Miracle-dz/UniFAR-FTUs huggingface dataset:
Pitfalls of polymyxin antimicrobial susceptibility testing of Pseudomonas aeruginosa isolated from cystic fibrosis patients.

OBJECTIVES AND METHODS With their potent activity against Gram-negative bacteria, the polymyxins are important alternative antibiotics for cystic fibrosis (CF) patients. A retrospective evaluation of polymyxin activity against 6001 Pseudomonas aeruginosa, 150 Achromobacter xylosoxidans and 506 Stenotrophomonas maltophilia CF isolates was initiated. In addition, we looked at how polymyxin susceptibility testing was affected by the testing method (agar dilution versus microdilution), the agent (polymyxin E versus polymyxin B), incubation time (24 h versus 48 h) and by different interpretative criteria (German DIN, French FSM, British BSAC). RESULTS Polymyxin B exhibited reasonable activity against P. aeruginosa (MIC(90)< or =2 mg/L), whereas it was less active against A. xylosoxidans (MIC(90)< or =16 mg/L) and S. maltophilia (MIC(90)< or =16 mg/L). During 2000-2002, polymyxin B resistance in P. aeruginosa, S. maltophilia and A. xylosoxidans was found to be 6.7%, 17.0% and 29.9% (corresponding to 12.4%, 20.7% and 35.4% of infected patients), respectively. When the agar dilution method was used, polymyxin E exhibited higher MICs than polymyxin B. The microdilution method produced lower polymyxin MICs than the agar dilution method. Therefore, the microdilution MICs after prolonged incubation (48 h) and the agar dilution MICs of polymyxin B correlated best (AUC of 0.93, r(2) of 0.44 and s of 0.83). CONCLUSIONS Polymyxin resistance among common CF pathogens is not rare, thus underlining the necessity of accurate susceptibility testing. When compared with the agar dilution method, it was found that the microdilution method is a valid, rapid and cost effective alternative for the determination of polymyxin activity. The performance of the microdilution method was most reliable after prolonged incubation (48 h) at a susceptibility breakpoint of < or =4 mg/L according to the BSAC guidelines (specificity 91%, sensitivity 89%, 1.5% very major errors).
Comparative analysis of continuous and discrete orthogonal moments for face recognition

In digital image processing, orthogonal moments play an important role in image reconstruction, comparison and enhancement. Orthogonal Moments are derived from the polynomials which are mutually perpendicular and may be discrete or continuous. Most prominent continuous orthogonal moments include Legendre, Zernike and Pseudo-Zernike Moments and primary discrete orthogonal moments are Krawtchouk and Tchebichef Moments. These moments involve minimum information redundancy and therefore can be applied to various fields like face recognition, edge detection, palm print verification and content based retrieval. This paper presents the comparative analysis of these moments in the field of face recognition. Due to robustness to image noise, invariance to rotation, scaling and transformation, these moments give better results than nonorthogonal moments. The paper summarizes the work done by various authors in face recognition field.
Human Cytomegalovirus Protein pUL38 Induces ATF4 Expression, Inhibits Persistent JNK Phosphorylation, and Suppresses Endoplasmic Reticulum Stress-Induced Cell Death

ABSTRACT The endoplasmic reticulum (ER) is a key organelle involved in sensing and responding to stressful conditions, including those resulting from infection of viruses, such as human cytomegalovirus (HCMV). Three signaling pathways collectively termed the unfolded protein response (UPR) are activated to resolve ER stress, but they will also lead to cell death if the stress cannot be alleviated. HCMV is able to modulate the UPR to promote its infection. The specific viral factors involved in such HCMV-mediated modulation, however, were unknown. We previously showed that HCMV protein pUL38 was required to maintain the viability of infected cells, and it blocked cell death induced by thapsigargin. Here, we report that pUL38 is an HCMV-encoded regulator to modulate the UPR. In infection, pUL38 allowed HCMV to upregulate phosphorylation of PKR-like ER kinase (PERK) and the α subunit of eukaryotic initiation factor 2 (eIF-2α), as well as induce robust accumulation of activating transcriptional factor 4 (ATF4), key components of the PERK pathway. pUL38 also allowed the virus to suppress persistent phosphorylation of c-Jun N-terminal kinase (JNK), which was induced by the inositol-requiring enzyme 1 pathway. In isolation, pUL38 overexpression elevated eIF-2α phosphorylation, induced ATF4 accumulation, limited JNK phosphorylation, and suppressed cell death induced by both thapsigargin and tunicamycin, two drugs that induce ER stress by different mechanisms. Importantly, ATF4 overexpression and JNK inhibition significantly reduced cell death in pUL38-deficient virus infection. Thus, pUL38 targets ATF4 expression and JNK activation, and this activity appears to be critical for protecting cells from ER stress induced by HCMV infection.
Adenylyl Cyclase Superactivation Induced by Long-Term Treatment with Opioid Agonist Is Dependent on Receptor Localized within Lipid Rafts and Is Independent of Receptor Internalization

