Miracle-dz/UniFAR-FTUs huggingface dataset:
Data preprocessing methods for robust Fourier ptychographic microscopy

Abstract. Fourier ptychographic microscopy (FPM) is a recently developed computational imaging technique that achieves gigapixel images with both high resolution and large field-of-view. In the current FPM experimental setup, the dark-field images with high-angle illuminations are easily overwhelmed by stray lights and background noises due to the low signal-to-noise ratio, thus significantly degrading the achievable resolution of the FPM approach. We provide an overall and systematic data preprocessing scheme to enhance the FPM’s performance, which involves sampling analysis, underexposed/overexposed treatments, background noises suppression, and stray lights elimination. It is demonstrated experimentally with both US Air Force (USAF) 1951 resolution target and biological samples that the benefit of the noise removal by these methods far outweighs the defect of the accompanying signal loss, as part of the lost signals can be compensated by the improved consistencies among the captured raw images. In addition, the reported nonparametric scheme could be further cooperated with the existing state-of-the-art algorithms with a great flexibility, facilitating a stronger noise-robust capability of the FPM approach in various applications.
Left‐ventricular outflow tract ventricular‐tachycardia event following corevalve transcatheter aortic‐valve implantation

We describe a patient with severe aortic stenosis who underwent CoreValve (Medtronic) implantation and presented several days later with a tachyarrhythmic episode. The electrocardiographic features of the arrhythmia were compatible with left‐ventricular outflow tract ventricular‐tachycardia. The life‐threatening event was not associated with ischemia or an electrolyte disorder and was not drug‐induced. A probable cause was the irritation of the myocardium by the prosthetic valve. Clinicians should be aware that the presence of anatomical parameters that increases the risk for myocardial injury and the need for pacemaker implantation might indicate an increased risk of a tachyarrhythmic episode. © 2011 Wiley Periodicals, Inc.
Association of Overtime Urine Volume and Ultrafiltration Changes with Patient Survival in Continuous Ambulatory Peritoneal Dialysis Patients

Background: Associations between patient survival and baseline urine volume (UV), ultrafiltration (UF) volume, and combined UV and UF were evaluated in Iranian continuous ambulatory peritoneal dialysis (CAPD) patients. Methods: From 1995 to 2006, data on 1472 CAPD patients from 26 centers were collected. Demographic, clinical, and laboratory characteristics were analyzed using STATA software. Baseline UV was considered as an indicator of residual renal function and patients with an annual decrease of more than 250 cc/day were placed in decreasing UV group. The role of a new variable, net positive fluid removal, which defines as the combination of baseline UV and UF, was also evaluated. Results: Patients with higher baseline UV were significantly more married and educated and candidate for CAPD based on positive selection criteria. In dichotomous categorization, mean of serum creatinine was lower and albumin was higher in patients with UV ≥ 1000 cc/day compared with UV < 250 cc/day. A significant correlation was found between baseline UV <250 cc/day and ≥1000 cc/day and patient survival. Patients with stable UV had better survival compared with patients with decreasing UV (p = 0.04). There was no correlation between UF and patient survival. Remarkable association with patient and technique survival and net positive fluid removal ≥2000 cc/day and <500 cc/day was observed. Multiple Cox regression analysis revealed significant correlation between net positive fluid removal ≥2000 cc/day and higher patient survival [p = 0.01, hazard ratio (HR) = 13.2], higher first albumin (albumin ≥ 3.5 mg/dL, p = 0.01, HR = 0.02), and lower negative selection (p = 0.0001, HR = 11.8). Conclusion: Loss of UV over time and lower net positive fluid removal increase mortality of PD patients.
Separation of Mixed Audio Sources By Independent Subspace Analysis

We propose the method of independent subspace analysis (ISA) for separating individual audio sources from a single-channel mixture. ISA is based on independent component analysis (ICA) but relaxes the constraint that requires at least as many mixture observation signals as sources. A second extension to ICA is the use of dynamic components to represent non-stationary signals. Sources are tracked by similarity of dynamic components over small time steps. We propose a method for grouping components by partitioning a matrix of independent component cross-entropies that we call an ixegram. The ixegram measures the mutual similarities of components in an audio segment and clustering the ixegram yields the source subspaces and time trajectories. To demonstrate the techniques we give examples of ISA applied to separation of musical and speech sources from single-channel mixtures
Subaperture Approach Based on Azimuth-Dependent Range Cell Migration Correction and Azimuth Focusing Parameter Equalization for Maneuvering High-Squint-Mode SAR

