Miracle-dz/UniFAR-FTUs huggingface dataset:
Lactic Acid Bacteria: Variability Due to Different Pork Breeds, Breeding Systems and Fermented Sausage Production Technology

Changes in the ecology of the various lactic acid bacteria (LAB) species, which are involved in traditional fermented sausages, were investigated in the light of the use of different breeds of pork, each of which was raised in two different environments and processed using two different technologies. The semi-quantitative molecular method was applied in order to understand how the different species alternate over time, as well as their concentration ratios. A significant increase in LAB over the first days of fermentation characterized the trials where the starter culture wasn’t added (T), reaching values of 107–108 cfu g−1. On the other hand, in the trials in which sausages were produced with starter addition, LAB counts had a less significant incremental jump from about 106 cfu g−1 (concentration of the inoculum) to 108 cfu g−1. Lactobacillus sakei and Lb. curvatus were detected as the prevalent population in all the observed fermentations. Pediococcus pentosaceus, Lb. casei, Leuconostoc mesenteroides, Lactococcus garviae, and Lb. graminis also appeared, but their concentration ratios varied depending on the diverse experimental settings. The results of cluster analysis showed that a plant- and breed-specific LAB ecology exists. In addition, it was also observed that the breeding system can influence the presence of certain LAB species.
Plasma Long Non-Coding RNA RP11-438N5.3 as a Novel Biomarker for Non-Small Cell Lung Cancer

Background Lung cancer is one of the most common malignancies around the world. The lack of early diagnosis and effective treatment strategies contributes to the poor prognosis of patients with lung cancer. Recent studies have implied the role of long non-coding RNAs (lncRNAs) in oncogenesis. The purpose of our study was to identify specific lncRNAs which were correlated with non-small cell lung cancer (NSCLC) and their potential functions. Materials and Methods The global plasma lncRNA profiling was performed using LncPathTM Human Cancer Array, and 11 lncRNAs were then selected for quantitative reverse transcription PCR (qRT-PCR) validation in 138 plasma samples from 69 NSCLC patients and 69 healthy controls (HCs). A noteworthy lncRNA, RP11-438N5.3, the function of which was previously unknown, was further explored on the aspect of the correlation of its expression level with clinicopathological factors. Results The results revealed that plasma level of RP11-438N5.3 was significantly lower in NSCLCs than that in HCs (p <0.01). Receiver operating characteristic (ROC) analyses showed that the area under the ROC curve (AUC) for plasma RP11-438N5.3 was 0.814 (95% CI, 0.743–0.885; p<0.01). High expression of RP11-438N5.3 in plasma correlated with favorable prognosis for NSCLC patients (Hazard ratio = 2.827; 95% CI: 1.036 to 7.718; p = 0.024; Cox regression analysis). Moreover, we found that the plasma level of stromal interaction molecule 1 (STIM1) mRNA was remarkably higher in NSCLC compared with HC (p<0.01), and the AUC for STIM1 was 0.753 (95% CI, 0.673–0.833; p<0.01), RP11-438N5.3 and STIM1 were inversely correlated with each other. Conclusion Our results indicated that RP11-438N5.3 and STIM1 might provide a new strategy for NSCLC diagnosis. Furthermore, increased circulating RP11-438N5.3 level holds great potential in indicating a beneficial prognosis in NSCLC patients.
Systematic re-evaluation of the long-used standard protocol of urease-dependent metabolome sample preparation

In the urinary metabolomics for finding biomarkers in urine, owing to high concentrations of urea, for chromatography-based metabolomic analysis, urea needed to be degraded by urease. This urease pretreatment has been the key step of sample preparation for standard urinary metabolomics until today even for mass spectrometry-based analysis. The urease pretreatment involving incubation of urine with urease contradicts the concept of metabolome sampling, which should immediately arrest metabolic reactions to prevent alterations of a metabolite profile. Nonetheless, the impact of urease pretreatment has not been clearly elucidated yet. We found that activities of urease and endogenous urinary enzymes and metabolite contaminants from the urease preparations introduce artefacts into metabolite profiles, thus leading to misinterpretation.
The Biology of Prostaglandins and Their Role as a Target for Allergic Airway Disease Therapy

Prostaglandins (PGs) are a family of lipid compounds that are derived from arachidonic acid via the cyclooxygenase pathway, and consist of PGD2, PGI2, PGE2, PGF2, and thromboxane B2. PGs signal through G-protein coupled receptors, and individual PGs affect allergic inflammation through different mechanisms according to the receptors with which they are associated. In this review article, we have focused on the metabolism of the cyclooxygenase pathway, and the distinct biological effect of each PG type on various cell types involved in allergic airway diseases, including asthma, allergic rhinitis, nasal polyposis, and aspirin-exacerbated respiratory disease.
Are Your Liposuction Cannulas and Handle-Cannulas a Potential Problem if Used for Autologous Fat Graft/Transfer?

