Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidation of Hosts, Native Distribution, and Habitat of the Coffee Berry Borer (Hypothenemus hampei) Using Herbaria and Other Museum Collections

The coffee berry borer (Hypothenemus hampei) is the most damaging insect pest of global coffee production. Despite its importance, our knowledge on the insect’s natural habitat, range, and wild host species remains poorly known. Using archival sources (mainly herbaria but also other museum collections), we surveyed 18,667 predominantly wild-collected herbarium specimens mostly from Africa, Madagascar, and Asia for coffee berry borer occurrence. A total of 72 incidences were confirmed for presence of the coffee berry borer, with identifications assisted by micro-CT for SEM. Of the 72 positive infestations, all were from tropical African coffee (Coffea) species, of which 32 were from wild (non-cultivated) plants. Of the 32 wild occurrences, 30 were found in C. canephora (robusta coffee), 1 in C. liberica (Liberica coffee), and 1 in C. arabica (Arabica coffee). Our herbarium survey confirms literature and anecdotal reports that the coffee berry borer is indigenous to tropical Africa, and that coffee species, and particularly robusta coffee, are important hosts. We identify the wetter type of Guineo-Congolian forest as either the preferred or exclusive native habitat of the coffee berry borer. Other than coffee, we find no evidence of other naturally occurring hosts. Characters of infestation (e.g., hole position on coffee fruits) infers a certain degree of specificity between the coffee berry borer and its host.
Evaluation of cognitive performance within the disease course of Alzheimer´s

Alzheimer disease (AD) is a progressive neurodegenerative disorder that is characterized by changes in cognition, behavior and daily functioning. The earliest change within cognition concerns episodic memory (EM) followed by other cognitive functions that will decline rather rapidly in the disease course of AD. Cognitive decline within EM and other cognitive domains may occur years before the actual diagnosis of AD. Although deposition of amyloidbeta (Aβ) plaques have been found to be associated with cognitive decline within AD, these linkages remains unclear. Furthermore, the cognitive reserve (CR) is thought to act as a mediator between neuropathological processes in the brain and clinical expression. In this study, we examined whether the amount of Aβ deposition, measured by posterior neocortical PIB (PIB) by PET imaging, and CR were able to predict cognitive performance, measured within 5 cognitive domains. In addition, we investigated whether medial temporal lobe atrophy (MTA) and posterior area atrophy (PA) would have an influence on the possible relationship between PIB and CR on cognitive performance. Results show that PIB was able to predict EM performance. However, MTA and PA appeared to account for this relationship. No significant results could be found within other cognitive domains. CR appeared to be a non significant predictor of cognitive performance. Findings indicate that within this study, ratings of atrophy were superior to measures of PIB retention on predicting EM performance and thus, may reflect upon the importance of using both MTA and PA in clinical settings on evaluating neurodegerenation within AD.
Quantifying the cost of cognitive stability and flexibility

Exerting cognitive control is well known to be accompanied by a subjective effort cost and people are generally biased to avoid it. However, the nature of cognitive control costs is currently unclear. Recent theorizing suggests that the cost of cognitive effort serves as a motivational signal to bias the system away from excessive focusing (i.e. cognitive stability) and towards more cognitive flexibility. We asked whether the effort cost of cognitive stability is higher than that of cognitive flexibility. Specifically, we tested this prediction in the domain of working memory by using (i) a delayed response paradigm that allows us to manipulate demands for stability (distractor resistance) and flexibility (flexible updating) of working memory representations, as well as (ii) a subsequent cognitive effort discounting paradigm that allows us to quantify the subjective effort costs assigned to performing the delayed response paradigm. We show strong evidence, in two different samples (28 and 62 participants respectively) that subjective cost increases as a function of demand. Moreover, we demonstrate that the subjective cost of performing a task requiring cognitive stability (distractor resistance) is higher than that requiring flexible updating, supporting the hypothesis that the subjective effort cost of cognitive stability is higher than that of flexibility.
Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi

The circadian clock drives time-specific gene expression, allowing for associated biological processes to be active during certain times of the 24 h day. Crassulacean acid metabolism (CAM) photosynthetic plants represent an interesting case of circadian regulation of gene expression as CO2 fixation and stomatal movement in CAM plants display strong circadian dynamics. The molecular mechanisms behind how the circadian clock enabled these physiological differences is not well understood. Therefore, we set out to investigate whether core circadian elements in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply connected to different core elements. We utilized a new metric for identifying candidate core genes of a periodic gene network and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between the candidate core clock genes and orthologs of known core clock genes in K. fedtschenkoi. We also used LEM to identify stomata-related gene targets for K. fedtschenkoi core clock genes and constructed a subsequent gene regulatory network. Our results provide new insights into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.
Risk of potential pesticide use to honeybee and bumblebee survival and distribution: A country‐wide analysis for The Netherlands