The challenge in the imaging of high-squint-mode synthetic aperture radar (SAR) mounted on maneuvering platforms is the azimuth dependence of both the range migration and the azimuth focusing parameters (the azimuth frequency-modulation rate and higher order coefficients), which are caused by range walk correction and acceleration. In order to accommodate the dependence, a modified subaperture imaging algorithm is proposed. Based on the fact that the azimuth times corresponding to the same Doppler frequency are different for targets in the same range gate, after making blocks in the azimuth frequency domain, the azimuth-dependent range cell migration correction is performed in the azimuth time domain for each block. Considering that the regions of support in the azimuth frequency domain are different for targets in the same range gate, the equalization of the azimuth focusing parameters is achieved by a new azimuth nonlinear chirp scaling method in the azimuth frequency domain. In order to verify the effectiveness of the proposed algorithm, the simulation of a point target array is presented. Furthermore, the real SAR data with a squint angle of 70° are processed, and high-quality images with a resolution of 1 m are provided.
Subjective response to alcohol and ADH polymorphisms in a select sample of young adult male East Indians and Africans in Trinidad and Tobago.

OBJECTIVE Level of response to alcohol has been associated with risk of alcohol dependence in a number of ethnic groups. In the present study, subjective and objective responses to alcohol were evaluated in Indo-Trinidadians (Indo-T) and Afro-Trinidadians (Afro-T). Associations of alcohol dehydrogenase polymorphisms with response to alcohol, using the Subjective High Assessment Scale (SHAS), and breath alcohol concentrations (BrAC) were tested. METHOD Regular male drinkers without alcohol dependence (n = 112) ages 18-25 years participated in alcohol challenge sessions consisting of placebo and two doses of alcohol (target BrAC: 0 g/dl for placebo, .04 g/dl low dose, and .08 g/dl high dose) and genotyped for variants in ADH1B*3 and ADH1C*2. RESULTS Indo-T had significantly higher BrAC, pulse rates, and cortisol levels when compared with Afro-T but did not have significantly higher SHAS values. Higher responses on the SHAS items muddle/confused and nauseated were significantly associated with the presence of at least one ADH1B*3 allele following the high dose of alcohol in Afro-T. Indo-T with at least one ADH1C*2 allele displayed significantly different Drug × Time interactions for the SHAS item effects of alcohol at the low dose and for the SHAS items clumsy, muddle/confused, effects of alcohol, floating, drunk, and total at the high dose from Indo-T with two ADH1C*1 alleles. CONCLUSIONS This is the first study that has investigated individual sensitivity to alcohol in a Caribbean population and in people of East Indian descent. Indo-T with at least one ADH1C*2 allele may be at higher risk for heavy drinking by feeling less of the effects of alcohol, including nausea. In Afro-T, having at least one ADH1B*3 allele appears to exert a protective effect by enhancing the unpleasant effects of alcohol, such as nausea and confusion.
Named Content Searching in Opportunistic Mobile Networks

In this letter, we study the adaptation of named data networking-based named content searching in opportunistic mobile networks (OMNs). Given the inherent uncertainty in OMNs, our goal is to replicate the content requests to a suitable set of nodes that can help improve users' experience in terms of requests satisfaction and latency. To this end, we propose a scheme, content searching as regret minimization (CHARM), based on the technique of random regret minimization. In CHARM, content interest replication and non-replication choices are expressed in terms of several measurable attributes. Regrets associated with the two choices indicate whether or not an interest should be replicated. Moreover, to reduce overhead, CHARM uses dynamic time-to-live adaptation, where the lifetime of a message is proactively scaled down. The results of performance evaluation based on real-life traces and synthetic mobility model indicate that CHARM can improve the number of interests satisfied and latency, respectively, by up to 1.6 and 1.4 times when compared with a contemporary scheme.
Role of a Bacterial Organic Hydroperoxide Detoxification System in Preventing Catalase Inactivation*

