Miracle-dz/UniFAR-FTUs huggingface dataset:
Inheritance of hormonal stress response and temperament in infant rhesus macaques (Macaca Mulatta): Nonadditive and sex-specific effects.

OBJECTIVE Early life interindividual variation in hypothalamic-pituitary-adrenal (HPA) reactivity to stress is predictive of later life psychological and physical well-being, including the development of many pathological syndromes that are often sex-biased. A complex and interactive set of environmental and genetic causes for such variation has been implicated by previous studies, though little attention has been paid to nonadditive effects (e.g. dominance, X-linked) or sex-specific genetic effects. METHOD We used a large pedigreed sample of captive 3-4 months old infant rhesus macaques (N = 2,661, 54% female) to fit univariate and multivariate linear mixed quantitative genetic models for four longitudinal blood cortisol samples and three reliable ratings of infant temperament (nervousness, gentleness, confidence) during a mother-infant separation protocol. RESULTS Each trait had a moderate narrow-sense heritability (h², 0.26-0.46), but dominance effects caused the first two cortisol samples to have much larger broad-sense heritabilities (H², 0.57 and 0.77). We found no evidence for X-linked variance or common maternal environment variance. There was a sex difference in heritability of the first cortisol sample (hf² < hm²), suggesting differing genetic architecture of perception of maternal separation and relocation during infancy. Otherwise, genetic covariance matrices for the sexes were very similar. Genetic correlations between cortisol levels and temperament were weak (< |0.4|) but stronger than residual or phenotypic correlations. CONCLUSIONS HPA reactivity and temperament had a primarily additive genetic basis in infant macaques, but there were important complexities to the genetic architecture of including genetic dominance and sex differences in heritability at this early life stage. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Archaeal overdominance close to life-limiting conditions in geothermally influenced hypersaline lakes at the Danakil Depression, Ethiopia.

The Dallol protovolcanic area on the Danakil Depression (Afar region, Ethiopia) exhibits unique hydrothermal manifestations in hypersaline context, yielding varied polyextreme physicochemical conditions. Previous studies identified a wide archaeal diversity in less extreme brines but failed to identify microorganisms thriving in either high-chaotropicity, low-water-activity brines or hyperacidic-hypersaline Na-Fe-rich brines. Recently, we accessed several small lakes under intense degassing activity adjacent to the Round Mountain, west to the Dallol dome (Western Canyon Lakes; WCL1-5). They exhibited intermediate parameter combinations (pH~5, 34-41% NaCl-dominated salts with relatively high levels of chaotropic Mg-Ca salts) that should allow to better constrain life limits. These lakes were overwhelmingly dominated by Archaea, encompassing up to 99% of prokaryotic 16S rRNA gene amplicon sequences in metabarcoding studies. The majority belonged to Halobacteriota and Nanohaloarchaeota, the latter representing up to half of prokaryotic sequences. Optical and epifluorescence microscopy showed active cells in natural samples and diverse morphotypes in enrichment cultures. Scanning electron microscopy coupled with energy-dispersive x-ray spectroscopy revealed tiny cells (200-300 nm diameter) epibiotically associated with somewhat larger cells (0.6-1 μm) but also the presence of silica-dominated precipitates of similar size and shape, highlighting the difficulty of distinguishing microbes from mineral biomorphs in this kind of low-biomass systems. This article is protected by copyright. All rights reserved.
Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins

The photo-functional chromophore retinal exhibits a wide variety of optical absorption properties depending on its intermolecular interactions with surrounding proteins and other chromophores. By utilizing these properties, microbial and animal rhodopsins express biological functions such as ion-transport and signal transduction. In this review, we present the molecular mechanisms underlying light absorption in rhodopsins, as revealed by quantum chemical calculations. Here, symmetry-adapted cluster-configuration interaction (SAC-CI), combined quantum mechanical and molecular mechanical (QM/MM), and transition-density-fragment interaction (TDFI) methods are used to describe the electronic structure of the retinal, the surrounding protein environment, and the electronic coupling between chromophores, respectively. These computational approaches provide successful reproductions of experimentally observed absorption and circular dichroism (CD) spectra, as well as insights into the mechanisms of unique optical properties in terms of chromophore-protein electrostatic interactions and chromophore-chromophore electronic couplings. On the basis of the molecular mechanisms revealed in these studies, we also discuss strategies for artificial design of the optical absorption properties of rhodopsins.
The Opinions of Turkish Older Adults Related to Frailty

