Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of region-specific glial homeostatic signature in prion diseases

Background Chronic neuroinflammation is recognized as a major neuropathological hallmark in a broad spectrum of neurodegenerative diseases including Alzheimer’s, Parkinson’s, Frontal Temporal Dementia, Amyotrophic Lateral Sclerosis, and prion diseases. Both microglia and astrocytes exhibit region-specific homeostatic transcriptional identities, which under chronic neurodegeneration, transform into reactive phenotypes in a region- and disease-specific manner. Little is known about region-specific identity of glia in prion diseases. The current study was designed to determine whether the region-specific homeostatic signature of glia changes with the progression of prion diseases, and whether these changes occur in a region-dependent or universal manner. Also of interest was whether different prion strains give rise to different reactive phenotypes. Methods To answer these questions, we analyzed gene expression in thalamus, cortex, hypothalamus and hippocampus of mice infected with 22L and ME7 prion strains using Nanostring Neuroinflammation panel at subclinical, early clinical and advanced stages of the disease. Results We found that at the preclinical stage of the disease, region-specific homeostatic identities were preserved. However, with the appearance of clinical signs, region-specific signatures were partially lost and replaced with a neuroinflammation signature. While the same sets of genes were activated by both prion strains, the timing of neuroinflammation and the degree of activation in different brain regions was strain-specific. Changes in astrocyte function scored at the top of activated pathways. Moreover, clustering analysis suggested that the astrocyte function pathway responded to prion infection prior to activated microglia or neuron and neurotransmission pathways. Conclusions The current work established neuroinflammation gene expression signature associated with prion diseases. Our results illustrate that with the disease progression, the region-specific homeostatic transcriptome signatures are replaced by region-independent neuroinflammation signature, which was common for prion strains with different cell tropism. The prion-associated neuroinflammation signature identified in the current study overlapped only partially with the microglia degenerative phenotype and the disease-associated microglia phenotype reported for animal models of other neurodegenerative diseases.
A dual functioning small RNA/Riboswitch controls the expression of the methionine biosynthesis regulator SahR in Desulfovibrio vulgaris Hildenborough

Riboswitches are cis-acting RNA regulatory elements that control expression of a downstream gene(s) by directly binding to a specific metabolite. Here we report a S-adenosylmethionine (SAM)-I riboswitch in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that plays an additional regulatory role as a trans small noncoding RNA (sRNA) targeting the methionine biosynthesis cycle transcriptional regulator SahR. Sequence and expression analyses indicated that DseA (Desulfovibrio SAM element A) is located upstream of a small hypothetical protein DVU1170 and that the two are co-transcribed. Multiple techniques were used to verify the riboswitch activity of DseA and its activity as a transcriptional terminator in response to SAM. While determining a potential role for DseA in the methionine biosynthesis pathway, a mRNA target encoding SahR was identified. Subsequent electrophoretic mobility shift assays confirmed the ability of DseA to bind the sahR transcript and qRT-PCR analysis of a DseA deletion strain suggested a negative regulatory role. This study presents the first regulatory role for a newly discovered sRNA in Desulfovibrio. Additionally, this study suggests that DseA acts not only as a riboswitch, but also as a trans regulatory molecule. IMPORTANCE Sulfate-reducing bacteria (SRB) are important contributors to global geochemical cycles while also causing major issues for the petroleum and oil industry due to biocorrosion and souring of oil wells. Despite their significance, gene regulatory networks and pathways remain poorly understood in SRB. Here, we report a trans acting small noncoding RNA that plays a dual role as a SAM sensing riboswitch that controls the expression of a small hypothetical protein. Our findings provide important insights into the regulatory repertoire of sulfate-reducing bacteria.
The complete chloroplast genome of Cerasus dictyoneura, an ornamental plant of China

Abstract The complete cp genome of Cerasus dictyoneura was 158,084 bp in length, consisting of a LSC of 86,275 bp and a SSC of 19,039 bp, which were separated by a pair of 26,385 bp IRs. The genome contained 131 genes, including 86 proteincoding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.6, 29.5, and 42.6%, respectively. Furthermore, phylogenetic analysis based on 16 complete cp genome sequences indicated that C. dictyoneura is within Eurosids I.
The Main Points and Principles of Isolating Total RNA from Ligneous Plant TIssues

According to the knowledge and experiences acquired in isolating total RNA from ligneous plant tissues, the authors probe in and discussed the problems that often occur in isolating total RNA from ligneous plant tissues, such as low RNA out-put, RNA degrading, the interference of hydroxybenzens, DNA, amylose, protein and other impurities, then bring forward the resolvable ways of these problems in particular. Meanwhile, sort the RNA isolating ways in common use into some categories, and also discusses their principles and evaluate their strongpoints and inferiors.
Another chemolithotrophic metabolism missing in nature—sulfur comproportionation

Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation-reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy (ΔGr) can identify whether a reaction is thermodynamically favorable, and the accompanying energy yield at the temperature, pressure, and chemical composition in the system of interest. Based on carefully calculated values of ΔGr, we predict a novel microbial metabolism—sulfur comproportionation (3H2S + SO42- + 2H+ = 4S0 + 4H2O). We show that at elevated concentrations of sulfide and sulfate in acidic environments over a broad temperature range, this putative metabolism can be exergonic (ΔGr<0), yielding ∼30-50 kJ/mol. We suggest that this may be sufficient energy to support a chemolithotrophic metabolism currently missing in nature. Other versions of this metabolism, to thiosulfate (H2S + SO42- = S2O32- + H2O) and to sulfite (H2S + 3SO42- = 4SO32- + 2H+), are only moderately exergonic or endergonic even at ideal geochemical conditions. Natural and impacted environments, including sulfidic karst systems, shallow-sea hydrothermal vents, sites of acid mine drainage, and acid-sulfate crater lakes, may be ideal hunting grounds for finding microbial sulfur comproportionators.
Feather Pecking of Laying Hens in Different Stocking Density and Type of Cage

Both stocking rate and housing systems are main factors influencing the occurrence of feather pecking in laying hens raised in conventional cage system. This study examines the effects of different type of cage and stock density on feather pecking behaviour in hens. Total of 216 Hisex Brown hens at 16 weeks of age were randomly selected and put into 2 types of battery cages: conventional cages and modified cages fitted with perch. Each groups comprised 3 subgroups: 2 hens per cage (943 cm2/hens), 3 hens per cage (627.7 cm2/hens), and 4 hens per cage (417.5 cm2/hens). The feather pecking behavior was observed at 25, 28, 31, 34, 37 and 40 weeks of age using time sampling scanning technique. Feather scoring of the hens was done at 42 weeks of age, neither cage type effect nor their interactions with stock densities on feather pecking behaviour and feather score were evident. The results showed that there were significant effect of stocking density on feather pecking behaviour, and feather score (P<0.05). Hens in 3 and 4 hens per cage displayed higher feather pecking bouts than those in 2 hens per cage (P<0.05). The feather condition scores in the areas of breast, wing, rump, tail, and belly of the birds in 2 hens per cage were better than those in other groups (P<0.05). The hens in 2 hens per cage also had higher body weight change than those in the other densities (P<0.05). This study demonstrated that the stock density had considering higher impact on feather pecking behavior than the type of cage. Therefore, using optimum stocking rate would be a potential choice following welfare consideration together with appropriate housing system currently applied.
Characterisation of the complete mitochondrial genome of Lucanus chengyuani (Coleoptera: Lucanidae)

Abstract We sequenced and assembled the complete mitochondrial genome of Lucanus chengyuani, from the Alishan, Chiayi County, Taiwan. The length of the complete mitogenome of L. chengyuani is 16,926 bp and the mitogenome contains 13 protein-coding, 22 tRNA, and 2 rDNA genes. Nucleotide compositions of the whole mitogenome of L. chengyuani are 38.37% for A, 27.96% for T, 23.03% for C, and 10.637% for G. The AT and GC skewness of mitogenome sequence are 0.157 and -0.368, showing the A-skew and C-skew. The reconstructed phylogenetic relationships of 9 Lucanidae species based on 13 mitochondrial protein-coding genes are highly supported. The clade including Neolucanus maximus and Odontolabis cuvera is sister to the rest of the stag beetle clades, which contains L. chengyuani and L. mazama. Mitogenomic data from this study will provide useful information for further studies for the population genetics, speciation, biogeography, and conservation of L. chengyuani in the future.
Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

The PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here we present the discovery and characterization of a novel pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K’s reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.
A cost-efficient open source laser engine for microscopy

Scientific-grade lasers are costly components of modern microscopes. For high-power applications, such as single-molecule localization microscopy, their price can become prohibitive. Here, we present an open-source high-power laser engine that can be built for a fraction of the cost. It uses affordable, yet powerful laser diodes at wavelengths of 405 nm, 488 nm and 640 nm and optionally a 561 nm diode-pumped solid-state laser. The light is delivered to the microscope via an agitated multimode fiber in order to suppress speckles. We provide the part lists, CAD files and detailed descriptions, allowing any research group to build their own laser engine.
Antiviral Activity of Extracts of Plocamium Brasiliense and Plocamium Cartilagineum at in Vitro Replication of Human Immunodeficiency Virus Type 1