In the gastric pathogen Helicobacter pylori, catalase (KatA) and alkyl hydroperoxide reductase (AhpC) are two highly abundant enzymes that are crucial for oxidative stress resistance and survival of the bacterium in the host. Here we report a connection unidentified previously between the two stress resistance enzymes. We observed that the catalase in ahpC mutant cells in comparison with the parent strain is inactivated partially (approximately 50%). The decrease of catalase activity is well correlated with the perturbation of the heme environment in catalase, as detected by electron paramagnetic resonance spectroscopy. To understand the reason for this catalase inactivation, we examined the inhibitory effects of hydroperoxides on H. pylori catalase (either present in cell extracts or added to the purified enzyme) by monitoring the enzyme activity and the EPR signal of catalase. H. pylori catalase is highly resistant to its own substrate, without the loss of enzyme activity by treatment with a molar ratio of 1:3000 H2 O2. However, it inactivated is by lower concentrations of organic hydroperoxides (the substrate of AhpC). Treatment with a molar ratio of 1:400 t-butyl hydroperoxide resulted in an inactivation of catalase by approximately 50%. UV-visible absorption spectra indicated that the catalase inactivation by organic hydroperoxides is caused by the formation of a catalytically incompetent compound II species. To further support the idea that organic hydroperoxides, which accumulate in the ahpC mutant cells, are responsible for the inactivation of catalase, we compared the level of lipid peroxidation found in ahpC mutant cells with that found in wild type cells. The results showed that the total amount of extractable lipid hydroperoxides in the ahpC mutant cells is approximately three times that in the wild type cells. Our findings reveal a novel role of the organic hydroperoxide detoxification system in preventing catalase inactivation.
The ComFor: an instrument for the indication of augmentative communication in people with autism and intellectual disability.

BACKGROUND The ComFor (Forerunners in Communication) is an instrument to explore underlying competence for augmentative communication. More specifically, it measures perception and sense-making of non-transient forms of communication at the levels of presentation and representation. The target group consists primarily of individuals with autism and intellectual disability (ID) without or with only limited verbal communication. The ComFor is suitable for children and adults with a developmental level between 12 and 60 months. This paper describes the theoretical framework and structure of the ComFor, the results of a study on its psychometric properties and its clinical uses. METHOD The ComFor was tested on a sample of 623 children and adults from the Netherlands and Flanders: a group with autism and ID (n = 310); a group with ID without autism (n = 174); and a control group of typically developing children (n = 139). RESULTS The data generally support the reliability and validity of the ComFor. Internal consistency, inter-rater and test-retest reliability were found to be good. Construct validity (internal structure, convergent and divergent patterns) was established in different ways. The criterion-related validity has yet to be established, as predictive data are not available at the moment. CONCLUSION Taken together, the results indicate that the ComFor is a promising instrument to explore underlying competence for augmentative communication. Areas for future research are outlined and the clinical relevance is discussed.
Concerted interaction between origin recognition complex (ORC), nucleosomes and replication origin DNA ensures stable ORC–origin binding

Chromosomal replication origins, where DNA replication is initiated, are determined in eukaryotic cells by specific binding of a six‐subunit origin recognition complex (ORC). Many biochemical analyses have showed the detailed properties of the ORC–DNA interaction. However, because of the lack of in vitro analysis, the molecular architecture of the ORC–chromatin interaction is unclear. Recently, mainly from in vivo analyses, a role of chromatin in the ORC–origin interaction has been reported, including the existence of a specific pattern of nucleosome positioning around origins and of a specific interaction between chromatin—or core histones—and Orc1, a subunit of ORC. Therefore, to understand how ORC establishes its interaction with origin in vivo, it is essential to know the molecular mechanisms of the ORC–chromatin interaction. Here, we show that ORC purified from yeast binds more stably to origin‐containing reconstituted chromatin than to naked DNA and forms a nucleosome‐free region at origins. Molecular imaging using atomic force microscopy (AFM) shows that ORC associates with the adjacent nucleosomes and forms a larger complex. Moreover, stable binding of ORC to chromatin requires linker DNA. Thus, ORC establishes its interaction with origin by binding to both nucleosome‐free origin DNA and neighboring nucleosomes.
Can We Use Historical Mean Returns?