Frailty is a geriatric syndrome characterized by decreased daily living activity, weight loss, weakness, and dependency caused by the cumulative decline in many physiological systems over the life span. This study examined older adults' perceptions of frailty. The study used a descriptive qualitative design. Data were collected using semistructured interviews with 14 older adults admitted to the geriatrics outpatient clinic in one Turkish institution from September to December 2019. The interviews were transcribed and analyzed using the MAXQDA data analysis software. Codes were combined into themes. The respondents were aged 74.5 ± 8.7 years. Two themes emerged from the qualitative data: (i) the conceptualization of frailty; and (ii) coping with frailty. Some of the participants self-identified as frail, a natural consequence of aging. Another group of participants emphasized the feelings of hopelessness and hopefulness in coping with frailty in their remaining lives. This study provides insights into older Turkish adults' opinions regarding frailty, including the development of frailty and its relationship with health status and daily life. This understanding may be used to detect frailty in older adults and to improve frail older adults' care interventions.
Molecular Epidemiology, Antifungal Susceptibility, and Virulence Evaluation of Candida Isolates Causing Invasive Infection in a Tertiary Care Teaching Hospital

Background The incidence of invasive candidiasis is increasing worldwide. However, the epidemiology, antifungal susceptibility, and virulence of Candida spp. in most hospitals remain unclear. This study aimed to evaluate invasive candidiasis in a tertiary care hospital in Nanchang City, China. Methods MALDI-TOF MS and 18S rDNA ITS sequencing were used to identify Candida strains. Randomly amplified polymorphic DNA analysis was used for molecular typing; biofilm production, caseinase, and hemolysin activities were used to evaluate virulence. The Sensititre™ YeastOne YO10 panel was used to examine antifungal susceptibility. Mutations in ERG11 and the hotspot regions of FKS1 of drug-resistant strains were sequenced to evaluate the possible mechanisms of antifungal resistance. Results We obtained 110 Candida strains, which included 40 Candida albicans (36.36%), 37 C. parapsilosis (33.64%), 21 C. tropicalis (19.09%), 9 C. glabrata (8.18%), 2 C. rugose (1.82%), and 1 C. haemulonii (0.91%) isolates. At a limiting point of 0.80, C. albicans isolates could be grouped into five clusters, C. parapsilosis and C. tropicalis isolates into seven clusters, and C. glabrata isolates into only one cluster comprising six strains by RAPD typing. Antifungal susceptibility testing revealed that the isolates showed the greatest overall resistance against fluconazole (6.36%), followed by voriconazole (4.55%). All C. albicans and C. parapsilosis isolates exhibited 100% susceptibility to echinocandins (i.e., anidulafungin, caspofungin, and micafungin), whereas one C. glabrata strain was resistant to echinocandins. The most common amino acid substitutions noted in our study was 132aa (Y132H, Y132F) in the azole-resistant strains. No missense mutation was identified in the hotpot regions of FKS1. Comparison of the selected virulence factors detectable in a laboratory environment, such as biofilm, caseinase, and hemolysin production, revealed that most Candida isolates were caseinase and hemolysin producers with a strong activity (Pz < 0.69). Furthermore, C. parapsilosis had greater total biofilm biomass (average Abs620 = 0.712) than C. albicans (average Abs620 = 0.214, p < 0.01) or C. tropicalis (average Abs620 = 0.450, p < 0.05), although all C. glabrata strains were either low- or no-biofilm producers. The virulence level of the isolates from different specimen sources or clusters showed no obvious correlation. Interesting, 75% of the C. albicans from cluster F demonstrated azole resistance, whereas two azole-resistant C. tropicalis strains belonged to the cluster Y. Conclusion This study provides vital information regarding the epidemiology, pathogenicity, and antifungal susceptibility of Candida spp. in patients admitted to Nanchang City Hospital.
Morphological and Mitochondrial DNA Analyses of Oysters in the Northern Bay of Bengal, Bangladesh