Objectives: To create surgeon awareness that some liposuction instruments should not be used for harvest and reinjection during autologous fat grafting (AFG), to outline which instruments need special cleaning techniques, and to increase awareness of available customized devices that will eliminate the accumulation of debris in defect areas. Methods: The author examined 13 common liposuction handles and 22 liposuction cannulas noting their construction and ease of cleaning by brush and pressured water. Internal examination of the handles was done by cutting them in half longitudinally observing the pathway of the fat during harvest. The cannulas were examined by probing the tips of the cannulas to determine if blind pockets were present. Results: A few of the instruments had an acceptable continuous pathway and no problem cleaning areas. However, 10 of the 13 liposuction handles had severe drop-offs and cracks that would be very difficult to clean, and 18 out of the 22 cannulas contained a blind pocket in their distal tip. The most common structural problem for the handles was the severe drop-off but the most serious problem for the handles was the crack. The most common and serious problem for the cannulas was the tip blind pocket. These areas would require special cleaning efforts to qualify for use during AFG/T. Discussion: When AFG became a more popular procedure, surgeons adapted by using liposuction instruments for harvest and reinjection. However, because fat transfer involves reinjecting fat back into the body, the instruments must be easy to clean. Most liposuction instruments are built to transport liposuction waste fat only; thus, they have a crude interior design with drop-offs and pockets that make them difficult to clean. Some of these devices can harbor pockets of old tissue. In general, if the pathway is continuous and is not interrupted by drop-offs or blind pockets, the instrument can be used for both liposuction and AFG. If, however, there are drop-offs and/or blind pockets, the surgeon should make certain the unit is dismantled and every area cleaned manually between procedures or should turn to the many customized instruments for AFG. Conclusions: The decision to purchase and use liposuction instruments for AFG should be made only after the surgeon has examined the product and is confident that the pathway has no drop-offs and/or blind pockets that make it difficult to clean. Custom AFG instruments are available that are constructed in a manner that negates the need for special cleaning procedures.
Application of a high-quality, high-volume trap–neuter–return model of community cats in Seoul, Korea

Background This study was performed to determine the characteristics of community cats that were admitted to trap–neuter–return(TNR) programs and the feasibility of the high-quality, high-volume spay/neuter (HQHVSN) model in Seoul, Korea. Methods TNR programs were performed eight times from 2017 to 2018, and a total of 375 community cats from the pilot areas were admitted. The pilot areas were selected regions wherein caregivers voluntarily participated in our TNR program. Each cat was anesthetized, assessed for health status, sterilized, vaccinated against feline viral rhinotracheitis, calicivirus and panleukopenia (FVR-CP), and rabies, and treated with insecticide after surgery. The time from anesthesia to recovery was evaluated to verify the efficiency of surgical time of the program. The TNR program at a local animal hospital and the program in this study were compared to assess the veterinary treatment administered and the cost for each cat. Results A total of 375 cats were underwent TNR in this study, including 192 (51.2%) intact females, 180 (48%) intact males, and three (0.8%) sterilized cats. Following surgery, 372 cats (99.2%) were returned to their original locations. Three cats (0.8%) died postoperatively. On average, 21.9% of the cats were pregnant during the TNRs, and the highest percentage of cats (63.9%) were pregnant in March. All cats presented to the TNR program were considered healthy enough to be part of the program after examination. For neutering one animal at a time, similar to conventional TNR ($140), it took 53 ± 16 mins for females and 30 ± 9 mins for males from anesthesia to recovery. In contrast, the standardized procedure can neuter multiple cats simultaneously, similar to the conveyor system, at an estimated rate of 6.8 mins per cat ($45 per female cat, $30 per male cat). Conclusions The TNR strategy in Seoul should be implemented by establishing dedicated clinics to concentrate on HQHVSN surgeries of cats. Through this pilot study, we were able to demonstrate that it is possible to effectively apply HQHVSN clinics in Korea. Future studies that perform intensive sterilization in targeted areas are necessary to confirm the efficacy of the TNR strategy.
Rapid On-Site Phenotyping via Field Fluorimeter Detects Differences in Photosynthetic Performance in a Hybrid—Parent Barley Germplasm Set