Recently tests of the CAPM are on the alternative proxies for the expected return as researchers believe that average realized return is an extremely poor proxy for the expected return. Like other researchers, we also believe on the failure of average realized return as an estimate for expected return. Unlike others, we believe that the inability of average realized return to explain risk-return relationship has led to this controversy. Besides, the differences in the information sets hinder realized return to be the ex-post realization of the ex-ante expectations. We argue that considering realized return as a sample of returns is misleading as we explain the differences between ex-post value and the realized return. If pricing is rational, we can show the validity of CAPM even when empirical tests deny CAPM.
Reconstitution and Anchoring of Cytoskeleton inside Giant Unilamellar Vesicles

Among the requirements for all life forms is the ability to self‐replicate. In eukaryotic cellular systems, this division is achieved through cytokinesis, and is facilitated by the (re)arrangement and interaction of cytoskeletal proteins with lipids and other proteins localized to the plasma membrane. A fascinating challenge of modern synthetic biology is the bottom‐up reconstitution of such processes for the generation of an artificial cell. One crucial step towards this goal is the functional reconstitution of the protein‐anchoring machinery to facilitate cytokinesis into lipid vesicles. True to the ideal of a minimal cell‐like system, we here describe the formation of an actin‐based cytoskeleton within giant unilamellar vesicles (GUVs) made from porcine brain lipid extracts. We demonstrate that the actin filaments are localised and anchored to the interior walls of the GUVs through the spectrin/ankyrin proteins, and produce tightly packed actin bundles. These studies allow for the examination of cytoskeletal rearrangements within a cell‐like model membrane system and represent important first steps in reconstituting the minimal machinery required for the division of an artificial cell. In addition, the study of such minimal systems can shed light on protein functions that are commonly unobservable or hidden within the overwhelming complexity of cells.
Enhanced Heat Transfer and Thermal Dose Using Magnetic Nanoparticles During HIFU Thermal Ablation—An In-Vitro Study

Avoiding collateral damage to healthy tissues during the high intensity focused ultrasound (HIFU) ablation of malignant tumors is one of the major challenges for effective thermal therapy. Such collateral damage can originate out of the need for using higher acoustic powers to treat deep seated or highly vascularized tumors. The objective of this study is to assess the utility of using magnetic nanoparticles (mNPs) during HIFU procedures to locally enhance heating at low powers, thereby reducing the likelihood of collateral thermal damage and undesired destruction due to cavitation. Tissue phantoms with 0% (control), 1% and 3% mNPs concentrations by volume were fabricated. Each tissue phantom was embedded with four thermocouples (TCs) and sonicated using transducer acoustic powers of 5.15 W, 9.17 W, and 14.26 W. The temperature profiles during the heating and cooling periods were recorded for each embedded TC. The measured transient temperature profiles were used for thermal-dose calculations. The increase in the concentration of mNPs in the tissue phantoms, from 0% to 3%, resulted in the rise in the peak temperatures for all the TCs for each acoustic power. The thermal dose also increased with the rise in the concentration of mNPs in the tissue phantoms. For the highest applied acoustic power (14.26 W), the peak temperature at TC 1 (T1) in tissue phantoms with 1% and 3% mNPs concentrations increased (with respect to tissue phantom with 0% (control) mNPs concentration) by 1.59 and 2.09 , respectively. For an acoustic power of 14.26 W, the time required to achieve cellular necrosis as defined by a 240 equivalent min thermal dose was approximately 75 s in the absence of mNPs, 14 s for the 1% concentration, and 8 s for the 3% concentration. Magnetic nanoparticles have the potential to significantly reduce the time for HIFU thermal-ablation procedures. They can also decrease the likelihood of collateral damage by the propagating beam in HIFU procedures by reducing the intensity required to achieve cellular necrosis. [DOI: 10.1115/1.4027340]
Handheld usability: design, prototyping, & usability testing for mobile phones

