Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Distinctiveness and Status of the Endangered Lake Eacham Rainbowfish (Melanotaenia eachamensis)

The Lake Eacham rainbowfish (Melanotaenia eachamensis) was declared extinct in the wild in the late 1980s after it disappeared from its only known locality, an isolated crater lake in northeast Queensland. Doubts have been raised about whether this taxon is distinct from surrounding populations of the eastern rainbowfish (Melanotaenia splendida splendida). We examined the evolutionary distinctiveness of M. eachamensis, obtained from captive stocks, relative to M. s. splendida through analysis of variation in mtDNA sequences, nuclear microsatellites, and morphometric characters. Captive M. eachamensis had mtDNAs that were highly divergent from those in most populations of M. s. splendida. A broader geographic survey using RFLPs revealed some populations, initially identified as M. s. splendida, that carried eachamensis mtDNA, whereas some others had mixtures of eachamensis and splendida mtDNA. The presence of eachamensis‐like mtDNA in these populations could in principle be due to (1) sorting of ancestral polymorphisms, (2) introgression of M. eachamensis mtDNA into M. s. splendida, or (3) incorrect species boundaries, such that some populations currently assigned to M. s. splendida are M. eachamensis or are mixtures of the two species. These alternative hypotheses were evaluated through comparisons of four nuclear microsatellite loci and morphometrics and meristics. In analyses of both data sets, populations of M. s. splendida with eachamensis mtDNA were more similar to captive M. eachamensis than to M. s. splendida with splendida mtDNA, supporting hypothesis 3. These results are significant for the management of M. eachamensis in several respects. First, the combined molecular and morphological evidence indicates that M. eachamensis is a distinct species and a discrete evolutionarily significant unit worthy of conservation effort. Second, it appears that the species boundary between M. eachamensis and M. s. splendida has been misdiagnosed, such that there are extant populations on the Atherton Tableland as well as areas where both forms coexist. Accordingly, we suggest that M. eachamensis be listed as vulnerable, rather than critical (or extinct in the wild). Third, the discovery of extant but genetically divergent populations of M. eachamensis on the Atherton Tableland broadens the options for future reintroductions to Lake Eacham.
Genetic susceptibility, plant-based dietary patterns, and risk of cardiovascular disease.

BACKGROUND Plant-based dietary patterns may be related to better cardiovascular profiles. Whether a healthy plant-based dietary index is predictive of future cardiovascular disease (CVD) across people with different genetic susceptibility remains uncertain. OBJECTIVE We investigated associations of adherence to healthy plant-based diets with the incidence of CVD considering the genetic susceptibility. METHODS This prospective cohort study included a total of 156,148 adults initially free of CVD and cancer. We calculated a healthful plant-based diet index (healthful-PDI) in which healthy plant foods received positive scores, and less healthy plant foods and animal foods received reverse scores. Genetic risk scores (GRSs) for myocardial infarction (MI) and stroke were calculated to assess interactions between healthful-PDI and GRSs. RESULTS During 5 y of follow-up, we observed 1812 incident cases of CVD. Higher healthful-PDI was associated with a lower CVD risk [HR per 10-unit increment: 0.87 (95% CI: 0.81, 0.93) after adjusting for demographic, lifestyle, and other dietary factors (model 1); HR 0.90 (0.84, 0.97) after further adjusting for obesity and metabolic factors (model 2)]. The risk of CVD was gradually decreased in association with higher adherence to healthful-PDI, regardless of genetic susceptibility. The inverse associations of healthful-PDI with CVD were consistently observed in people with low GRS-MI [HR 0.85 (95% CI: 0.76, 0.94) in model 1; HR 0.88 (0.79, 0.97) in model 2] and those with high GRS-MI [HR 0.91 (0.82, 0.99) in model 1; HR 0.94 (0.86, 1.04) in model 2], without significant interactions (Pinteraction = 0.59 in model 1; Pinteraction = 0.66 in model 2). Similarly, higher healthful-PDI was related to a lower risk of CVD, regardless of low/high GRS-stroke. CONCLUSION Adherence to healthy plant-based diets may be associated with a decreased incidence of CVD in the entire population, suggesting that plant-based dietary patterns may modify the risk of CVD, regardless of genetic susceptibility.
High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution

The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.
Alphatorquevirus is the most prevalent virus identified in blood from a matched maternal-infant preterm cohort

Abstract Objective To determine the prevalence of virus in a previously uncharacterized matched maternal-infant preterm cohort and test if viral presence or viral load correlate with histologic chorioamnionitis, spontaneous preterm labor or pre-eclampsia. Study Design Using qRT-PCR/qPCR we tested plasma or whole blood samples from 56 matched maternal and premature infant dyads for: adenovirus, anellovirus (alphatorquevirus and betatorquevirus), cytomegalovirus (CMV), Epstein-Barr virus (EBV), enterovirus, human herpesvirus 6 (HHV6), parechovirus, and parvovirus B19. Result Viral detection was more common in maternal samples 29/56 (52%) than in cord blood from their infants (4/56 (7%)) (p ≤ .0001). No significant difference in viral load or viral prevalence was identified between pregnancies with and without histologic chorioamnionitis, spontaneous preterm labor or pre-eclampsia. Conclusion Despite frequent detection of virus in maternal samples, virus was less frequently detected in the infants. Additionally, there was no association of presence or quantity of virus in maternal blood with histologic chorioamnionitis, spontaneous preterm labor or pre-eclampsia in this small, but well-defined cohort. Future studies are necessary to further characterize the role of virus in placental inflammatory states and pregnancy outcomes.
Effects of Light, Temperature and Osmotic Stress on Seed Germination of Eucalyptus occidentalis Endl

Seed germination of E. occidentalis was examined under different combinations of light, temperature and osmotic potential. The effects of all three factors were found to be interrelated. Germination rates are directly related to the temperature of the environment between 15 and 30°C and to the osmotic potentials of the medium between -9.1 and 0 bars. The relative require- ment for light, i.e. the ratio of light germination to dark germination, increases with the rise in temperature. Light is a decisive factor in improving germination under osmotic stress; its effect is directly related to the intensity of stress. In media with an osmotic potential of -9.1 bars, the effect of light on germination is directly related to temperature. Optimum germination occurs at 30" under continuous light and under no osmotic styes. Very low germination is obtained under the same temperature in the absence of light and in a medium with an osmotic potential of -9.1 bars. Inhibition of germination caused by osmotic stress is 2-3 times as great as that caused by dark stress. Seed germination was found to vary according to an annual rhythm. Lower rates of germination were obtained in July and January, whereas maximum germination occurred from March to May.
Amylopectin Staling of Cooked Milled Rices and Properties of Amylopectin and Amylose

ABSTRACT Starches of waxy rices that showed varietal differences in hardness testing of cooked rice after amylopectin staling and high-amylose content (AC) rices differing in gel consistency (GC) and starch gelatinization temperature (GT) were studied to determine the factors related to varietal differences in amylopectin staling of cooked rice. Intermediate- and high-GT starches showed greater amylopectin staling of gelatinized rice by hardness testing values or differential scanning calorimetry (DSC) endotherm than did low-GT starches in both waxy and nonwaxy rices. Isoamylase-debranched amylopectins of waxy rices differed in the ratio of weight-average degree of polymerization (DPw) fractions, but these fraction ratios were not simply related to differences in amylopectin staling of cooked rice. Among high-AC rices, amylopectin from low-GT starch was confirmed to have higher iodine affinity (2.3–2.5%) than amylopectin from intermediate-GT starches (1.7–1.8%), regardless of GC. Within high-AC starch of .
The Six Isomers of the Cyclohexanol Dimer: A Delicate Test for Dispersion Models.