ABSTRACT The geographic boundaries of many important habitat-building shallow estuarine oyster (Family Ostreidae) species are poorly understood, especially in subtropical and tropical waters. These keystone species often have extensive historical and extant ranges, in part because of their ability to adapt to diverse environmental conditions and the transfer and introduction of a few species worldwide for aquaculture production. In addition, oysters exhibit morphological plasticity additionally confounding species identification and taxonomy. Molecular techniques have led to significant improvements in oyster systematics and taxonomy but have not been applied to oysters from many tropical regions, including the coastal areas of the Indian Ocean such as Bangladesh. Because species' identification based on morphological traits alone, in this case primarily shell characteristics, were inadequate, phylogenetic analyses of mitochondrial cytochrome oxidase subunit I gene fragments was also done to confirm the identity of oyster specimens collected from Bangladesh coastal waters. Phylogenetic analyses of collected oyster samples confirmed the two monophyletic subclades of the Ostreidae family Crassostrea and Saccostrea, and five oyster lineages from the region of Bangladesh were identified: Crassostrea gryphoides, Crassostrea belcheri, Saccostrea cuccullata lineage B, S. cuccullata lineage F, and Saccostrea mordax. A new addition to the list of Crassostrea species, C. belcheri was found in Bangladesh, but C. belcheri, C. gryphoides, and S. cuccullata are considered “common” species in the neighboring states of India and Myanmar indicating a widespread distribution of these species along the entire coast of the Bay of Bengal. However, S. mordax, is a new record for the Bay of Bengal region including the coastal waters of Andaman and Nicobar Islands, and thus extends the geographical distribution of this species.
Circular RNA SMEK1 promotes neuropathic pain in rats through targeting microRNA-216a-5p to mediate Thioredoxin Interacting Protein (TXNIP) expression

ABSTRACT Neuropathic pain (NP) is a disease induced by damage to the nervous system. A large number of studies have manifested that circular RNAs (circRNAs) are key in the development of neurological diseases. However, the role of circRNA in NP remains ambiguous. In this study, the biological function and molecular mechanism of circSMEK1 were investigated in NP. NP rat and cell models were established by chronic contractile injury (CCI) surgery and lipopolysaccharide (LPS) treatment, separately. The results exposed that circSMEK1 and TXNIP were up-regulated in NP, while miR-216a-5p was down-regulated. The claw retraction threshold and claw retraction latency in rats were elevated and reduced separately via knockdown circSMEK1 and miR-216a-5p. Meanwhile, knockout circSMEK1 or elevated miR-216a-5p declined inflammatory cytokines tumor necrosis factor-α (TNF-α), interleukin (IL)-1β and IL6 in spinal cord, and the activation of microglia, but promoted the polarization of microglia into anti-inflammatory type, while up-regulation of circSMEK1 or knockdown of miR-216a-5p was opposite. Mechanism studies demonstrated that circSMEK1 mediated TXNIP expression through competitive adsorption of miR-216a-5p. Functional rescue experiments manifested that the suppressive effect of circSMEK1 knockdown on NP was reversed by declined miR-216a-5p simultaneously. In conclusion, the results of this study affirmed that circSMEK1 facilitates NP inflammation and microglia M1 polarization by modulating miR-216a-5p/TXNIP axis, providing a new molecular target for the future treatment of NP.
Non-biodegradable objects may boost microbial growth in water bodies by harnessing bubbles