Long-term opioid agonist treatment results in adenylyl cyclase superactivation. A recent “RAVE” theory implicates a direct correlation between the ability of agonist to induce receptor internalization and the magnitude of adenylyl cyclase superactivation. We decided to test such a theory by examining the adenylyl cyclase superactivation after long-term activation of μ-opioid receptor (MOR) in an EcR293 cell model. We examined the magnitudes of adenylyl cyclase superactivation in the presence of naloxone after long-term treatment with morphine, etorphine, and methadone, three agonists reported to have differential activities in promoting MOR internalization. It can be shown that the magnitudes of adenylyl cyclase superactivation after treating with these three agonists, although different, were dependent on MOR density. Blunting MOR internalization with the dominant-negative mutant of dynamin, K44E, did not alter the magnitude of either morphine- or etorphine-induced adenylyl cyclase superactivation. In the presence of diprenorphine, the magnitude of adenylyl cyclase superactivation after etorphine treatment was identical to that observed with morphine. It could be demonstrated further that adenylyl cyclase superactivation is dependent on the cell surface-located MOR. Sucrose gradient fractionation demonstrated the colocalization of MOR and adenylyl cyclase V/VI with caveolin-1, a marker for lipid rafts. After long-term agonist treatment, the majority of MOR remained at the lipid rafts. Methyl-β-cyclodextrin (MβCD) completely blunted the adenylyl cyclase superactivation and agonist-induced receptor internalization. These MβCD actions were reversed by incubating the cells with cholesterol. Thus, the adenylyl cyclase superactivation is not dependent on agonist-induced receptor internalization. Rather, the location of MOR at lipid rafts is an absolute requirement for the observed adenylyl cyclase superactivation.
Equivalent Representation of Real and Illusory Contours in Macaque V4

The cortical processing of illusory contours provides a unique window for exploring the brain mechanisms underlying visual perception. Previous electrophysiological single-cell recordings demonstrate that a subgroup of cells in macaque V1 and V2 signal the presence of illusory contours, whereas recent human brain imaging studies reveal higher-order visual cortices playing a central role in illusory figure processing. It seems that the processing of illusory contours/figures may engage multiple cortical interactions between hierarchically organized processing stages in the ventral visual pathway of primates. However, it is not yet known in which brain areas illusory contours are represented in the same manner as real contours at both the population and single-cell levels. Here, by combining intrinsic optical imaging in anesthetized rhesus macaques with single-cell recordings in awake ones, we found a complete overlap of orientation domains in visual cortical area V4 for processing real and illusory contours. In contrast, the orientation domains mapped in early visual areas V1 and V2 mainly encoded the local physical stimulus features inducing the subjective perception of global illusory contours. Our results indicate that real and illusory contours are encoded equivalently by the same functional domains in V4, suggesting that V4 is a key cortical locus for integration of local features into global contours.
A Novel Framework to Identify Non-Contiguous Clones

Software refactoring is the process of changing the code without changing its behavior and is done to reduce the maintenance effort of the system. Maintenance is a difficult activity which involves adapting the new environment and the difficulty level is increased due to the poor structure of the program. In this paper a new framework is proposed in which the task of removing the clones is done by the developer irrespective of the language in which the project is being made. It also identifies the unique clones which should be removed without changing the behavior of the program thereby the effort at the maintenance side is reduced to a very large extent. This framework has been developed keeping non-contiguous clones in consideration since these types of clones are difficult to extract specially in cases where the flow of program switches from one module to another module.
Drug Target Mining and Analysis of the Chinese Tree Shrew for Pharmacological Testing

The discovery of new drugs requires the development of improved animal models for drug testing. The Chinese tree shrew is considered to be a realistic candidate model. To assess the potential of the Chinese tree shrew for pharmacological testing, we performed drug target prediction and analysis on genomic and transcriptomic scales. Using our pipeline, 3,482 proteins were predicted to be drug targets. Of these predicted targets, 446 and 1,049 proteins with the highest rank and total scores, respectively, included homologs of targets for cancer chemotherapy, depression, age-related decline and cardiovascular disease. Based on comparative analyses, more than half of drug target proteins identified from the tree shrew genome were shown to be higher similarity to human targets than in the mouse. Target validation also demonstrated that the constitutive expression of the proteinase-activated receptors of tree shrew platelets is similar to that of human platelets but differs from that of mouse platelets. We developed an effective pipeline and search strategy for drug target prediction and the evaluation of model-based target identification for drug testing. This work provides useful information for future studies of the Chinese tree shrew as a source of novel targets for drug discovery research.
Revolving speed control of ultrasonic motor based on feedback of piezoelectric sensor