The cyclohexanol homodimer is a delicate test model of the role of dispersion forces in intermolecular association. While phenol produces a single dimer, suppression of π interactions and larger conformational flexibility in cyclohexanol results in multiple isomerism, as six competing dimers of the free molecule are observed in a supersonic jet expansion. Rotational spectroscopy reveals accurate structural data, specifically the formation of homo- and heterochiral diasteroisomers and the presence of both equatorial and axial forms in the dimers. Four dispersion-corrected density-functional molecular orbital calculations were tested against the experiment, with B3LYP-D3(BJ) offering good structural reproducibility with an Alrich's triple-ζ basis set. However, the prediction of the dimer energetics is largely model-dependent, offering a testbed for validation of dispersion-corrected computational models.
Maternal glyphosate exposure causes autism-like behaviors in offspring through increased expression of soluble epoxide hydrolase

Significance Maternal exposure to high levels of the herbicide glyphosate may increase the risk for autism spectrum disorder (ASD) in offspring; however, the underlying mechanisms remain largely unknown. Maternal glyphosate exposure during pregnancy and lactation caused ASD-like behavioral abnormalities and abnormal composition of gut microbiota in murine male offspring. Soluble epoxide hydrolase (sEH) in the brain of offspring after maternal glyphosate exposure was higher than controls. Treatment with an sEH inhibitor from pregnancy to weaning prevented the onset of ASD-like behavioral abnormalities in offspring after maternal glyphosate exposure. The glyphosate exposures used here exceed any reasonable dietary, environmental, or occupational exposure, but they indicate that increased sEH plays a role in ASD-like behaviors in offspring. Epidemiological studies suggest that exposure to herbicides during pregnancy might increase risk for autism spectrum disorder (ASD) in offspring. However, the precise mechanisms underlying the risk of ASD by herbicides such as glyphosate remain unclear. Soluble epoxide hydrolase (sEH) in the metabolism of polyunsaturated fatty acids is shown to play a key role in the development of ASD in offspring after maternal immune activation. Here, we found ASD-like behavioral abnormalities in juvenile offspring after maternal exposure to high levels of formulated glyphosate. Furthermore, we found higher levels of sEH in the prefrontal cortex (PFC), hippocampus, and striatum of juvenile offspring, and oxylipin analysis showed decreased levels of epoxy-fatty acids such as 8 (9)-EpETrE in the blood, PFC, hippocampus, and striatum of juvenile offspring after maternal glyphosate exposure, supporting increased activity of sEH in the offspring. Moreover, we found abnormal composition of gut microbiota and short-chain fatty acids in fecal samples of juvenile offspring after maternal glyphosate exposure. Interestingly, oral administration of TPPU (an sEH inhibitor) to pregnant mothers from E5 to P21 prevented ASD-like behaviors such as social interaction deficits and increased grooming time in the juvenile offspring after maternal glyphosate exposure. These findings suggest that maternal exposure to high levels of glyphosate causes ASD-like behavioral abnormalities and abnormal composition of gut microbiota in juvenile offspring, and that increased activity of sEH might play a role in ASD-like behaviors in offspring after maternal glyphosate exposure. Therefore, sEH may represent a target for ASD in offspring after maternal stress from occupational exposure to contaminants.
Pan-Genomic Analysis of Clostridium botulinum Group II (Non-Proteolytic C. botulinum) Associated with Foodborne Botulism and Isolated from the Environment

The neurotoxin formed by Clostridium botulinum Group II is a major cause of foodborne botulism, a deadly intoxication. This study aims to understand the genetic diversity and spread of C. botulinum Group II strains and their neurotoxin genes. A comparative genomic study has been conducted with 208 highly diverse C. botulinum Group II strains (180 newly sequenced strains isolated from 16 countries over 80 years, 28 sequences from Genbank). Strains possessed a single type B, E, or F neurotoxin gene or were closely related strains with no neurotoxin gene. Botulinum neurotoxin subtype variants (including novel variants) with a unique amino acid sequence were identified. Core genome single-nucleotide polymorphism (SNP) analysis identified two major lineages—one with type E strains, and the second dominated by subtype B4 strains with subtype F6 strains. This study revealed novel details of population structure/diversity and established relationships between whole-genome lineage, botulinum neurotoxin subtype variant, association with foodborne botulism, epidemiology, and geographical source. Additionally, the genome sequences represent a valuable resource for the research community (e.g., understanding evolution of C. botulinum and its neurotoxin genes, dissecting key aspects of C. botulinum Group II biology). This may contribute to improved risk assessments and the prevention of foodborne botulism.
Adjuvant chemotherapy in rectal cancer: state of the art and future perspectives.