Crop productivity can be expressed as the product of the amount of radiation intercepted, radiation use efficiency and harvest index. Genetic variation for components of radiation use efficiency has rarely been explored due to the lack of appropriate equipment to determine parameters at the scale needed in plant breeding. On the other hand, responses of the photosynthetic apparatus to environmental conditions have not been extensively investigated under field conditions, due to the challenges posed by the fluctuating environmental conditions. This study applies a rapid, low-cost, and reliable high-throughput phenotyping tool to explore genotypic variation for photosynthetic performance of a set of hybrid barleys and their parents under mild water-stress and unstressed field conditions. We found differences among the genotypic sets that are relevant for plant breeders and geneticists. Hybrids showed lower leaf temperature differential and higher non-photochemical quenching, resembling closer the male parents. The combination of traits detected in hybrids seems favorable, and could indicate improved photoprotection and better fitness under stress conditions. Additionally, we proved the potential of a low-cost, field-based phenotyping equipment to be used routinely in barley breeding programs for early screening for stress tolerance.
Reducing Hypermuscularization of the Transitional Segment Between Arterioles and Capillaries Protects Against Spontaneous Intracerebral Hemorrhage

Supplemental Digital Content is available in the text. Background: Spontaneous deep intracerebral hemorrhage (ICH) is a devastating subtype of stroke without specific treatments. It has been thought that smooth muscle cell (SMC) degeneration at the site of arteriolar wall rupture may be sufficient to cause hemorrhage. However, deep ICHs are rare in some aggressive small vessel diseases that are characterized by significant arteriolar SMC degeneration. Here we hypothesized that a second cellular defect may be required for the occurrence of ICH. Methods: We studied a genetic model of spontaneous deep ICH using Col4a1+/G498V and Col4a1+/G1064D mouse lines that are mutated for the α1 chain of collagen type IV. We analyzed cerebroretinal microvessels, performed genetic rescue experiments, vascular reactivity analysis, and computational modeling. We examined postmortem brain tissues from patients with sporadic deep ICH. Results: We identified in the normal cerebroretinal vasculature a novel segment between arterioles and capillaries, herein called the transitional segment (TS), which is covered by mural cells distinct from SMCs and pericytes. In Col4a1 mutant mice, this TS was hypermuscularized, with a hyperplasia of mural cells expressing more contractile proteins, whereas the upstream arteriole exhibited a loss of SMCs. TSs mechanistically showed a transient increase in proliferation of mural cells during postnatal maturation. Mutant brain microvessels, unlike mutant arteries, displayed a significant upregulation of SM genes and Notch3 target genes, and genetic reduction of Notch3 in Col4a1+/G498V mice protected against ICH. Retina analysis showed that hypermuscularization of the TS was attenuated, but arteriolar SMC loss was unchanged in Col4a1+/G498V, Notch3+/− mice. Moreover, hypermuscularization of the retinal TS increased its contractility and tone and raised the intravascular pressure in the upstream feeding arteriole. We similarly found hypermuscularization of the TS and focal arteriolar SMC loss in brain tissues from patients with sporadic deep ICH. Conclusions: Our results suggest that hypermuscularization of the TS, through increased Notch3 activity, is involved in the occurrence of ICH in Col4a1 mutant mice, by raising the intravascular pressure in the upstream feeding arteriole and promoting its rupture at the site of SMC loss. Our human data indicate that these 2 mutually reinforcing vascular defects may represent a general mechanism of deep ICH.
Identification of Candidate Genes Involved in Curd Riceyness in Cauliflower

“Riceyness” refers to the precocious development of flower bud initials over the curd surface of cauliflower, and it is regarded as undesirable for the market. The present study aimed to identify the candidate loci and genes responsible for the morphological difference in riceyness between a pair of cauliflower sister lines. Genetic analysis revealed that riceyness is controlled by a single dominant locus. An F2 population derived from the cross between these sister lines was used to construct “riceyness” and “non-riceyness” bulks, and then it was subjected to BSA-seq. On the basis of the results of Δ(SNP-index) analysis, a 4.0 Mb candidate region including 22 putative SNPs was mapped on chromosome C04. Combining the RNA-seq, gene function annotation, and target sequence analysis among two parents and other breeding lines, an orthologous gene of the Arabidopsis gene SOC1, Bo4g024850 was presumed as the candidate gene, and an upstream SNP likely resulted in riceyness phenotype via influencing the expression levels of Bo4g024850. These results are helpful to understand the genetic mechanism regulating riceyness, and to facilitate the molecular improvement on cauliflower curds.
A High Reliability 3D Scanning Measurement of the Complex Shape Rail Surface of the Electromagnetic Launcher