Bees play an important role in natural ecosystems and the world's food supply. In the past decades, bee abundance and diversity have declined globally. This has resulted in decreased pollination services for natural ecosystems and the agricultural sector at the field scale. One of the causes of the decline in bee abundance and diversity is the use of pesticides. Linking pesticide use, land use and bee presence could provide crucial insights into areas, and pesticides that pose a significant threat to the abundance and diversity of bees. Obtaining actual figures of farmer pesticide use is rarely possible. Therefore, we designed a method to study the effects of potential pesticide use on the survival and distribution of honeybees and bumblebees.
Adverse childhood experiences in families with multiple members diagnosed to have psychiatric illnesses

Objective: Adverse childhood experiences are linked to the development of a number of psychiatric illnesses in adulthood. Our study examined the pattern of adverse childhood experiences and their relation to the age of onset of major psychiatric conditions in individuals from families that had ⩾2 first-degree relatives with major psychiatric conditions (multiplex families), identified as part of an ongoing longitudinal study. Methods: Our sample consisted of 509 individuals from 215 families. Of these, 268 were affected, i.e., diagnosed with bipolar disorder (n = 61), obsessive–compulsive disorder (n = 58), schizophrenia (n = 52), substance dependence (n = 59) or co-occurring diagnoses (n = 38), while 241 were at-risk first-degree relatives who were either unaffected (n = 210) or had other depressive or anxiety disorders (n = 31). All individuals were evaluated using the Adverse Childhood Experiences – International Questionnaire and total adverse childhood experiences exposure and severity scores were calculated. Results: It was seen that affected males, as a group, had the greatest adverse childhood experiences exposure and severity scores in our sample. A Cox mixed effects model fit by gender revealed that a higher total adverse childhood experiences severity score was associated with significantly increased risk for an earlier age of onset of psychiatric diagnoses in males. A similar model that evaluated the interaction of diagnosis revealed an earlier age of onset in obsessive–compulsive disorder and substance dependence, but not in schizophrenia and bipolar disorder. Conclusion: Our study indicates that adverse childhood experiences were associated with an earlier onset of major psychiatric conditions in men and individuals diagnosed with obsessive–compulsive disorder and substance dependence. Ongoing longitudinal assessments in first-degree relatives from these families are expected to identify mechanisms underlying this relationship.
Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites

“Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, for example, Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.
Introduction history and population genetics of intracontinental scotch broom (Cytisus scoparius) invasion

Biological invasions at the intracontinental scale are poorly studied, and intracontinental invasions often remain cryptic. Here, we investigate the recent range expansion of scotch broom (Cytisus scoparius) into Norway and clarify whether the genetic patterns indicate natural spread or human introduction. Furthermore, we investigate whether plants were moved within the native range and how this influences invasion success. We also infer the level and structuring of genetic diversity within and between the putative native and introduced range.
Integrative taxonomy of an arctic bumblebee species complex highlights a new cryptic species (Apidae: Bombus)

Bumblebees have been the focus of much research, but the taxonomy of many species groups is still unclear, especially for circumpolar species. Delimiting species based on multisource datasets provides a solution to overcome current systematic issues of closely related populations. Here, we use an integrative taxonomic approach based on new genetic and eco-chemical datasets to resolve the taxonomic status of Bombus lapponicus and Bombus sylvicola. Our results support the conspecific status of B. lapponicus and B. sylvicola and that the low gradual divergence around the Arctic Circle between Fennoscandia and Alaska does not imply speciation in this species complex. Therefore, based on our molecular and morphological analyses, we propose to assign them subspecific status: Bombus lapponicus lapponicus from Fennoscandia and West Siberia and Bombus lapponicus sylvicola comb. nov. from Alaska and Yukon. In addition, our analyses reveal a cryptic species in the B. lapponicus complex from Alaska, which we describe here as new: Bombus (Pyrobombus) interacti sp. nov.
The Management of Pain in Older People

