Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of husbandry systems and Chinese indigenous chicken strain on cecum microbial diversity

Objective This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions. Methods A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment. Results i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens. Conclusion The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.
Vicente´s poison frog (Oophaga vicentei) in the wild: calling activity, bioacoustics and diet

Calling activity, bioacoustics and the diet of males is reported for three different populations of Oophaga vicentei in central Panama. Calling activity was predicted by time of day, season and temperature with peaks between 08:00 h to 10:00 h and was more frequent during the dry season. Only at one location was calling activity positively correlated with air temperature. The temperature was also positively correlated with call repetition rates and negatively with call duration. Within the ten first calls of a call-bout, there was a cline variation in dominant frequency, call duration and silent intervals. The stomach contents of males comprised mainly insects but also a large number of oribatid mites.
Genotypic variations in the inhibitory potentials of four combined botanicals on mycelia growth of Macrophomina phaseolina of cowpea [Vigna unguiculata (L) Walp.]

The ethanol extracts of Ficus asperifolia, Mormordica charantia, Anacardium occidentals and Psidium guajava were evaluated sole and in treatment combinations at 25, 50 and 75mg ml concentration levels against the mycelial growth of Macrophomina phaseolina of Cowpea. The pathogen was cultured on plates containing botanicals amended Potato Dextrose Agar (PDA) in three replicates while only ethanol treated PDA tested plates served the control experiment. The radial growths were recorded at 4, 6 and 8 day after inoculation. Data obtained were analysed using the SAS software program version 9.2. The extract of Mormordica charantia was the most effective in the botanical treatments alone. The most significant inhibition of Macrophomina phaseolina were observed from the combined treatments of Ficus asperifolia, Mormordica charantia and Anacardium occidentals (3.11 cm), followed by Mormordica charantia and Psidium guajava (3.29 cm), then combination of four extracts; Ficus asperifolia, Mormordica charantia, Anacardium occidentals and Psidium guajava (3.53 cm), then Mormordica charantia and Anacardium occidentals (3.84 cm). Other treatments, either alone or in combination produced significant result compared to the control experiment (6.94 cm). However, the efficacy of botanicals increased with concentration and also significantly correlated with time and reduction in mycelia extension of the pathogen. More so, variability in the antifungicidal potentials of the botanicals on Macrophomina phaseolina ranges from 15.93% to 34.06% according to Eigen proportions. The treatment combinations of; Ficus asperifolia, Mormordica charantia and Anacardium occidentals at 75mg ml concentration level produced the most inhibitory effect against Macrophomina phaseolina in vitro. However, the untreated plates did not show inhibitory effect on the mycelial growth of the pathogen. Therefore, combined treatments of botanicals could be a potential source in the practise of plant disease control.
A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1

Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long distances, there were gaps of significant size that were stochastically distributed throughout the actin core. Actin crosslinkers were distributed through the stereocilium, but did not occupy all possible binding sites. At stereocilia tips, protein density extended beyond actin filaments, especially on the side of the tip where a tip link should anchor. Along the shaft, repeating density was observed that corresponds to actin-to-membrane connectors. In the taper region, most actin filaments terminated near the plasma membrane. The remaining filaments twisted together to make a tighter bundle than was present in the shaft region; the spacing between them decreased from 13 nm to 9 nm. Our models illustrate detailed features of distinct structural domains that are present within the stereocilium.
Gene-environment interactions using a Bayesian whole genome regression model

The contribution of gene-environment (GxE) interactions for many human traits and diseases is poorly characterised. We propose a method, LEMMA, that estimates an interpretable environmental score (ES) that interacts with genetic markers throughout the genome. When applied to body mass index, systolic, diastolic and pulse pressure in the UK Biobank we estimate that 9.3%, 3.9%, 1.6% and 12.5% of phenotypic variance is explained by GxE interactions, and that rare variants explain most of this variance. We also identify 3 loci that interact with the estimated environmental scores (−log10 p > 7).
Meta-analytic activation maps can help identify affective processes captured by contrast-based task fMRI: the case of threat-related facial expressions