This tutorial presents handheld device UI design, prototyping, and usability strategies. Handheld devices include pagers, PDAs, and mobile telephone handsets. Hardware UI, operating environments, and wireless networking will be presented. Information architecture, paper prototyping, and usability testing of handheld devices will be taught with team exercises.
The Spectrum of Skin Disease Among Indian Children

Abstract: Skin diseases in children are encountered frequently and their characterization is essential for the preparation of academic, research and health plans. A retrospective study was designed to evaluate the epidemiologic features of pediatric dermatoses in India. The setting was a tertiary care referral center in India (Kalawati Saran Children’s Hospital, New Delhi) during January 1997 to December 2003. A total of 30,078 children less than 12 years of age with 32,341 new dermatoses were recorded, with a male to female ratio of 1.07:1. Most of the disease was seen in the 1‐ to 5‐year age group (44.94%). The most common skin diseases were infections and infestations (47.15%) consisting of bacterial infections (58.09%) and scabies (21.54%), followed by eczemas (26.95%), infantile seborrheic dermatitis, scabies, and pityriasis alba. Other unique dermatoses in our settings were papular uticaria (3.59%), miliaria (5.46%), postinflammatory pigmentary abnormalities (1.68%), and nutritional deficiency dermatoses (0.45%). A majority of patients were diagnosed clinically and special diagnostic tests were conducted in 2.6% of patients. The most common diagnostic test used was KOH mount (59.2%), followed by skin biopsy (39%). Nearly 90% of patients were seen without any referral and in the remaining, a majority were referred by pediatricians (75%). A majority of patients were diagnosed to have infection followed by dermatitis in our setting.
Joint channel and delay aware user scheduling for multiuser MIMO system over LTE-A network

Existing mobile video applications are continuously driving up the demand for throughput and better quality of service (QoS) for future Long Term Evolution-Advanced (LTE-A) networks. Multi-User Multiple-Input Multiple-Output (MU-MIMO) is one of the most promising technologies that would meet the throughput demand. Unfortunately, existing MU-MIMO schemes do not consider metrics such as delay, and therefore, cannot meet the QoS requirement of delay sensitive applications, such as mobile video. We propose a new cross-layer MU-MIMO scheduling algorithm, which is referred to as joint channel and delay aware user scheduling (CDAUS), satisfies both the throughput and delay requirements. The key idea of the CDAUS algorithm is to select users to form MU-MIMO based on the delay requirements of individual users, as well as their channel correlations. The priority of the users is carefully designed to leverage their delay and throughput. Simulation results show that the proposed CDAUS algorithm is able to reduce the average delay by up to 30% with a marginal 2% sacrifice of throughput, compared to previous work. It also reduces delay variations and improves fairness among the users.
Evidence for a Regulated Interaction between Heterotrimeric G Proteins and Caveolin

Caveolae are flask-shaped plasma membrane specializations. A 22-kDa protein, caveolin, is a principal component of caveolar membranes in vivo. As recent evidence suggests that caveolae may participate in G protein-coupled signaling events, we have investigated the potential interaction of caveolin with heterotrimeric G proteins. Using cell fractionation techniques, we found that mutational or pharmacologic activation of G prevents its cofractionation with caveolin. In a second independent approach, we directly examined the interaction of G proteins with caveolin. For this purpose, we recombinantly expressed caveolin as a glutathione S-transferase fusion protein. Using an in vitro binding assay, we found that caveolin interacts with G protein α subunits (G, G, and G). Mutational or pharmacologic activation (with guanosine 5′-O-(thiotriphosphate)) of G subunits prevents this interaction, indicating that the inactive GDP-bound form of G subunits preferentially interacts with caveolin. This G protein binding activity is located within a 41-amino acid region of caveolin's cytoplasmic N-terminal domain (residues 61-101). Further functional analysis shows that a polypeptide derived from this region of caveolin (residues 82-101) effectively suppresses the basal activity of purified G proteins, apparently by inhibiting GDP/GTP exchange. This caveolin sequence is homologous to a region of the Rab GDP dissociation inhibitor, a known inhibitor of GDP/GTP exchange for Rab proteins. These data suggest that caveolin could function to negatively regulate the activation state of heterotrimeric G proteins.