those of NO. This would provide the overall plethysmography system with the ability to provide useful diagnostic and prognostic information for preclinical and, potentially, clinical thoracic dose escalation studies.
Insole Pedometer With Piezoelectric Energy Harvester and 2 V Organic Circuits

A shoe insole pedometer, which consists of a piezoelectric energy harvester and a 2 V organic pedometer circuit, has been developed as a first step toward the application of flexible large-area energy harvesting. A pseudo-CMOS 14 bit step counter records the number of steps up to 16383 steps using the harvested power. To increase the noise margin of the pseudo-CMOS logic circuits, a negative voltage is generated by an organic charge pump circuit and is applied to the pseudo-CMOS inverters and transmission gates in the flip-flops in the step counter. A pseudo-CMOS Schmitt trigger inverter used to feed clean square pulses to the step counter is presented. This paper describes the details of the insole pedometer and provides measurement results and some discussion.
Increase of 10% in the Rate of Adverse Drug Reactions for Each Drug Administered in Hospitalized Patients

OBJECTIVE: To assess the risk factors, incidence and severity of adverse drug reactions in in-patients. METHODS: This prospective study evaluated 472 patients treated at a teaching hospital in Brazil between 2010 and 2013 by five medical specialties: Internal Medicine, General Surgery, Geriatrics, Neurology, and Clinical Immunology and Allergy. The following variables were assessed: patient age, gender, comorbidities, family history of hypersensitivity, personal and family history of atopy, number of prescribed drugs before and during hospitalization, hospital diagnoses, days of hospitalization. The patients were visited every other day, and medical records were reviewed by the investigators to detect adverse drug reactions. RESULTS: There were a total of 94 adverse drug reactions in 75 patients. Most reactions were predictable and of moderate severity. The incidence of adverse drug reactions was 16.2%, and the incidence varied, according to the medical specialty; it was higher in Internal Medicine (30%). Antibiotics were the most commonly involved medication. Chronic renal failure, longer hospital stay, greater number of diagnoses and greater number of medications upon admission were risk factors. For each medication introduced during hospitalization, there was a 10% increase in the rate of adverse drug reaction. In the present study, the probability of observing an adverse drug reaction was 1 in 104 patients per day. CONCLUSIONS: Adverse drug reactions are frequent and potentially serious and should be better monitored in patients with chronic renal failure or prolonged hospitalization and especially in those on ‘polypharmacy’ regimens. The rational use of medications plays an important role in preventing adverse drug reactions.
A review of earthworm impact on soil function and ecosystem services

Biodiversity is responsible for the provision of many ecosystem services; human well‐being is based on these services, and consequently on biodiversity. In soil, earthworms represent the largest component of the animal biomass and are commonly termed ‘ecosystem engineers’. This review considers the contribution of earthworms to ecosystem services through pedogenesis, development of soil structure, water regulation, nutrient cycling, primary production, climate regulation, pollution remediation and cultural services. Although there has been much research into the role of earthworms in soil ecology, this review demonstrates substantial gaps in our knowledge related in particular to difficulties in identifying the effects of species, land use and climate. The review aims to assist people involved in all aspects of land management, including conservation, agriculture, mining or other industries, to obtain a broad knowledge of earthworms and ecosystem services.