Ingrid De Barcelos Oliveira1,4,5, Rainiomar Raimundo Fonseca2,4, Claudio Cesar Cirne-Santos1,3,4, Caroline de Souza Barros1,3,4, Valeria Launeville Teixeira2,3,4, Izabel Christina Nunes de Palmer Paixao1,3* 1Department of Celular and Molecular Biology, Laboratory of Molecular Virology, Federal Fluminense University, Brazil 2Department of Marine Biology, Laboratory of Marine Natural Products, Institute of Biology, Federal Fluminense University, Brazil 3Post-graduate Program in Science and Biotecnology, Federal Fluminense University, Brazil 4Post-graduate Program in Chemistry, Institute of Chemistry, Federal Fluminense University, Brazil
Mammals and long‐distance over‐water colonization: The case for rafting dispersal; the case against phantom causeways

In the absence of evidence suggesting former ice or land bridges, the colonization of remote landmasses by non‐aquatic, non‐flying vertebrates is thought to result from long‐distance over‐water rafting (LDOR). However, Mazza et al. (2019) challenge the notion that mammals can make such journeys citing their perceived physiological inadequacies. They claim that lengthy transits combined with lack of food and water plus the stresses imposed by temperature, humidity and salinity render such passages impossible. We, though, contend that this reasoning is wrong. The few cases where LDOR has been invoked for mammal colonization have all involved small‐bodied animals, several of which are able to drastically reduce their metabolic rates through torpor/hibernation when food and water are scarce. Furthermore, there may be sustenance. Crucially, LDOR obviates the need for miraculous short‐lived causeways and the attendant issue of unrecognized large‐scale bidirectional invasions being made by other organisms that had access to the conduits.
Improving teamwork and engagement: the case for self and peer assessment

There is a reported competency gap between the teamwork skills required by employers and those developed by engineering students during their undergraduate courses. While project-based learning increases the opportunities for team interaction, it does not necessarily produce the skills required to function effectively in a team. Students also report negative perceptions of project-based learning due to problems with free-riding team members. Appropriately supported assessment and practice activities must be included to motivate students to learn and develop these skills. We report the impact of introducing instruction (lectures), practice (team project) and more importantly assessment (rewarding individual contributions) to develop team skills. Oral team presentations have an individual component and the team mark for written reports is adjusted for individual contributions using self and peer assessment. A confidential online tool is used to collect and collate the student self and peer assessment ratings used both for formative feedback and improvement as well assessment purposes. The online collection of assessment ratings and their automated conversion to two assessment factors significantly reduced the administrative burden of using self and peer assessment with large classes. We found the method reported here improved student teamwork, engagement and satisfaction. In addition, it facilitated students supporting each 2 AJEE 2006-02 Willey & Freeman other to develop their teamwork skills in an engineering context while requiring only a small commitment of academic resources.
Semantic Reversal Anomalies under the Microscope: Task and Modality Influences on Language-Associated Event-Related Potentials

Semantic reversal anomalies (SRAs) – sentences where an implausibility is created by reversing participant roles – have attracted much attention in the literature on the electrophysiology of language. In spite of being syntactically well-formed but semantically implausible, these sentences unexpectedly elicited a monophasic P600 effect in English and Dutch rather than an N400 effect. Subsequent research revealed variability in the presence/absence of an N400 effect to SRAs depending on the language examined and the choice of verb type in English. However, most previous studies employed the same presentation modality (visual) and task (acceptability judgement). Here, we conducted two experiments and three statistical analyses to investigate the influence of stimulus modality, task demand, and statistical choices on event-related potential (ERP) response patterns to SRAs in English. We reproduced a previous study’s procedure and analysis (Bourguignon et al., 2012), and further introduced between-subjects factors of task type and modality, using mixed effects modelling to analyse the data. We observed an N400 effect to typical English SRAs (agent subject verbs, e.g. the fries will eat the boys), which contrasts existing literature and was not predicted by existing theories that account for SRA processing. Task demand modulated the ERPs elicited by SRAs, while auditory presentation led to increased comprehension accuracy and a more broadly distributed ERP. Finally, the statistical methods used influenced the presence/absence of ERP effects. Our results suggest a sensitivity of language-related ERP patterns to methodological parameters and we conclude that future experiments should take this into careful consideration.
Basic Principles of Ethics for Psychiatry

Since the beginning of the 21st century, ethics has been at the core of the practice of psychiatry. This pa- per discusses the basic principles of ethics that are rele- vant to psychiatry and focuses on recent developments in ethics, particularly since 1960. Further, it revisits notions of deontology and codes of ethics and discusses how these regulations can be made relevant to psychiatric practice through clinical ethics consultation services. Finally, two specific issues are highlighted: the teaching of ethics to residents and the relationship of psychiatrists and resi- dents to the pharmaceutical industry.
Pathologic complete response (pCR) in patient subgroups: An analysis of ABCSG-24, a phase III, randomized study of anthracycline- and taxane-based neoadjuvant therapy with or without capecitabine in early breast cancer (EBC).

