Miracle-dz/UniFAR-FTUs huggingface dataset:
Folic acid, either solely or combined with L‐citrulline, improves NO signaling and ameliorates chronic hypoxia‐induced pulmonary hypertension in newborn pigs

Concomitant with developing pulmonary hypertension (PH), newborn piglets exposed to chronic hypoxia develop pulmonary vascular NO signaling impairments. PH is reduced and NO signaling is improved in chronically hypoxic piglets treated with the NO‐arginine precursor, L‐citrulline. Folic acid positively impacts NO signaling. We evaluated whether the effect on NO signaling and PH is greater using co‐treatment with folic acid and L‐citrulline than either alone. From day 3 to day 10 of hypoxia, piglets were treated solely with folic acid, solely with L‐citrulline, or co‐treated with both. Catheters were placed to measure in vivo hemodynamics. NO production was measured in vitro in dissected pulmonary arteries. Compared to normoxic piglets, pulmonary vascular resistance (PVR) was elevated and NO production was reduced in untreated hypoxic piglets. Regardless of treatment strategy, PVR was less in all three treated groups of hypoxic piglets when compared to the untreated hypoxic group. In addition, for all three groups of treated hypoxic piglets, NO production was higher than the untreated group. Improvements in PVR and NO production did not differ between piglets co‐treated with folic acid and L‐citrulline and those treated solely with either. Thus, the impact on NO production and PVR was not augmented by combining folic acid and L‐citrulline treatments. Nonetheless, treatment with folic acid, either singly or when combined with L‐citrulline, increases NO production and inhibits PH in chronically hypoxic newborn piglets. Folic acid merits consideration as a therapy for PH in human infants with chronic heart and lung conditions that are associated with chronic hypoxia.
Effects of early hemodynamics, oxygen metabolism, and lactate dynamics on prognosis of post-cardiac arrest syndrome

With an annual incidence of 0.5 to 1.5/1000, cardiac arrest (CA) has emerged as a major global public health concern. Although the American Heart Association (AHA)-International Liaison Committee on Resuscitation updates the cardiopulmonary resuscitation (CPR) guidelines every 5 years, the survival rate and percentage of patients with good neurologic outcomes post-CA after hospital discharge have been relatively low. Therefore, the AHA 2010 CPR guidelines mention the treatment of postcardiac arrest syndrome (PCAS) in the intensive care unit (ICU) as the fifth link in the CA survival chain. PCAS is a pathophysiological process that includes (1) brain injury, (2) myocardial dysfunction leading to hemodynamic instability, and (3) systemic ischemia/reperfusion response leading to lactate accumulation. These key factors affect the survival and neurological prognosis of CA patients in the early stages. We assessed the effects of early hemodynamics, oxygen metabolism, and lactate dynamics during PCAS on a 28-day survival rate and neurological outcomes.
Endocrine disruptor chemicals. A review of their effects on male reproduction and antioxidants as a strategy to counter it

Endocrine disruptor chemicals are exogenous molecules that generate adverse effects on human health by destabilizing the homeostasis of endocrine system and affecting directly human reproductive system by inhibiting or activating oestrogenic or androgenic receptors. Endocrine disruptor chemicals generate transgenerational epigenetic problems, besides being associated with male infertility. Epidemiological data indicate that the increase in reproductive problems in males in the last 50 years is correlated with the increase of endocrine disrupting chemicals in the environment, being associated with a decrease in semen quality and direct effects on spermatozoa, such as alterations in motility, viability and acrosomal reaction, due to the generation of oxidative stress, and have also been postulated as a possible cause of testicular dysgenesis syndrome. Diverse antioxidants, such as C and E vitamins, N‐acetylcysteine, selenium and natural vegetable extracts, are among the alternatives under study to counter the effects of endocrine disruptor chemicals. In some cases, the usage of them has given positive results and the opposite in others. In this review, we summarize the recent information about the effects of endocrine disruptor chemicals on male reproduction, on sperm cells, and the results of studies that have tested antioxidants as a strategy to diminish their harmful effects.
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species

Abstract Previous studies on enhancers and their target genes were largely based on bulk samples that represent ‘average’ regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populations. In recent years, single-cell sequencing technology has enabled the profiling of open chromatin accessibility at the single-cell level (scATAC-seq), which can be used to annotate the enhancers and promoters in specific cell types. A comprehensive resource is highly desirable for exploring how the enhancers regulate the target genes at the single-cell level. Hence, we designed a single-cell database scEnhancer (http://enhanceratlas.net/scenhancer/), covering 14 527 776 enhancers and 63 658 600 enhancer-gene interactions from 1 196 906 single cells across 775 tissue/cell types in three species. An unsupervised learning method was employed to sort and combine tens or hundreds of single cells in each tissue/cell type to obtain the consensus enhancers. In addition, we utilized a cis-regulatory network algorithm to identify the enhancer-gene connections. Finally, we provided a user-friendly platform with seven useful modules to search, visualize, and browse the enhancers/genes. This database will facilitate the research community towards a functional analysis of enhancers at the single-cell level.
Immune Efficacy of different immunization doses of divalent combination DNA vaccine pOPRL+pOPRF of Pseudomonas aeruginosa