At present, the feedback control of Ultrasonic Motor (USM) is mainly based on the direct feedback of USM's revolving speed. With this method, the photoelectric encoding is essential. When we need to control the USM at low speed, the demand of the precision of the photo-electricity encoding is high, resulting in significant increase the cost of the control system. Hence this paper proposes the feedback based on the piezoelectric sensor to control the USM.
Formation control of autonomous robots following desired formation during tracking a moving target

In this paper, we propose a novel method for control the formation of the autonomous robots following to the desired formations during tracking a moving target under the influence of the dynamic environment. The V-shape formation is used to track a moving target when the distance from this formation to the target is longer than the target approaching radius. Furthermore, when the leader moves in the target approaching range, the circling shape formation is used to encircle the target. The motion of the robots to the optimal positions in the desired formations are controlled by the artificial force fields, which consist of local and global potential fields around the virtual nodes in the desired formations. Using the global attractive force field around the target, the formation of robots is always driven towards the target position. Moreover, using the repulsive/rotational vector fields in the obstacle avoiding controller, robots can easily escape the obstacle without collisions. The success of the proposed method is verified in simulations.
Nanofabrication of high aspect ratio structures using an evaporated resist containing metal

Organic electron beam resists are typically not resistant to the plasma etching employed to transfer the pattern into the underlying layer. Here, the authors present the incorporation of a metal hard mask material into negative resist polystyrene by co-evaporation of the polystyrene and the metal onto a substrate. With a volume ratio of 1:15 between Cr and polystyrene, this nanocomposite resist showed an etching selectivity to silicon one order higher than pure polystyrene resist. Silicon structures of 100 nm width and 3.5 μm height (aspect ratio 1:35) were obtained using a non-switching deep silicon etching recipe with SF6 and C4F8 gas. Moreover, unlike the common spin coating method, evaporated nanocomposite resist can be coated onto irregular and non-flat surfaces such as optical fibers and AFM cantilevers. As a proof of concept, we fabricated high aspect ratio structures on top of an AFM cantilever. Nanofabrication on non-flat surfaces may find applications in the fields of (AFM) tip enhanced Raman spectroscopy for chemical analysis and lab-on-fiber technology.
Analysis of some Krylov subspace approximations to the matrix exponential operator

In this note a theoretical analysis of some Krylov subspace approximations to the matrix exponential operation $\exp (A)v$ is presented, and a priori and a posteriors error estimates are established. Several such approximations are considered. The main idea of these techniquesis to approximately project the exponential operator onto a small Krylov subspace and to carry out the resulting small exponential matrix computation accurately. This general approach, which has been used with success in several applications, provides a systematic way of defining high-order explicit-type schemes for solving systems of ordinary differential equations or time-dependent partial differential equations.
Does specific psychopathology predict development of psychosis in ultra high-risk (UHR) patients?

Objectives: Studies have attempted to identify additional risk factors within the group identified as ‘ultra high risk’ (UHR) for developing psychotic disorders in order to characterise those at highest risk. However, these studies have often neglected clinical symptom types as additional risk factors. We aimed to investigate the relationship between baseline clinical psychotic or psychotic-like symptoms and the subsequent transition to a psychotic disorder in a UHR sample. Method: A retrospective ‘case–control’ methodology was used. We identified all individuals from a UHR clinic who had subsequently developed a psychotic disorder (cases) and compared these to a random sample of individuals from the clinic who did not become psychotic within the sampling time frame (controls). The sample consisted of 120 patients (60 cases, 60 controls). An audit tool was used to identify clinical symptoms reported at entry to the clinic (baseline) using the clinical file. Diagnosis at transition was assessed using the Operational Criteria for Psychotic Illness (OPCRIT) computer program. The relationship between transition to a psychotic disorder and baseline symptoms was explored using survival analysis. Results: Presence of thought disorder, any delusions and elevated mood significantly predicted transition to a psychotic disorder. When other symptoms were adjusted for, only the presence of elevated mood significantly predicted subsequent transition (hazard ratio 2.69, p = 0.002). Thought disorder was a predictor of transition to a schizophrenia-like psychotic disorder (hazard ratio 3.69, p = 0.008). Conclusions: Few individual clinical symptoms appear to be predictive of transition to a psychotic disorder in the UHR group. Clinicians should be cautious about the use of clinical profile alone in such individuals when determining who is at highest risk.
Factors influencing driving 10 years after brain injury

