Long-term COVID-19 sequelae by Theta and SARS-CoV-2 variants in a Philippine cohort.

Introduction: Millions have been infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) since its emergence in 2019, but most patients make a full recovery. The long-term consequences of the infection are anticipated to unravel in the succeeding years with reports of patients experiencing chronic, debilitating sequelae post-infection commonly referred to as Long COVID. Various Variants of Concern (VoCs) have emerged as the SARS-CoV-2 virus evolved displaying increased infectivity and immune evasiveness.

Pathogen genomic surveillance status among lower resource settings in Asia.

Asia remains vulnerable to new and emerging infectious diseases. Understanding how to improve next generation sequencing (NGS) use in pathogen surveillance is an urgent priority for regional health security. Here we developed a pathogen genomic surveillance assessment framework to assess capacity in low-resource settings in South and Southeast Asia.

Genomic analysis of strain PH1009, a potential multi-drug resistant pathogen due to acquisition of toxin genes.

In has increasingly been observed that viral and bacterial coinfection frequently occurs among cultured shrimp and this coinfection could exacerbate the disease phenotype. Here, we describe a newly discovered bacterial strain, PH1009 collected from Masbate Island, Philippines that was found to be co-infecting with the White Spot Syndrome virus in a sample of black tiger prawn, . The genome of PH1009 was sequenced, assembled, and annotated.

Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines.

The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, while other Omicron lineages, including BA.

Detection and Genome Sequencing of SARS-CoV-2 Variants Belonging to the B.1.1.7 Lineage in the Philippines.

We report the sequencing and detection of 36 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations specific to viruses belonging to the B.1.1.

Draft Genome Sequence of Multidrug-Resistant Vibrio parahaemolyticus Strain PH698, Infecting Penaeid Shrimp in the Philippines.

The emergence of multidrug-resistant bacterial strains in diverse settings has been reported globally. In the Philippine shrimp aquaculture industry, antibiotics are used for the treatment of bacterial diseases during the production cycle. We report the draft genome of PH698, a multidrug-resistant strain isolated from a Philippine shrimp farm.

Draft Genome Sequence of Vibrio parahaemolyticus Strain PH1339, Which Causes Acute Hepatopancreatic Necrosis Disease in Shrimp in the Philippines.

We report the first draft genome sequence of an acute hepatopancreatic necrosis disease (AHPND)-causing strain isolated from a sample from the Philippines. The strain carries the genes encoding the Pir-like toxin pair PirA and PirB.

The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae.

The impact of modern agriculture on the evolutionary trajectory of plant pathogens is a central question for crop sustainability. The Green Revolution replaced traditional rice landraces with high-yielding varieties, creating a uniform selection pressure that allows measuring the effect of such intervention. In this study, we analyzed a unique historical pathogen record to assess the impact of a major resistance gene, Xa4, in the population structure of Xanthomonas oryzae pv.

Acute hepatopancreatic necrosis disease (AHPND) outbreaks in Penaeus vannamei and P. monodon cultured in the Philippines.

Acute hepatopancreatic necrosis disease (AHPND) has recently emerged as a serious disease of cultured shrimp. It has also been described as early mortality syndrome (EMS) due to mass mortalities occurring within 20 to 30 d after stocking of ponds with postlarvae. Here, Penaeus vannamei and Penaeus monodon from shrimp farms in the Philippines were examined for the toxin-producing strain of Vibrio parahaemolyticus due to AHPND-like symptoms occurring in marketable size shrimp.

Prior individual training and self-organized queuing during group emergency escape of mice from water pool.

We study the impact of prior individual training during group emergency evacuation using mice that escape from an enclosed water pool to a dry platform via any of two possible exits. Experimenting with mice avoids serious ethical and legal issues that arise when dealing with unwitting human participants while minimizing concerns regarding the reliability of results obtained from simulated experiments using 'actors'. First, mice were trained separately and their individual escape times measured over several trials.

A bioinformatics survey for conotoxin-like sequences in three turrid snail venom duct transcriptomes.

The repertoire of venom peptides produced by Conoidean snails has shown to be useful for therapeutic and neuropharmacologic applications. Despite their dominance in terms of species number, the Family Turridae is the least studied among their other Conoidean counterparts. They provide a vast resource of pharmacological material only hindered by the inaccessibility of their deep water habitat for sample collection and their small size that allows only a limited amount of material from their venom duct amenable for analysis.

Superantigen involvement and susceptibility factors in Kawasaki disease: profiles of TCR Vβ2+ T cells and HLA-DRB1, TNF-α and ITPKC genes among Filipino patients.

Superantigens and genetic factors may play roles in the etiology and susceptibility to Kawasaki disease (KD). To investigate these roles, percentages of TCR-Vβ2+ T cells were compared by flow cytometry using anti-Vβ2 monoclonal antibodies and genotyping was done on HLA-DRB1 exon 2, the -308 site of the TNF-α promoter region, and ITPKC SNP rs28493229 by polymerase chain reaction followed by direct sequencing. There were higher percentages of Vβ2+ T-cells in KD patients (9.

Two-color excitation fluorescence microscopy through highly scattering media.

We study the performance of two-color excitation (2CE) fluorescence microscopy [Opt. Lett. 24, 1505 (1999)] in turbid media of different densities and anisotropy.

Noise-Enhanced Measurement of Weak Doublet Spectra with a Fourier-Transform Spectrometer and a 1-Bit Analog-to-Digital Converter.

We demonstrate an efficient noise dithering procedure for measuring the power spectrum of a weak spectral doublet with a Fourier-transform spectrometer in which the subthreshold interferogram is measured by a 1-bit analog-to-digital converter without oversampling. In the absence of noise, no information is obtained regarding the doublet spectrum because the modulation term s(x) of its interferogram is below the instrumental detection limit B, i.e.