At present, there is no vaccine available against Pseudomonas aeruginosa, a common zoonotic pathogenic bacterium. In a previous study, the authors prepared a divalent combination DNA vaccine, pOPRL+pOPRF, which exhibited good protective efficacy. To explore the optimal immunization dose of this divalent combination DNA vaccine, in the present study, chickens were vaccinated with 25, 50, 100, and 200 µg doses. The levels of serum antibody, interferon-γ (IFN-γ), and interleukin-2 (IL-2) were determined, and lymphocyte proliferation assays were performed. After challenge with virulent P. aeruginosa, the protective efficacy was evaluated. Following vaccination, the serum antibodies, stimulation index values, and concentrations of IFN-γ and IL-2 were significantly higher in chickens vaccinated with 100 and 200 µg vaccines than in those vaccinated with 25 and 50 µg doses (P<0.05). IFN-γ and IL-2 concentrations in chickens immunized with 100 µg vaccine were slightly higher than those in chickens immunized with 200 µg vaccine, although the difference was not statistically significant. The protective rates were 55%, 65%, 85%, and 85% with 25, 50, 100, and 200 µg of the pOPRL+pOPRF DNA vaccine, respectively. Thus, the immune efficacy of the pOPRL+pOPRF DNA vaccine increased with an increase in immunization dose, but this does not imply that a higher dose necessarily achieves a better outcome. The optimal immunization dose of pOPRL+pOPRF DNA vaccine in chickens was 100 µg.
Convex optimization algorithms in medical image reconstruction—in the age of AI

The past decade has seen the rapid growth of model based image reconstruction (MBIR) algorithms, which are often applications or adaptations of convex optimization algorithms from the optimization community. We review some state-of-the-art algorithms that have enjoyed wide popularity in medical image reconstruction, emphasize known connections between different algorithms, and discuss practical issues such as computation and memory cost. More recently, deep learning (DL) has forayed into medical imaging, where the latest development tries to exploit the synergy between DL and MBIR to elevate the MBIR's performance. We present existing approaches and emerging trends in DL-enhanced MBIR methods, with particular attention to the underlying role of convexity and convex algorithms on network architecture. We also discuss how convexity can be employed to improve the generalizability and representation power of DL networks in general.
Nonstarter Bacterial Communities in Aged Cheddar Cheese: Patterns on Two Timescales

Long production schedules used in modern cheese manufacturing can create circumstances that support the growth of microorganisms in the cheese processing environment. This work demonstrates that this growth can lead to significant changes in the microbial quality of aged cheese produced later in the production day. ABSTRACT The aim of this study was to investigate the temporal stability of microbial contamination during cheddar cheese production by examining patterns of nonstarter bacteria in 60-day aged cheddar collected from the start and end of 30 consecutive production days. Further, we explored the source of these temporal microbial variations by comparing microbial communities in the aged cheese to those on food contact surfaces from a piece of cheesemaking equipment previously identified as a major source of nonstarter bacteria in the same processing environment. 16S rRNA metabarcoding and culture-based sequencing methods identified two Streptococcus sequence variants significantly associated with the end of the production day in both the aged cheese and the cheese processing environment. Closer inspection of these sequence variants in the aged cheese over the 40-day sampling period revealed sinusoidal-like fluctuations in their relative ratios, which appeared to coincide with the Lactococcus starter rotation schedule. These results demonstrate that the microbial composition of finished cheese can vary according to the timing of processing within a production day. Further, our results demonstrate that time-of-day microbial differences in cheese can result from bacterial growth on food contact surfaces and that the composition of these microbial differences is subject to change day-to-day and may be linked to routine changes in the Lactococcus starter culture. IMPORTANCE Long production schedules used in modern cheese manufacturing can create circumstances that support the growth of microorganisms in the cheese processing environment. This work demonstrates that this growth can lead to significant changes in the microbial quality of aged cheese produced later in the production day. Further, we demonstrate that the dominant bacteria associated with these microbial changes throughout production are subject to change between days and might be influenced by specific cheese manufacturing practices. These findings improve understanding of microbial contamination patterns in modern food manufacturing facilities, thereby improving our ability to develop strategies to minimize quality losses due to microbial spoilage.
Direct localised measurement of electrical resistivity profile in rat and embryonic chick retinas using a microprobe