Meta-analysis of functional magnetic resonance imaging (fMRI) data is an effective method for capturing the distributed patterns of brain activity supporting discrete cognitive and affective processes. One opportunity presented by the resulting meta-analysis maps (MAMs) is as a reference for better understanding the nature of individual contrast maps (ICMs) derived from specific task fMRI data. Here, we compared MAMs from 148 neuroimaging studies representing the broad emotion categories of fear, anger, disgust, happiness, and sadness with ICMs from fearful > neutral and angry > neutral facial expressions from an independent dataset of task fMRI (n = 1263). Analyses revealed that both fear and anger ICMs exhibited the greatest pattern similarity to fear MAMs. As the number of voxels included for the computation of pattern similarity became more selective, the specificity of MAM-ICM correspondence decreased. Notably, amygdala activity long considered critical for processing threat-related facial expressions was neither sufficient nor necessary for detecting MAM-ICM pattern similarity effects. Our analyses suggest that both fearful and angry facial expressions are best captured by distributed patterns of brain activity associated with fear. More generally, our analyses demonstrate how MAMs can be leveraged to better understand affective processes captured by ICMs in task fMRI data.
Identification, mechanisms and treatment of perinatal brain injury

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Examining the Sustainability of Tropical Island Forests: Advances and Challenges in Measurement, Monitoring, and Reporting in the U.S. Caribbean and Pacific

Forests across the U.S. and U.S. affiliated islands of the Caribbean and Pacific constitute rich and dynamic social-ecological systems that, while heterogeneous in many ways, share certain characteristics and trends that underscore the utility of sustainability assessments that go beyond single jurisdictional efforts. This paper summarizes a recent effort to assess the sustainability of tropical island forests of and politically affiliated with the U.S. using the Montréal Process criteria and indicator framework (MP C&I), which address ecological, social, economic, and institutional dimensions of forests. Forests cover 45 percent of the total area and more than 50 percent of each island jurisdiction, except Hawaii (36 percent). Forest cover is generally stable over much of the area in terms of recent reference conditions. The history of human occupation and land alteration is a prominent determinant of current conditions throughout the islands, which exhibit relatively high rates of threatened species in comparison to mainland counterparts and particularly where endemism is high. The islands also harbor significant areas of new or novel assemblages of native and non-native forest species, predominately on abandoned agricultural lands cleared of native forests long ago, which have been shown to contribute to the restoration of these degraded lands and provide many other ecosystem services at levels as high as and in some cases higher than native forests. Although industrial-level commercial timber harvest is small to nonexistent on most islands, socioeconomic and cultural linkages to forests are extensive but difficult to quantify. Amassing a foundation of data sufficient to address the MP C&I was challenging, in part due to the heterogeneity of the islands, island geography, and limited reporting capacities. We document significant improvements in the availability of data important for sustainability assessments in the last decade or so, especially with the extension of the U.S. Department of Agriculture Forest Service Forest Inventory and Analysis program to the islands. Likewise, we find the MP C&I to be a useful tool for organizing and presenting information important for assessing forest sustainability. Nevertheless, considerable data gaps remain in the areas of biodiversity, forest functions and processes, and socioeconomic conditions of forests, which are critical elements to track across the islands, particularly in the context of climate change and ongoing anthropogenic pressures.
Improving secondary metabolite accumulation, mineral content, and growth of coriander (Coriandrum sativum L.) by regulating light quality in a plant factory

ABSTRACT A plant factory with artificial lighting is an advanced indoor cultivation system that has been being developed rapidly for producing high-quality vegetables in many countries. Coriander is an important herbal vegetable and contains abundant secondary metabolites, vitamins, and minerals, which are essential for human health. Five different light qualities, red (R), blue (B), green (G), red:blue (RB, ratio of 87:13), and red:blue:far-red (RBFr, ratio of 81.5:12.5:6) were applied to identify the optimal light quality for enhancing the growth and accumulation of minerals and bioactive metabolites in coriander. Results showed that biomass, chlorophyll index, and ascorbic acid content of coriander plants were significantly higher in RB or RBFr light treatments than in other light treatments. The antioxidant capacity and total phenolic content were the highest under B light. The total phenolic content per plant was the highest under RBFr light due to the high growth rate and biomass production of the plants. Besides, tipburn occurrence in coriander was not affected by total Ca content in the shoot. RBFr was found to be the optimal light spectrum for producing coriander with high yield and contents of ascorbic acid, total phenolics, Ca, and P in a plant factory.
INADVERTENT TREATMENT WITH A PURE IKR BLOCKER IN LQT2 SYNDROME