Chapter 1: Anatomy & Physiology of Pain. Pain & Sensation. Neural Pain Pathways. A Delta fibres. Dorsal Roots. Spinal cord to brain. Descending tracts & Substantia gelatinosa. The pain gate. Chronic pain. Peripheral sensitisation. Central Senstization. Older People. Chapter 2: Relating socio-economic issues with older people and pain: Independence dignity and choice. Health Economics. Cultural issues in older age. Resources linked with being older and in pain . Policy in health services, economics and older people. Diet and health in older age, related to economics. Independence. Dignity. Choice. Chapter 3: Creaking joints, a bit of arthritis, and aches and pains': Older people's experiences and perceptions of pain. The Study. Is pain different for older people Equating older age with aches and pains. Salience of older age linked to whether people experienced pain. Effect of pain on everyday lives. Managing the pain Keeping a positive attitude. Others in relation to pain. Implications for practice Exercises. Case studies. Mr Uddim. Violet Jones. Learning points. Chapter 4: Assessment of Pain. Visual Analogue Scale. Numerical Rating Scale. Verbal Descriptors. Faces Pain Scale. Colour Scale. McGill Pain Questionnaire (MPQ). Sensory Impairment. Learning disability. Cognitive impairment. Perception of Pain. Behavioural Pain Assessment Tools. DS DAT Scale. Checklist of non-verbal Pain Indicators (CNPI). ADD Protocol. DOLOPLUS Scale. The NOPAIN Scale. Pain Assessment Scale for Dementing Elderly (PADE). PAINAD. PACSLAC. Abbey Scale. Terminal Care. Chapter 5 : Communication. Research. Care workers and mentioning dementia. Explaining memory loss. Chapter 6: Acute versus Chronic Pain. Assessing Acute with Chronic Pain. Treatment for Acute with Treatment for Chronic. Opiophobia and Other Barriers. Chapter 7: Cancer Pain in the elderly in palliative care settings. How is cancer pain addressed in palliative care settings? The total pain concept - the patient experience. Multidimensional assessment. The family in palliative care. What are the issues for older people Expectations of pain in later life. Co-morbidity. Lack of access to specialist palliative care services. Compliance with pharmacological treatments. Age related alterations in drug disposition Management of cancer pain in the elderly in palliative care. Drugs compliance/concordance. Other treatments. Recommendations for practice Assessment and management Roles of MDT. SPCS intervention. Chapter 8: Care Settings. Problems with Chronic Pain in Older people. Physiological Changes. Getting used to pain. Assessment. Management. Education. Assets. Research Ongoing. Reluctance to report pain/ an acceptance that being in pain is normal and low expectations for help with medical interventions Age related perceptions of pain. Lack of Awareness of potential strategies for dealing with pain. Multidisciplinary Management. Cognitive Behavioural Therapy. Care Home Settings.
Effects of Increasing Phytase Inclusion Levels on Broiler Performance, Nutrient Digestibility, and Bone Mineralization in Low-Phosphorus Diets

SUMMARY The objective of the current study was to evaluate the impact of increasing levels of phytase in corn-soy diets fed to male broilers. Experimental treatments included a positive control (PC) with a calculated non-phytate phosphorus (nPP) level of 0.43 and 0.39% for the starter and grower, respectively. The negative control (NC) diet included a reduction in nPP to 0.25 and 0.23% in the starter and grower, respectively, and phytase added to NC diet with increasing levels of 250, 500, 750, 1,000, 2,000, and 3,000/1,000 FTU/kg. All phytase treatments were fed throughout the study with the exception of the 3,000 FTU/kg treatment, which utilized a “step-down” program consisting of 3,000 FTU/kg in the starter being reduced to 1,000 FTU/kg in the grower. Treatment effects on performance, apparent metabolizable energy, apparent ileal digestibility of amino acids, phosphorus, and calcium, and bone mineralization were evaluated on days 14 and 28. The NC diet decreased feed consumption (FC) (P
Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants

Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but comprise only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large dataset of published and newly generated sRNA sequencing data (1,333 sRNA-seq libraries containing over 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding over 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24 nucleotide and 21 nucleotide siRNAs, respectively. 24 nucleotide-dominated siRNA loci usually occurred in intergenic regions, especially at the 5’-flanking regions of protein-coding genes. In contrast, 21 nucleotide-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21 nucleotide-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, while mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible at http://plantsmallrnagenes.science. psu.edu.
Effect of post-fermentative yeast biomass as a substitute for soybean meal on feed utilization and rumen ecology in Thai native beef cattle