Optical-feedback semiconductor laser Michelson interferometer for displacement measurements with directional discrimination.

An optical-feedback semiconductor laser Michelson interferometer (OSMI) is presented for measuring microscopic linear displacements without ambiguity in the direction of motion. The two waves from the interferometer arms, one from the reference mirror and the other from the reflecting moving target, are fed back into the lasing medium (lambda = 830 nm), causing variations in the laser output power. We model the OSMI into an equivalent Fabry-Perot resonator and derive the dependence of the output power (and the junction voltage) on the path difference between the two interferometer arms.

Excitation with a focused, pulsed optical beam in scattering media: diffraction effects.

To gain a better understanding of the spatiotemporal problems that are encountered in two-photon excitation fluorescence imaging through highly scattering media, we investigate how diffraction affects the three-dimensional intensity distribution of a focused, pulsed optical beam propagating inside a scattering medium. In practice, the full potential of the two-photon excitation fluorescence imaging is unrealized at long scattering depths, owing to the unwanted temporal and spatial broadening of the femtosecond excitation light pulse that reduces the energy density at the geometric focus while it increases the excitation energy density in the out-of-focus regions. To analyze the excitation intensity distribution, we modify the Monte Carlo-based photon-transport model to a semi-quantum-mechanical representation that combines the wave properties of light with the particle behavior of the propagating photons.

Third-harmonic generation microscopy in highly scattering media.

The performance of third-harmonic generation (THG) microscopy in highly scattering media is analyzed with the Monte Carlo technique. The three-dimensional point-spread function (PSF) of the laser-scanning THG microscope with a pulsed excitation light source is derived for both isotropic and anisotropic scattering media and at different h/d(s) values, where h is the scattering depth as measured from the geometric focus of the objective lens and d(s) is the mean free path of the scattering medium. The generated THG signal is detected by a large-area photodetector.

High-accuracy fourier transform interferometry, without oversampling, with a 1-bit analog-to-digital converter.

We demonstrate a new technique for performing accurate Fourier transform interferometry with a 1-bit analog-to-digital (AD) converter that does not require oversampling of the interferogram, unlike in other 1-bit coding schemes that rely on delta-sigma modulation. Sampling aims at locating the intersections {z(i)} of the modulation term s(z) of the interferogram and a reference sinusoid r(z) = A cos(2pif(r)z), where z is the optical path difference. A new autocorrelation-based procedure that includes the accurate recovery of the equally sampled amplitude representation {s(k)} of s(z) from {z(i)} is utilized to calculate the square of the emission spectrum of the light source (sample).

Efficient analysis of temporal broadening of a pulsed focused Gaussian beam in scattering media.

We show that the temporal broadening of a pulsed, tightly focused TEM(00) beam propagating in a scattering medium can be accurately modeled as a convolution between the initial pulse profile and an effective impulse response that is given by the propagation behavior of an infinitely thin pulse in the said medium. The impulse response is obtained with a Monte Carlo (MC) analysis of the propagating photons in the impulse. Our algorithm is 2 orders of magnitude less complex than the full MC solution of the pulse propagation problem.

Image compression by vector quantization with noniterative derivation of a codebook: applications to video and confocal images.

We demonstrate an image-compression technique that uses what we believe is a new noniterative codebook generation algorithm for vector quantization. The technique supports rapid decompression and is equally applicable to individual images or to a set of images without the need for interframe processing. Compression with a single-image codebook is tested on (1) ten confocal images of the hindbrain of a mouse embryo, (2) video images of a polystyrene microsphere that is manipulated by a focused laser light, and (3) five fluorescence images of the embryo eye lens taken at different magnifications.

Monte carlo analysis of two-photon fluorescence imaging through a scattering medium.

The behavior of two-photon fluorescence imaging through a scattering medium is analyzed by use of the Monte Carlo technique. The axial and transverse distributions of the excitation photons in the focused Gaussian beam are derived for both isotropic and anisotropic scatterers at different numerical apertures and at various ratios of the scattering depth with the mean free path. The two-photon fluorescence profiles of the sample are determined from the square of the normalized excitation intensity distributions.

Image contrast enhancement for two-photon fluorescence microscopy in a turbid medium.

Image contrast enhancement is investigated for two-photon excitation fluorescence images of a microscopic sample that is buried underneath a turbid medium. The image contrast, which deteriorates rapidly with sample depth because of scattering loss, is enhanced by an increase in the average excitation power of the focused Gaussian (the TEM(00) mode) beam according to a compensation relation that has been derived by use of a Monte Carlo analysis of the scattering problem. A correct increase in the excitation power results in a detected fluorescence signal that remains invariant with sample depth.

Improved classification robustness for noisy cell images represented as principal-component projections in a hybrid recognition system.

Different types of cells are recognized from their noisy images by use of a hybrid recognition system that consists of a learning principal-component analyzer and an image-classifier network. The inputs to the feed-forward backpropagation classifier are the first 15 principal components of the 10 x 10 pixel image to be classified. The classifier was trained with clear images of cells in metaphase, unburst cells, and other erroneous patterns.

Signal Recovery in Sinusoid-Crossing Sampling by use of the Minimum-Negativity Constraint.

High-frequency components that are lost when a signal s(x) of bandwidth W is low-pass filtered in sinusoid-crossing sampling are recovered by use of the minimum-negativity constraint. The lost high-frequency components are recovered from the information that is available in the Fourier spectrum, which is computed directly from locations of intersections {x(i)} between s(x) and the reference sinusoid r(x) = A cos(2pif(r)x), where the index i = 1, 2, ..