PURPOSE OF REVIEW The value of adjuvant chemotherapy in rectal cancer is controversial with opinions varying from 'not be used' since randomized trials have not shown significant gains to 'be used as in colon cancer' as the need is the same and colon and rectal cancers are quite similar. This review will look upon data critically and with open eyes. RECENT FINDINGS With the exception of one randomized phase II trial (ADORE) revealing a significant gain in disease-free survival using one more effective regimen (mFOLFOX) than bolus 5-fluorouracil leucovorin, no new data have been presented. However, bringing up aspects in previous trials, either considered irrelevant for the present situation or overall negative, of what adjuvant treatment can achieve, a small reduction (hazard ratio about 0.8) in the risk of recurrence is present. This reduction is not fundamentally different from that in colon cancer considering that adjuvant treatment for rectal cancer cannot be initiated as rapidly as it can after a colon cancer diagnosis. SUMMARY Adjuvant chemotherapy after rectal cancer surgery reduces recurrence risks but the benefit is limited and for most patients not clinically relevant. Neoadjuvant therapy can be more effective but results from randomized trials are not yet available.
Oxidative Stress and BPA Toxicity: An Antioxidant Approach for Male and Female Reproductive Dysfunction

Bisphenol A (BPA) is a non-persistent anthropic and environmentally ubiquitous compound widely employed and detected in many consumer products and food items; thus, human exposure is prolonged. Over the last ten years, many studies have examined the underlying molecular mechanisms of BPA toxicity and revealed links among BPA-induced oxidative stress, male and female reproductive defects, and human disease. Because of its hormone-like feature, BPA shows tissue effects on specific hormone receptors in target cells, triggering noxious cellular responses associated with oxidative stress and inflammation. As a metabolic and endocrine disruptor, BPA impairs redox homeostasis via the increase of oxidative mediators and the reduction of antioxidant enzymes, causing mitochondrial dysfunction, alteration in cell signaling pathways, and induction of apoptosis. This review aims to examine the scenery of the current BPA literature on understanding how the induction of oxidative stress can be considered the “fil rouge” of BPA’s toxic mechanisms of action with pleiotropic outcomes on reproduction. Here, we focus on the protective effects of five classes of antioxidants—vitamins and co-factors, natural products (herbals and phytochemicals), melatonin, selenium, and methyl donors (used alone or in combination)—that have been found useful to counteract BPA toxicity in male and female reproductive functions.
Tensile Properties of Composite Reinforced with Three-Dimensional Printed Fibers

This study used melt-electrospinning writing to fabricate three-dimensional fiber constructs by embedding them in a polyvinyl alcohol (PVA) matrix to obtain thin composite films. Fourier transform infrared spectroscopy (FTIR) and dynamic scanning calorimetry (DSC) were used to demonstrate an interaction between the polycaprolactone (PCL) fibrous phase and the PVA matrix phase. Following this, the mechanical deformation behavior of the composite was investigated, and the effect of reinforcement with three-dimensional fibrous constructs was illustrated. The specific strength of the composite was found to be five times higher than the specific strength of the neat PVA matrix. Additionally, the specific toughness of the composite was determined to be roughly four times higher than the specific toughness determined for the neat PVA matrix. These results demonstrate the potential of using melt-electrospinning writing for producing three-dimensional fibrous constructs for composite reinforcement purposes.
Intraventricular Hemorrhage Clearance in Human Neonatal Cerebrospinal Fluid