1 Khon Kaen University, Faculty of Agriculture, Department of Animal Science, Tropical Feed Resources Research and Development Center (TROFREC), Khon Kaen 40002, Thailand 2 Maejo University, Faculty of Animal Science and Technology, Chiangmai 50290, Thailand 3 KSL Green Innovation Public Company Limited, Rajathevi 10400, Bangkok, Thailand 4 Prince of Songkla University, Faculty of Natural Resources, Department of Animal Science, Songkhla 90112, Thailand 5 Udon Thani Rajabhat University, Faculty of Technology, Program in Animal Production Technology, Udon Thani 41000, Thailand 6 Rajamangala University of Technology-Isan, Faculty of Natural Resources, Department of Animal Science, Sakon Nakhon Campus, Phangkhon 47160, Sakon Nakhon, Thailand
Green synthesis of AgNPs@PPE and its Pseudomonas aeruginosa biofilm formation activity compared to pomegranate peel extract

Background Bacteria are able to form biofilm on the biotic and abiotic surfaces which helps to protect themselves from deleterious conditions, predation, desiccation, and exposure to antibacterial substances. About 80% of bacterial infections are caused by those bacteria living in the biofilm. Pseudomonas aeruginosa, a gram-negative, non-fermentative bacillus, and the ubiquitous bacterium is an important opportunistic pathogen notorious for biofilm formation and is remarkably resistant against most antibiotics multiple front-line antibiotics, which significantly contributes to eradication failure. The aim of this paper was to evaluate the anti-biofilm formation activity of Ag@PPEs gainst P. aeruginosa bacteria. Methods An aqueous extract of black pomegranate peel was used for the synthesis of silver nanoparticles (AgNPs@PPE). The characteristics, anti-biofilm formation and cell toxicity of AgNPs@PPE were examined in vitro. Results Absorbance at λmax 372 nm which is related to the surface plasmon resonance, confirms the AgNPs@PPE formation. XRD pattern showed the face-centered qubic (fcc) crystalline structure of AgNPs. TEM images showed that spherical AgNPs size is ranged between 32 and 85 nm. The AgNPs@PPE showed inhibition effect against P. aeruginosa biofilm formation at 0.1 to 0.5 mg/ml concentrations. Cell toxicity assay showed that at 400 µg/ml, AgNPs@PPE were safe without a significant toxicity in L929 cell line. Conclusion These data indicate that co-treatment of PPE and AgNPs@PPE significantly decreased the biofilm formation rate. Furthermore, no significant toxicity of AgNPs@PPE was shown against L929 cell line at 400 µg/ml concentration.
The CTCF Anatomy of Topologically Associating Domains

Topologically associated domains (TADs) are defined as regions of self-interaction. To date, it is unclear how to reconcile TAD structure with CTCF site orientation, which is known to coordinate chromatin loops anchored by Cohesin rings at convergent CTCF site pairs. We first approached this problem by 4C analysis of the FKBP5 locus. This uncovered a CTCF loop encompassing FKBP5 but not its entire TAD. However, adjacent CTCF sites were able to form ‘back-up’ loops and these were located at TAD boundaries. We then analysed the spatial distribution of CTCF patterns along the genome together with a boundary identity conservation ‘gradient’ obtained from primary blood cells. This revealed that divergent CTCF sites are enriched at boundaries and that convergent CTCF sites mark the interior of TADs. This conciliation of CTCF site orientation and TAD structure has deep implications for the further study and engineering of TADs and their boundaries.
Fitting of decomposition of sewage sludge and oat straw by nonlinear models

An economic and environmentally feasible way to recycle sewage sludge is its use in agriculture.Information on carbon mineralization curves allows us to seek improvements in soil quality andcrop productivity. The objective of this work was to evaluate the nonlinear models that describecarbon mineralization in the soil. The experiment was conducted in laboratory and the design wascompletely randomized, with four replicates and three treatments. The following treatments wereevaluated: sewage sludge, black oat straw and sewage sludge + oat straw, incorporated into the soil.Pots with soil and the applied treatment were incubated for 110 days. The Stanford and Smith andCabrera models were used, considering structure of autoregressive errors AR (1) when necessary.The fittings were compared using the Akaike Information Criterion (AIC). The evaluated nonlinearmodels described the carbon decomposition dynamics of the treatments satisfactorily. The Stanfordand Smith model is suitable for describing the carbon decomposition in the soil + sludge and soil +oat straw treatments. The Cabrera model is suitable to describe the carbon decomposition of the soil+ sludge + straw treatment.Keywords: Mineralization. Stanford and Smith model. Cabrera model. Half-life.