530 Background: pCR is a predictor of better outcomes, including improved survival. The integration of capecitabine (C) into a standard neoadjuvant regimen of epirubicin and docetaxel (ED) has been shown to significantly improve pCR rate in patients with EBC. This preplanned subgroup analysis was undertaken to determine whether the pCR benefit with C was achieved irrespective of baseline risk factors. Methods: Patients with biopsy proven operable breast cancer ± nodal involvement without distant disease who were scheduled to receive neoadjuvant therapy were randomized to 6x ED every 21 days (d1: E 75 mg/m2 iv and D 75 mg/m2 iv, d2: pegfilgrastim 6 mg2) with or without C (1,000 mg/m2 bid d1–14). The accrual target was 536 patients (510 eligible pts, power = 83%, p < 0.05) to detect a difference in pCR of 16% (ED±T) vs. 27% (EDC±T). Patients were stratified according to tumor stage (T1-4), clinical nodal stage (neg vs. pos), menopausal status (pre vs post), histology (ductal + mixed vs. lobular), hormone re.
Historical biogeography of the hyperdiverse hidden snout weevils (Coleoptera, Curculionidae, Cryptorhynchinae)

The first dated phylogeny of the weevil subfamily Cryptorhynchinae is presented within a framework of Curculionoidea. The inferred pattern and timing of weevil family relationships are generally congruent with previous studies, but our data are the first to suggest a highly supported sister‐group relationship between Attelabidae and Belidae. Our biogeographical inferences suggest that Cryptorhynchinae s.s. originated in the Late Cretaceous (c. 86 Ma) in South America. Within the ‘Acalles group’ and the ‘Cryptorhynchus group’, several independent dispersal events to the Western Palaearctic via the Nearctic occurred in the Late Cretaceous and Early Paleogene. A second southern route via Antarctica may have facilitated the colonization of Australia in the Late Cretaceous (c. 82 Ma), where a diverse Indo‐Australian clade probably emerged c. 73 Ma. In the Early Eocene (c. 50–55 Ma), several clades independently dispersed from Australia to proto‐New Guinea, i.e. the tribe Arachnopodini s.l. , the ‘Rhynchodes group’ and the genus Trigonopterus. New Zealand was first colonized in the Late Palaeocene (c. 60 Ma). Divergence time estimations and biogeographical reconstructions indicate that the colonization of New Guinea is older than expected from current geological reconstructions of the region.
Using National Health Interview Survey Data and State and Local Area Integrated Telephone Survey Data to Study Health Disparities 1

Examples from published analyses show the usefulness of data from the National Health Interview Survey (NHIS) and the State and Local Area Integrated Telephone Survey (SLAITS) for studying health disparities: Married adults were generally healthier than adults in other marital status categories (NHIS results); the prevalence of diabetes was higher among non-Hispanic black persons and Hispanic persons than among non-Hispanic white persons (NHIS results); Hispanic persons were more likely to be without health insurance coverage than non-Hispanic black persons and non-Hispanic white persons (NHIS results); and children in step, single-mother, or grandparent-only families had poorer health than children living with two biological parents (SLAITS results). Also, the major role played by the NHIS in providing data to track disparity-reducing objectives of the Healthy People Program is described.
Cranial variation in common dolphins Delphinus spp. off South Africa, with the inclusion of information from the holotype of Delphinus capensis

The common dolphins (genus Delphinus) are widely distributed in all temperate and tropical oceans. Over this wide geographical distribution they show considerable range in morphological variation, which has led to descriptions of several species in the genus. Until recently, only two species of Delphinus were accepted, but this classification has become contentious. This study investigated the occurrence of morphologically different types of Delphinus in South African waters and assessed geographic and morphometric variations within each type. A total of 296 skulls of Delphinus spp. , obtained from the Port Elizabeth Museum and the Iziko South African Museum, were photographed in their dorsal and ventral aspects for geometric morphometric analysis. Our results revealed three clusters of specimens based on analysis of the dorsal aspect of the skull, and two clusters for the ventral aspect. Significant differences in cranial size were found between clusters. Both cranial aspects showed that the main variations in skull shape occurred in the rostral region and braincase area, indicating divergent adaptations relating to these features. There was a substantial difference between the composition of the dorsal-aspect and ventral- aspect clusters, suggesting the presence of only one species in South African waters. Significant differences between morphological clusters associated with the three regions within the study area (cold-temperate, warm-temperate and subtropical) are probably mediated through differences in local environmental conditions (e.g. different water temperatures and productivity).