Long QT syndrome (LQTS) results from structural abnormalities in the potassium channels of the heart, which predispose affected persons to an accelerated heart rhythm (arrhythmia). Nifekalant, a new class III antiarrhythmic agent developed in US, blocks selectively a rapidly-activating component of the delayed rectifier potassium channel (IKr) in cardiac myocytes, and causes dose-dependent increase in artrial and ventricular refractory periods and repolarization. We report a case of congenital long QT syndrome (LQTS) with recurrent ventricular fibrillation inadvertently treated with intravenous nifekalant. Treatment neither modified the rate-corrected QT interval nor induced torsades de points. Subsequent genotyping of the patient revealed a missense mutation in the extracellular loop between S5 and the pore region of HERG (K595E). Since HERG encodes the IKr channel, LQT2 patient may be more tolerant of pure IKr blockers than other LQTS genotypes.
Regulation of chalcone synthase gene expression in wild-type and mutant Arabidopsis

The regulation of chalcone synthase (CHS) gene expression in Arabidopsis thaliana plants was investigated, icxl {increased chalcone synthase egression, Jackson et al.,1995, Plant J. 8; 369-380), a mutant altered in the light regulation of CHS expression, was studied in detail. Mature icxl leaf tissue was found to have increased CHS expression compared to that of wild type plants in UVA /b lue, UV-A and UV-B light. Dark grown icxl seedlings displayed an increase in CHS expression in the above light qualities and also in far red light. These results indicate that ICXl acts as a negative regulator downstream of phytochrome, cryptochrome and UV-B photoreceptors and in both mature leaves and seedlings. The synergistic effect of UV-B plus blue light or UV-B plus UV-A light on CHS expression is not altered in the icxl mutant. A model is presented to explain the position of ICXl in relation to the inductive and synergistic pathways. Genetic analysis shows that hy5 is epistatic to icxl and it is proposed that the HY5 transcription factor functions downstream of ICXl in the light signalling pathway. In addition, the cold induction of CHS is increased in icxl. Therefore ICXl also regulates a non-light signalling pathway, icxl has increased expression of other genes involved in flavonoid biosynthesis, encoding dihydroflavonol reductase and chalcone isomerase. The ICXl gene product does not affect the light regulation of CAB and rbcS genes which are expressed in mesophyll cells. It is proposed that ICXl acts principally in the epidermis. The induction of CHS expression by UV light was found to be regulated by phytochrom e. W hen m utant plants lacking phytochrom e B or both phytochrome B and phytochrome A, were exposed to UV-A light, the resultant CHS expression was lower than that seen in the wild type plants.A red light exposure given to wild type plants prior to UV-A illumination resulted in an increase in CHS expression. In the phyA phyB double m utant the overall induction of CHS was reduced but the increase in CHS expression in red
Isolated classic Kaposi Sarcoma in an old female patient

Kaposi sarcoma (KS) is an angio-proliferative disorder and classified in terms of four clearly differentiated variants. Classic variant is an uncommon disease that it has an overwhelming male predominance and majority of cases patients are positive for HIV infections. We present HIV-negative female patient presenting multiple nodules on palmar and dorsal aspect of right wrist. Considering the male predominance of classic KS and positivity of HIV infections in majority of KS cases the patient presented to contribute to the literature.
Mean body weight gains in standard mink depending on the number of kits in a litter

Mean body weight gains in standard mink depending on the number of kits in a litter. The objective of the study is to determine the effect of litter size from which animals came on their weight at weaning and pre-slaughter, and as a consequence also on their mean daily gains. The study was conducted on a population of 330 minks, divided into groups depending on the size of litter from which they came: I (2–4 kits) – 74 animals (44 ♂, 30 ♀), II (5–7 kits) – 170 animals (92 ♂, 78 ♀), III (8–10 kits) – 86 animals (44 ♂, 42 ♀). We established a signifi cant effect of litter size on body weight at weaning and mean daily gains. Animals from smaller litters were found to have a higher body weight at weaning; whereas higher gains were observed in animals coming from bigger litters. Pre-slaughter body weight was similar in all assessed groups.
BACH: A randomized phase II trial of doxorubicin-cyclophosphamide (AC) versus pegylated liposomal doxorubicin (PLD)-cyclophosphamide-trastuzumab (CCH) followed by paclitaxel-trastuzumab (TH) as adjuvant therapy for HER2-positive breast cancer (BC)--Cardiac safety analysis.