Abstract We report an alternative technique to perform a direct and local measurement of electrical resistivities in a layered retinal tissue. Information on resistivity changes along the depth in a retina is important for modelling retinal stimulation by retinal prostheses. Existing techniques for resistivity-depth profiling have the drawbacks of a complicated experimental setup, a less localised resistivity probing and/or lower stability for measurements. We employed a flexible microprobe to measure local resistivity with bipolar impedance spectroscopy at various depths in isolated rat and chick embryo retinas for the first time. Small electrode spacing permitted high resolution measurements and the probe flexibility contributed to stable resistivity profiling. The resistivity was directly calculated based on the resistive part of the impedance measured with the Peak Resistance Frequency (PRF) methodology. The resistivity-depth profiles for both rat and chick embryo models are in accordance with previous mammalian and avian studies in literature. We demonstrate that the measured resistivity at each depth has its own PRF signature. Resistivity profiles obtained with our setup provide the basis for the construction of an electric model of the retina. This model can be used to predict variations in parameters related to retinal stimulation and especially in the design and optimisation of efficient retinal implants.
Consistent VIV Fatigue Analysis Methodology of Umbilicals

The fatigue life assessment of umbilicals due to vortex induced vibrations (VIV) requires special attention to the structural properties of the umbilical due to the stick/slip behavior of helix elements in bending. Essential parameters for assessment of the VIV response are the structural damping in the stick regime (i.e. umbilical behaves as a solid cross section due to friction between the helix elements) as well as the additional damping introduced by the hysteretic damping due to the stick/slip behavior in bending. Furthermore, consistent fatigue stress recovery considering the stick/slip behavior in bending is essential for fatigue life predictions. The expected VIV response characteristics of different types of umbilicals (steel tube umbilicals, control umilicals and power umbilicals) are discussed with basis of typical mechanical properties of the different types. It is shown that these main types of umbilicals may experience distinctive different VIV response characteristics underlining the need for a consistent VIV fatigue analysis scheme. The overall objective of the paper is to establish consistent VIV analysis methodology for umbilicals in compliance with requirements given in ISO 13628-5 ‘Subsea Umbilicals’. A consistent VIV fatigue analysis scheme is outlined using commercially available state-of-the-art computer programs for global system modeling/eigenmode analysis (Riflex), VIV response analysis (Shear7) and cross sectional stress analysis (Helica). The performance of the calculation scheme is demonstrated by case studies of deepwater umbilicals in a complex long-term current loading environment. It is show that consistent treatment of the mechanical properties of umbilicals is essential for VIV fatigue life assessments. It is furthermore shown that the VIV fatigue damage in umbilicals may be significant underlining, the practical importance in design of deepwater dynamic umbilicals.Copyright © 2011 by ASME
Analytical treatment of uniform multiconductor transmission lines

The authors study a certain class of solutions of the multiconductor-transmission-line (MTL) equations. This class is basically defined by two reasonable but otherwise arbitrary demands: the commutativity between the propagation matrix and the characteristic impedance matrix, and the assumption that the matrices of interest are real matrices times complex-valued functions (e.g., functions of the constitutive parameters of the medium). On the basis of the above requirements, it can be shown that all matrices that are relevant for the MTL equations and for their solutions can be simultaneously diagonalized with only one set of eigenvectors (e.g., the eigenvectors of the per-unit-length inductance matrix). Of course, the sets of eigenvalues corresponding to different matrices are different. The authors investigate the MTL equations and their solutions for different environments and different properties, including lossy lines and lossy media. Mechanisms that can cause splitting of natural frequencies are considered. >
The Lack of Contribution of 7-Hydroxymitragynine to the Antinociceptive Effects of Mitragynine in Mice: A Pharmacokinetic and Pharmacodynamic Study

Kratom (Mitragyna speciosa), a Southeast Asian tree, has been used for centuries in pain relief and mitigation of opium withdrawal symptoms. Mitragynine (MTG), the major kratom alkaloid, is being investigated for its potential to provide analgesia without the deleterious effects associated with typical opioids. Concerns have been raised regarding the active metabolite of MTG, 7-hydroxymitragynine (7HMG), which has higher affinity and efficacy at µ-opioid receptors than MTG. Here we investigated the hotplate antinociception, pharmacokinetics, and tissue distribution of MTG and 7HMG at equianalgesic oral doses in male and female C57BL/6 mice to determine the extent to which 7HMG metabolized from MTG accounts for the antinociceptive effects of MTG and investigate any sex differences. The mechanism of action was examined by performing studies with the opioid receptor antagonist naltrexone. A population pharmacokinetic/pharmacodynamic model was developed to predict the behavioral effects after administration of various doses of MTG and 7HMG. When administered alone, 7HMG was 2.8-fold more potent than MTG to produce antinociception. At equivalent effective doses of MTG and 7HMG, there was a marked difference in the maximum brain concentration of 7HMG achieved, i.e., 11-fold lower as a metabolite of MTG. The brain concentration of 7HMG observed 4 hours post administration, producing an analgesic effect <10%, was still 1.5-fold higher than the maximum concentration of 7HMG as a metabolite of MTG. These results provide strong evidence that 7HMG has a negligible role in the antinociceptive effects of MTG in mice. SIGNIFICANCE STATEMENT Mitragynine (MTG) is being investigated for its potential to aid in pain relief, opioid withdrawal syndrome, and opioid use disorder. The active metabolite of MTG, 7-hydroxymitragynine (7HMG), has been shown to have abuse potential and has been implicated in the opioid-like analgesic effect after MTG administration. The results of this study suggest a lack of involvement of 7HMG in the antinociceptive effects of MTG in mice.
Sofosbuvir-based antiviral therapy provided highly treatment efficacy, safety, and good tolerability for Taiwanese chronic hepatitis C patients with decompensated cirrhosis