Supplemental Digital Content is available in the text. Background and Purpose— Preterm neonates with intraventricular hemorrhage (IVH) are at risk for posthemorrhagic hydrocephalus and poor neurological outcomes. Iron has been implicated in ventriculomegaly, hippocampal injury, and poor outcomes following IVH. We hypothesized that levels of cerebrospinal fluid blood breakdown products and endogenous iron clearance proteins in neonates with IVH differ from those of neonates with IVH who subsequently develop posthemorrhagic hydrocephalus. Methods— Premature neonates with an estimated gestational age at birth <30 weeks who underwent lumbar puncture for clinical evaluation an average of 2 weeks after birth were evaluated. Groups consisted of controls (n=16), low-grade IVH (grades I–II; n=4), high-grade IVH (grades III–IV; n=6), and posthemorrhagic hydrocephalus (n=9). Control subjects were preterm neonates born at <30 weeks’ gestation without brain abnormality or hemorrhage on cranial ultrasound, who underwent lumbar puncture for clinical purposes. Cerebrospinal fluid hemoglobin, total bilirubin, total iron, ferritin, ceruloplasmin, transferrin, haptoglobin, and hemopexin were quantified. Results— Cerebrospinal fluid hemoglobin levels were increased in posthemorrhagic hydrocephalus compared with high-grade IVH (9.45 versus 6.06 µg/mL, P<0.05) and cerebrospinal fluid ferritin levels were increased in posthemorrhagic hydrocephalus compared with controls (511.33 versus 67.08, P<0.01). No significant group differences existed for the other cerebrospinal fluid blood breakdown and iron-handling proteins tested. We observed positive correlations between ventricular enlargement (frontal occipital horn ratio) and ferritin (Pearson r=0.67), hemoglobin (Pearson r=0.68), and total bilirubin (Pearson r=0.69). Conclusions— Neonates with posthemorrhagic hydrocephalus had significantly higher levels of hemoglobin than those with high-grade IVH. Levels of blood breakdown products, hemoglobin, ferritin, and bilirubin correlated with ventricular size. There was no elevation of several iron-scavenging proteins in cerebrospinal fluid in neonates with posthemorrhagic hydrocpehalus, indicative of posthemorrhagic hydrocephalus as a disease state occurring when endogenous iron clearance mechanisms are overwhelmed.
Nomogram to predict the risk of septic acute kidney injury in the first 24 h of admission: an analysis of intensive care unit data

Abstract Background Acute kidney injury (AKI) is a significant cause of morbidity and mortality, especially in sepsis patients. Early prediction of AKI can help physicians determine the appropriate intervention, and thus, improve the outcome. This study aimed to develop a nomogram to predict the risk of AKI in sepsis patients (S-AKI) in the initial 24 h following admission. Methods Sepsis patients with AKI who met the Sepsis 3.0 criteria and Kidney Disease: Improving Global Outcomes criteria in the Massachusetts Institute of Technology critical care database, Medical Information Mart for Intensive Care (MIMIC-III), were identified for analysis. Data were analyzed using multiple logistic regression, and the performance of the proposed nomogram was evaluated based on Harrell’s concordance index (C-index) and the area under the receiver operating characteristic curve. Results We included 2917 patients in the analysis; 1167 of 2042 patients (57.14%) and 469 of 875 patients (53.6%) had AKI in the training and validation cohorts, respectively. The predictive factors identified by multivariate logistic regression were blood urea nitrogen level, infusion volume, lactate level, weight, blood chloride level, body temperature, and age. With the incorporation of these factors, our model had well-fitted calibration curves and achieved good C-indexes of 0.80 [95% confidence interval (CI): 0.78–0.82] and 0.79 (95% CI: 0.76–0.82) in predicting S-AKI in the training and validation cohorts, respectively. Conclusion The proposed nomogram effectively predicted AKI risk in sepsis patients admitted to the intensive care unit in the first 24 h.