559 Background: For patients (pts) with HER2+ BC, concurrent AC-H results in unacceptable cardiotoxicity rates. Substituting PLD for A in an adjuvant regimen may minimize cardiotoxic risk and permit earlier integration of adjuvant H. Methods: Inthis randomized phase II trial, pts with resected lymph node+ or high-risk, node-negative HER2+ BC were stratified by age and randomized (1:2) to: Arm A: AC (60/600 mg/m2 q21d × 4) followed by T 80 mg/m2 + H 2 mg/kg qwk × 12 or Arm B: PLD 35 mg/m2 + C 600 mg/m2 q21d × 4 + H 2 mg/kg/wk × 12, followed by T 80 mg/m2 + H 2 mg/kg qwk × 12. Subsequent H for a total of 1y was given as per institutional standards. Primary objective was incidence of level 1 (cardiac death or severe heart failure with left ventricular ejection fraction [LVEF] drop > 10% to 10% to < 50%) cardiac event rates during the 8 cycles of chemotherapy (CT). This analysis reports cardiotoxicity for the entire patient population comple.
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set

RNA molecules play many pivotal roles in the cellular functioning that are still not fully understood. Any detailed understanding of RNA function requires knowledge of its three-dimensional structure, yet experimental RNA structure resolution remains demanding. Recent advances in sequencing provide unprecedented amounts of sequence data that can be statistically analysed by methods such as Direct Coupling Analysis (DCA) to determine spatial proximity or contacts of specific nucleic acid pairs, which improve the quality of structure prediction. To quantify this structure prediction improvement, we here present a well curated dataset of about seventy RNA structures with high resolution and compare different nucleotide-nucleotide contact prediction methods available in the literature. We observe only minor difference between the performances of the different methods. Moreover, we discuss how these predictions are robust for different contact definitions and how strongly depend on procedures used to curate and align the families of homologous RNA sequences.
Virulence markers, phylogenetic evolution, and molecular techniques of uropathogenic Escherichia coli

Urinary tract infections are very significant public health concerns globally with most of them being caused by uropathogenic Escherichia coli (UPEC). The wide range of genetic makeup of UPEC due to the acquisition of specialized virulence genes located on mobile genetic elements called pathogenicity islands is the rationale behind colonization of the urinary tracts of humans as against diarrheagenic E. coli pathotype. Indebt understanding of the virulence mechanisms and pathogenesis of UPEC lies in the knowledge of the molecular techniques of UPEC which have advanced tremendously. This review has carefully summarized the unique virulence markers, the phylogenetic evolution, and molecular techniques used in the studies of pathogenesis and virulence of UPEC.
The postmortem microbiome and gene expression in vertebrates

In life, most internal organs of a healthy adult vertebrate are essentially ‘microbial-cell-free’ – but in death, microorganisms invade and proliferate these internal organs and genes are expressed by the host presumably in response. We recently investigated how these two interconnected processes change with postmortem time and examined the feasibility of using this information to determine the postmortem interval, i.e. the elapsed-time-since-death. Although more research is needed, our findings suggest one of them has a significant potential to determine the length of time from the person dying until discovery of the body.
Reconstruction of the disturbance history of a temperate coniferous forest through stand-level analysis of airborne LiDAR data

Spatially explicit information about stand-level Time Since the last stand-replacing Disturbance (TSD) is fundamental for modelling many forest ecosystem processes, but most of the current satellite remote sensing mapping approaches are based on change detection and time series analysis, and can detect only disturbances that have occurred since the start of the optical satellite data record. The spatial legacy of stand-replacing disturbances can however persist on the landscape for several decades to centuries, in the form of distinct horizontal and vertical stand structure features. We propose a new approach to reconstruct the long-term disturbance history of a forest, estimating TSD through stand-level analysis of LiDAR data, which are highly sensitive to the three-dimensional forest canopy structure. The study area is in the Nez Perce-Clearwater National Forest in north-central Idaho, where airborne LiDAR covering about 52,000 ha and ancillary TSD reference data for a period of more than 140 years were available. The root mean square difference (RSMD) between predicted and reference TSD was 17.5 years with a BIAS of 0.8 years; and on 72.8% of the stands the predicted TSD was less than 10 years apart from the reference TSD (78.2% of the stands when considering only disturbances occurred in the last 100 years). The results demonstrate that airborne LiDAR-derived data have enough explanatory power to reconstruct the long-term, stand-replacing disturbance history of temperate forested areas at regional scales.