Background: For patients with hepatitis C virus (HCV)-related decompensated cirrhosis, poor prognosis was documented due to the development of portal hypertension-related complications and hepatocellular carcinoma. Sofosbuvir-based direct-acting antiviral agents (DAAs) has revolutionized the treatment landscape of HCV, particularly in this subpopulation. To date, real-world efficacy, tolerability, and safety profiles for Taiwanese HCV-related decompensated cirrhosis treated by DAAs have not been reported. Methods: Between December 2015 and June 2020, 50 consecutive HCV-related Child-Turcotte-Pugh (CTP) classes B or C cirrhotics treated by sofosbuvir-based DAAs (with daclatasvir: 7, with ledipasvir: 32, with velpatasvir: 10, with ledipasvir then shifted to velpatasvir: 1) were enrolled. Forty-seven (94%) patients used DAAs in combination with low-dose ribavirin. SVR12 was defined by undetectable HCV RNA (<15 IU/mL) at treatment end and 12 weeks after the completion of therapy. Results: The mean age of the enrolled patients was 68.1 ± 11.2 years, 18% of the patients were CTP class C, and the baseline HCV RNA level was 5.42 ± 1.2 log10 IU/mL. The genotype distribution was as follows: 1a: 3; 1b: 34; 2: 9; 6: 3; and one patient with an unclassified HCV genotype. After DAAs treatment, the rates of undetectable HCV RNA at week 4 and at the end of the treatment were 88.9% and 98.0%, respectively. Subjective adverse events were reported by 42.0% of the patients, but they were generally mild and could be relieved by medications. One patient did not finish therapy due to sepsis with multiple organ dysfunction. The overall SVR12 rate was 96.0% (CTP class B: 97.6%, CTP class C: 88.9%). A significant improvement in hepatic functional reserve was noted after successful antiviral therapy. Conclusion: For patients with HCV-related decompensated cirrhosis, which has been considered a contraindication for interferon-based therapy, sofosbuvir-based all-oral DAAs provided high treatment efficacy, acceptable safety, and good tolerability.
A closed frequencies estimation by using the phase property of an all-pass filter

The purpose of this paper is to shorten the analytical duration with keeping high resolution in frequency for the closed frequencies estimation. Existence of the closed frequencies in an input signal makes difficult the estimation with high resolution, because of a spectral leakage. It is difficult to eliminate the leakage. We utilize the leakage to estimate the closed frequencies without attempt to eliminate it. In general, the magnitude of leakage changes with the phase of an input signal. For changing the phase, an all-pass filter (APF) is used. This paper makes clear the relationships among three factors: the leakage, the phase, and the input frequencies (i.e., periodic components forming an input signal). The experimental results for estimating closed frequencies clearly show that the use of APF results in the duration shorter than 60% of the conventional methods with high resolution in frequency.
Complete Genome Sequence of Leptospira kobayashii Strain E30, Isolated from Soil in Japan

The spirochete bacterium Leptospira kobayashii is a recently designated species of the genus Leptospira. Here, we report the complete genome sequence of L. kobayashii strain E30, consisting of two circular chromosomes and two plasmids. ABSTRACT The spirochete bacterium Leptospira kobayashii is a recently designated species of the genus Leptospira. Here, we report the complete genome sequence of L. kobayashii strain E30, consisting of two circular chromosomes and two plasmids.
ODF: An Efficient OWL-Based Linked Course Data Generating Framework

Although the intention of OWL is to provide an open, minimally constraining way for representing to represent rich and complex knowledge about things, there exists an increasing demands for the efficiency of course data generating. Addressing this issue, we present the ODF: a new OWL-based Linked Course Data generating framework, which makes it possible to specify semantic data directly. Generating such data directly does not only help in maintaining course data quality, but also opens up new optimization opportunities for link sources and, most importantly, makes generating process easier for users and system developers. We present OWL-based Linked Course Data generating framework and discuss the impact on Linked Data.