Objective: To study long-term consequences of brain injury on health status, driving characteristics and car accidents. To study whether driving 10 years after brain injury was retrospectively related to cognitive functioning and on-road driving performance 10 years before. Research design: A semi-structured telephone interview with 38 patients with sequelae of brain injury and 49 healthy controls was used. Results: Hypertension, heart disease and vascular disorder were the most frequently reported diseases. The patients reported fatigue, irritability, memory and initiative problems. Concentration and vision problems influenced their driving. Patients had more car accidents reported to an insurance company during the observation period than control subjects. Present driving was retrospectively significantly related to neuropsychological test results but not to on-road test outcome 10 years before. Car accidents were not related to neuropsychological test results or to on-road test outcome 10 years back. Half of the dropouts were stroke patients and they performed significantly worse on the neuropsychological tests but not on the on-road test 10 years before. Conclusion: Neuropsychological tests focusing on information processing speed and attention is a useful screening tool for predicting driving competence. Stroke patients are vulnerable if they continue to drive and need to be evaluated for their driving capacity to drive.
Performance differences in the fingers, wrist, and forearm in computer input control

Recent work in computer input control has sought to maximize the use of the fingers in the operation of computer pointing devices. The main rationale is the hypothesis that the muscle groups conmolling the fingers have a higher bandwidth than those controlling other segments of the human upper limb. Evidence which supports this, however, is inconclusive. We conducted an experiment to determine the relative bandwidths of the fingers, wrist, and forearm and found that the fingers do not necessarily outperform the other limb segments. Our results indicate that the bandwidth of the unsupported index finger is approximately 3.0 bits/s while the wrist and forearm have bandwidths of about 4.1 bits/s. We also show that the thumb and index finger working together in a pinch grip have an information processing rate of about 4.5 bits/s. Other factors which influence the relative performance of the different limbs in manipulation tasks are considered.
Performance-aware reliability assessment of heterogeneous chips

Technology evolution has raised serious reliability considerations, as transistor dimensions shrink and modern microprocessors become denser and more vulnerable to faults. Reliability studies have proposed a plethora of methodologies for assessing system vulnerability which, however, highly rely on traditional reliability metrics that solely express failure rate over time. Although Failures In Time (FIT) is a very strong and representative reliability metric, it may fail to offer an objective comparison of highly diverse systems, such as CPUs against GPUs or other accelerators that are often employed to execute the same algorithms implemented for these platforms.
The rule-based method for the non-intrusive electrical appliances identification

The paper presents the application of the rules-based method to the non-intrusive identification of electrical energy appliances in the household. This up-to-date problem consists in three stages: detection of turning the device on or off, calculating its features based on the measured current and identifying the specific device. All stages were described in detail, including the description of the newly proposed rules induction algorithm. The tests conducted on the laboratory data show the advantages and disadvantages of the approach with the suggested modifications in the future.
ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis

The degradation of small RNAs in plants and animals is associated with small RNA 3′ truncation and 3′ uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we show that SMALL RNA DEGRADING NUCLEASES (SDNs) initiate miRNA degradation by acting on AGO1-bound miRNAs to cause their 3′ truncation, and the truncated species are uridylated and degraded. We report that AGO10 reduces miR165/6 accumulation by enhancing its degradation by SDN1 and SDN2 in vivo. In vitro, AGO10-bound miR165/6 is more susceptible to SDN1-mediated 3′ truncation than AGO1-bound miR165/6. Thus, AGO10 promotes the degradation of miR165/6, which is contrary to the stabilizing effect of AGO1. Our work identifies a class of exonucleases responsible for miRNA 3′ truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, suggests that spatially regulated miRNA degradation underlies stem cell maintenance in plants.
Design and verification of an integrated current mode switching regulator

In this paper, a design of current-mode control switching regulator was presented with loop gain analysis. The analysis was verified by the chip implementation and measurement. A current mirror based current sensor was used to sensing the inductor current information. This chip has been fabricated with a TSMC 2P4M 0. 35μm polyside CMOS process. The measurement result verify the buck converter with on-chip current sensing can operate with load current from 200mA-500mA in a supply voltage from 2.7–4.2V and the output voltage of 1.8V with no sub-harmonic condition occur. By the loop gain measurement, the correctness of the loop gain analysis is verified. The stability of proposed buck converter was guaranteed by the loop gain measurement, too.
On effective data clustering in bitemporal databases

Temporal databases provide built-in supports for efficient recording and querying of time-evolving data. In this paper, data clustering issues in temporal database environment are addressed. Data clustering is one of the most effective techniques that can improve performance of a database system. However, data clustering methods for conventional databases do not perform well in temporal databases because there exist crucial differences between their query patterns. We propose a data clustering measure, called Temporal Affinity, that can be used for the clustering of temporal data. The temporal affinity, which is based on the analysis of query patterns in temporal databases, reflects the closeness of temporal data objects in viewpoints of temporal query processing. We perform experiments to evaluate the proposed measure. The experimental results show that a data clustering method with the temporal affinity works better than other methods.