After an electromagnetic railgun launch, a series of damage phenomena may cause the inner bore surface to become complex, such as gouging and deposition. Furthermore, the rail surface will be uneven and blackened by oxidation. To understand these forms of rail degradation, many previous studies have mentioned several surface scanning methods, but none of these can be used in the complex inner bore. Therefore, we present a 3D scanning system based on binocular stereovision technology combined with the active illumination, which can be used to obtain the rail surface topography under a complex inner bore environment. The laser dot projection is applied as the active illumination. In contrast with other active illumination, laser dot projection has high reconstruction reliability. By combining laser dot projection with binocular stereovision, the object can be completely reconstructed. In addition, an image acquisition method which can improve image signal-to-noise ratio is proposed. The proof-of-principle experiment of the system is done under dim light conditions. Through the experiment, the 3D depth map of the rail surface is obtained and the gouge crater is scanned out. Meanwhile, system evaluation and measurement uncertainty analysis have also been carried out.
Executive function deficits contribute to poor theory of mind abilities in adults with ADHD

Abstract Introduction Studies exploring the theory of mind (ToM) in adults with Attention/Deficit Hyperactivity Disorder (ADHD), have tended to result in mixed findings. The contribution of neuropsychologic functions to ToM has not been investigated yet in adults with ADHD. The aim of this study was to investigate ToM abilities and the role of attention and executive functions in ToM of adults with ADHD. Methods This study was conducted in Bakirkoy Training and Research Hospital. Forty adults with ADHD and 40 healthy controls were administered a sociodemographic data form, and scales. Both groups were also assessed by Reading Mind From the Eyes Test (RMET), Trail Making Test (TMT) Part A-B and Continuous Performance Test (CPT). Results ToM was significantly impaired in adults with ADHD relative to controls (23.50 ± 3.44 and 26.25 ± 1.67, t(77) = 4.543, p = 0.003). Adults with ADHD performed worse on TMT Part B (76.02 ± 51.47 and 46.39 ± 18.33 seconds, t(78) = −3.429, p < 0.001), and CPT than the controls (46.20 ± 8.09 and 52.00 ± 3.56, t(78) = 4.145, p < 0.001). A significant regression equation was found: F (1,38) = 6.494, β = −0.382, p < 0.05 with an R² of 0.146. Conclusion Our findings suggest that adults with ADHD demonstrated social cognition difficulties and executive function deficits contributed to poor ToM abilities in ADHD.
Defatted Rice Bran Supplementation in Diets of Finishing Pigs: Effects on Physiological, Intestinal Barrier, and Oxidative Stress Parameters

Simple Summary Most studies on dietary fiber mainly focus on the digestibility of feed nutrients and microbial flora, etc. However, insufficient attention has been paid to the regulation of immune and oxidative stress of the intestinal tract by dietary fiber. This study investigated the effects of varying levels of defatted rice bran replacing corn on physiological, intestinal barrier, and oxidative stress parameters in finishing pigs. Based on the current findings, a high diet of rice bran will not only reduce the level of inflammatory factors in the peripheral blood of finishing pigs, but also enhance the healthy level of the colon through mucin2 and keap1-Nrf2 pathways. Our results can be used as reference for dietary rice bran to improve intestinal health in finishing pigs. Abstract Rice bran is a waste product with low cost and high fiber content, giving it an added advantage over corn and soybean meal, which have to be purchased and always at a relatively higher cost. Under the background of increased attention to sustainable agriculture, it is significant to find alternative uses for this byproduct. A total of 35 finishing pigs were allotted to five dietary treatments: a control group with basal diet and four experimental diets where corn was equivalently substituted by 7%, 14%, 21%, and 28% defatted rice bran (DFRB), respectively. With increasing levels of DFRB, the neutrophil to lymphocyte ratio (NLR) linearly decreased (p < 0.05). In the jejunum, the mRNA level of nuclear factor erythroid-2 related factor-2 (Nrf2) exhibited a quadratic response (p < 0.01) with incremental levels of DFRB. In the colon, the mRNA levels of mucin 2 (MUC2), Nrf2, and NAD(P)H: quinone oxidoreductase 1 (NQO1) were upregulated (linear, p < 0.05) and heme oxygenase-1 (HO-1) was upregulated (linear, p < 0.01). Overall, using DFRB to replace corn decreased the inflammatory biomarkers of serum and showed potential function in modulating the intestinal barrier by upregulating the mRNA expression levels of MUC2 and downregulating that of Nrf2, NQO1, and HO-1 in the colon.
Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems

The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and—among nitrifiers—unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations. ABSTRACT The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions. IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and—among nitrifiers—unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.