Given the ubiquity of bubbles and non-biodegradable wastes in aqueous environments, their transport through bubbles should be widely extant in water bodies. In this study, we investigate the effect of bubble-induced waste transport on microbial growth by using yeasts as model microbes and a silicone rubber object as model waste. Noteworthily, this object repeatedly rises and sinks in fluid through fluctuations in bubble-acquired buoyant forces produced by cyclic nucleation, growth and release of bubbles from object's surface. The rise–sink movement of the object gives rise to a strong bulk mixing and an enhanced resuspension of cells from the floor. Such spatially dynamic contaminant inside a nutrient-rich medium also leads to an increment in the total microbe concentration in the fluid. The enhanced concentration is caused by strong nutrient mixing generated by the object's movement which increases the nutrient supply to growing microbes and thereby, prolonging their growth phases. We confirm these findings through a theoretical model for cell concentration and nutrient distribution in fluid medium. The model is based on the continuum hypothesis and it uses the general conservation law which takes an advection–diffusion growth form. We conclude the study with the demonstration of bubble-induced digging of objects from model sand.
Evolution of Leaf Fusion in Honeysuckle (Periclymenum, Lonicera)

Premise of research. Fused or connate leaves are a well-known phenomenon observed across a limited number of angiosperm clades, and no study has attempted to examine this form of fusion from an evolutionary, morphometric, or functional perspective. We examined leaf fusion in honeysuckles, specifically the Periclymenum clade (∼22 species) of Lonicera (Caprifoliaceae, Dipsacales), which exhibits variation in leaf shape, degree of fusion, and the position of fused leaves. As fused leaves co-occurred with reproductive structures, evolutionary correlations between leaf fusion and inflorescence architecture were also examined. Methodology. Variation of leaf fusion was assessed using elliptical Fourier analysis, and multiple individuals of 19 of the 22 species of Periclymenum were sampled. As fused leaves occurred only on reproductive shoots, a suite of inflorescence characters were also studied. A phylogeny for Periclymenum was reconstructed using published sequence data, and this tree was used for ancestral character state reconstructions and correlation analyses. Pivotal results. Leaves directly subtending inflorescences of Periclymenum were free or fused but were rarely partially fused. Fused leaves were ancestral to Periclymenum and were lost in parallel. Leaf fusion was not correlated with inflorescence architecture features, yet inflorescence architecture has become more complex among Periclymenum species. Conclusions. While free leaves are the ancestral condition in the Dipsacales, fused leaves have been gained at least three times and lost at least twice. Given the proximity of fused leaves to reproductive structures, particularly in Lonicera, fused leaves may play a role in protection or in the discovery of flowers and fruits by pollinators and seed dispersers, respectively.
Macrophage migration inhibitory factor is a valid drug target at the intersection of herpes simplex virus 1 replication and Alzheimer’s disease-relevant cellular pathology

Herpes virus infections are endemic and ubiquitous. While only rarely leading to overt encephalitis, subchronic or latent infections have been associated to a variety of conditions, including Alzheimer’s disease (AD). The cellular consequences of herpes virus infection are determined by the host proteins recruited during virus replication and assembly. Identifying such virus-recruited host proteins therefore allows the interrogation fundamental cellular events leading to associated “sporadic” diseases.A host protein-targeted small molecule drug highly active against herpes simplex virus 1 (HSV-1) infection in human brain organoids and cell lines was identified to interact with macrophage migration inhibitory factor (MIF) where it acted by intercalating between MIF units within a trimer, as determined by nuclear magnetic resonance (NMR). MIF knockout cells showed a decreased viral antigen/titer ratio corroborating its role in virus assembly.From post-mortem brain homogenates of patients with Braak 6-staged AD the small molecule lead compound specifically eluted a MIF subpopulation that correlated with the oxidized conformer of MIF (oxMIF). HSV-1 led to an increase in tau phosphorylation at distinct residues, and the lead compound decreased tau phosphorylation in recombinant cell lines expressing mutant tau and in neuron-differentiated iPSCs also in the absence of HSV-1 infection.We conclude that MIF is a cellular host factor involved in HSV-1 replication and a drug target with antiviral efficacy. At the same time, MIF also plays a role in tau phosphorylation and is enriched in an oxidized conformation in brains of AD patients. MIF thus presents as a molecular link connecting HSV-1 infection and cellular pathology characteristic of neurodegenerative diseases involving aberrant tau phosphorylation.
DriverSonar

Dangerous driving due to drowsiness and distraction is the main cause of traffic accidents, resulting in casualties and economic loss. There is an urgent need to address this problem by accurately detecting dangerous driving behaviors and generating real-time alerts. Inspired by the observation that dangerous driving actions induce unique acoustic features that respond to the signal of an acoustic source, we present the DriverSonar system in this paper. The proposed system detects dangerous driving actions and generates real-time alarms using off-the-shelf smartphones. Compared with the state-of-the-arts, the DriverSonar system does not require dedicated sensors but just uses the built-in speaker and microphone in a smartphone. Specifically, DriverSonar is able to recognize head/hand motions such as nodding, yawning, and abrupt adjustment of the steering wheel. We design, implement and evaluate DriverSonar with extensive experiments. We conduct both simulator-based and and real driving-based experiments (IRB-approved) with 30 volunteers for a period over 12 months. Experiment results show that the proposed system can detect drowsy and distraction related dangerous driving actions at an precision up to 93.2% and a low false acceptance rate of 3.6%.
District nurses’ experiences of using a clinical decision support system and an assessment tool at elderly care units in primary health care: a qualitative study

Abstract Aim: The present study aimed to describe the experience of district nurses (DNs) in using a clinical decision support system (CDSS) and the safe medication assessment (SMA) tool during patient visits to elderly care units at primary health care centres. Background: In Swedish primary health care, general practitioners (GPs) prescribe and have the responsibility to regularly review older adults’ medications, while DN (nurses specialised in primary health care) play an important role in assessing older adults’ ability to manage their medications, detecting potential drug-related problems and communicating with patients and GPs about such problems. In a previous feasibility study, we found that DNs who use a combination of a CDSS and the SMA tool identified numerous potentially harmful or dangerous factors and took a number of nursing care actions to improve the safety and quality of patients’ medication use. In telephone interviews, patients indicated that they were positive towards the assessment and interventions. Methods: Individual interviews with seven DNs who worked at six different primary health care centres in Region Stockholm were carried out in 2018. In 2019, an additional group interview was conducted with two of the seven DNs so they could discuss and comment on preliminary findings. Qualitative content analysis was used to analyse the interview transcripts. Findings: Using the tools, the DNs could have a natural conversation about medication use with older adults. They could get a clear picture of the older adults’ medication use and thus obtain information that could facilitate collaboration with GPs about this important component of health care for older adults. However, for the tools to be used in clinical practice, some barriers would have to be overcome, such as the time-consuming nature of using the tools and the lack of established routines for interprofessional collaboration regarding medication discussions.
Multi environmental evaluation of persistence and drought tolerance in smooth bromegrass (Bromus inermis): genetic analysis for stability in combining ability

Abstract. Information on the nature and amount of genotype × environment (GE) interaction for economic traits and persistence is extremely rare in smooth bromegrass (Bromus inermis Leyss.), especially under drought stress. In this study, 25 half-sib (HS) families of smooth bromegrass were evaluated in the field during five consecutive years under normal and water deficit conditions. The effect of water deficit on dry forage yield was increased from the first year to the fifth, and manifested as a decline in persistence of HS families. Based on narrow-sense heritability estimates, additive gene action was found to be an effective factor in the control of yield components, whereas forage yield is controlled by both additive and non-additive gene actions. Considering the three parameters of stability of combining ability, mean performance and drought tolerance simultaneously, it was inferred that four parental genotypes were superior and stable with high values of general combining ability. This indicates that when developing synthetic varieties from these genotypes, both stability and plant productivity are transmitted to their progenies.