Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut microbiota in wild and captive Guizhou snub‐nosed monkeys, Rhinopithecus brelichi

Many colobine species—including the endangered Guizhou snub‐nosed monkey (Rhinopithecus brelichi) are difficult to maintain in captivity and frequently exhibit gastrointestinal (GI) problems. GI problems are commonly linked to alterations in the gut microbiota, which lead us to examine the gut microbial communities of wild and captive R. brelichi. We used high‐throughput sequencing of the 16S rRNA gene to compare the gut microbiota of wild (N = 7) and captive (N = 8) R. brelichi. Wild monkeys exhibited increased gut microbial diversity based on the Chao1 but not Shannon diversity metric and greater relative abundances of bacteria in the Lachnospiraceae and Ruminococcaceae families. Microbes in these families digest complex plant materials and produce butyrate, a short chain fatty acid critical to colonocyte health. Captive monkeys had greater relative abundances of Prevotella and Bacteroides species, which degrade simple sugars and carbohydrates, like those present in fruits and cornmeal, two staples of the captive R. brelichi diet. Captive monkeys also had a greater abundance of Akkermansia species, a microbe that can thrive in the face of host malnutrition. Taken together, these findings suggest that poor health in captive R. brelichi may be linked to diet and an altered gut microbiota.
Molecular and Immunological Analyses of the Mycobacterium avium Homolog of the Immunodominant Mycobacterium leprae 35-Kilodalton Protein

ABSTRACT The analysis of host immunity to mycobacteria and the development of discriminatory diagnostic reagents relies on the characterization of conserved and species-specific mycobacterial antigens. In this report, we have characterized the Mycobacterium avium homolog of the highly immunogenic M. leprae 35-kDa protein. The genes encoding these two proteins were well conserved, having 82% DNA identity and 90% identity at the amino acid level. Moreover both proteins, purified from the fast-growing host M. smegmatis, formed multimeric complexes of around 1000 kDa in size and were antigenically related as assessed through their recognition by antibodies and T cells from M. leprae-infected individuals. The 35-kDa protein exhibited significant sequence identity with proteins from Streptomyces griseus and the cyanobacterium Synechoccocus sp. strain PCC 7942 that are up-regulated under conditions of nutrient deprivation. The 67% amino acid identity between the M. avium 35-kDa protein and SrpI of Synechoccocus was spread across the sequences of both proteins, while the homologous regions of the 35-kDa protein and the P3 sporulation protein of S. griseus were interrupted in the P3 protein by a divergent central region. Assessment by PCR demonstrated that the gene encoding the M. avium35-kDa protein was present in all 30 M. avium clinical isolates tested but absent from M. intracellulare,M. tuberculosis, or M. bovis BCG. Mice infected with M. avium, but not M. bovis BCG, developed specific immunoglobulin G antibodies to the 35-kDa protein, consistent with the observation that tuberculosis patients do not recognize the antigen. Strong delayed-type hypersensitivity was elicited by the protein in guinea pigs sensitized with M. avium.
Non‐trisomic homeobox gene expression during craniofacial development in the Ts65Dn mouse model of Down syndrome

Trisomy 21 in humans causes cognitive impairment, craniofacial dysmorphology, and heart defects collectively referred to as Down syndrome. Yet, the pathophysiology of these phenotypes is not well understood. Craniofacial alterations may lead to complications in breathing, eating, and communication. Ts65Dn mice exhibit craniofacial alterations that model Down syndrome including a small mandible. We show that Ts65Dn embryos at 13.5 days gestation (E13.5) have a smaller mandibular precursor but a normal sized tongue as compared to euploid embryos, suggesting a relative instead of actual macroglossia originates during development. Neurological tissues were also altered in E13.5 trisomic embryos. Our array analysis found 155 differentially expressed non‐trisomic genes in the trisomic E13.5 mandible, including 20 genes containing a homeobox DNA binding domain. Additionally, Sox9, important in skeletal formation and cell proliferation, was upregulated in Ts65Dn mandible precursors. Our results suggest trisomy causes altered expression of non‐trisomic genes in development leading to structural changes associated with DS. Identification of genetic pathways disrupted by trisomy is an important step in proposing rational therapies at relevant time points to ameliorate craniofacial abnormalities in DS and other congenital disorders. © 2013 Wiley Periodicals, Inc.
Unmet supportive care needs mediate the relationship between functional status and quality of life in patients with amyotrophic lateral sclerosis

Abstract Objective The aims of this study were to identify the unmet care needs and to examine the mediating effect of unmet supportive care needs in the relationship between functional status and quality of life (QOL) in Korean patients with amyotrophic lateral sclerosis (ALS). Method This was a cross-sectional study conducted among 186 patients with ALS recruited from a tertiary hospital in Seoul, South Korea. ALS patients' functional status, unmet supportive care needs, and QOL were assessed by Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised, the Amyotrophic Lateral Sclerosis Supportive Care Needs Instrument, and the Amyotrophic Lateral Sclerosis Specific Quality of Life – Revised Instrument, respectively. Mediation analysis was tested using Baron and Kenny's regression analysis and a Sobel test. Result The mean score for functional status was 33.35 ± 8.89; for unmet supportive care needs it was 2.40 ± 0.66; and for QOL it was 4.95 ± 1.29. Functional status was significantly correlated with unmet care needs and QOL. Unmet care needs satisfaction demonstrated a complete mediating effect on the relationship between functional status and QOL of the patients with ALS (β = –0.53, p < 0.001) and the effect was significant (Sobel test; Z = 5.48, p < 0.001). Significance of results Although QOL was negatively affected by the functional status in our sample, the relationship was fully mediated via unmet supportive care needs. Because there is no cure for ALS, and the condition is rapidly progressive with a lethal outcome, providing care by meeting patients’ needs is a critical aspect of caring for these patients. Early assessment of supportive care needs, providing services, and referring ALS patients to appropriate resources could enhance their QOL.
Brain functional impairment in beta‐thalassaemia: the cognitive profile in Italian neurologically asymptomatic adult patients in comparison to the reported literature

Cognitive involvement in beta‐thalassaemia is strikingly controversial and poorly studied in adulthood. This multicentre prospective study investigated 74 adult neurologically‐asymptomatic beta‐thalassaemia patients (mean‐age 34·5 ± 10·3 years; 53 transfusion‐dependent [TDT], 21 non‐transfusion dependent [NTDT]) and 45 healthy volunteers (mean‐age 33·9 ± 10·7 years). Participants underwent testing with Wechsler Adult Intelligence Scale‐Fourth Edition (WAIS‐IV), Brief Psychiatric Rating Scale (BPRS) and multiparametric brain 3T‐magnetic resonance imaging (MRI) for parenchymal, vascular and iron content evaluation. Patients had lower Full‐Scale Intelligence Quotient (FSIQ) than controls (75·5 ± 17·9 vs. 97·4 ± 18·1, P < 0·0001) even after correction for education level. Compared to TDT, NTDT showed a trend of higher FSIQ (P = 0·08) but a similar cognitive profile at WAIS‐subtests. FSIQ correlated with total and indirect bilirubin (P < 0·0001 and P = 0·002, respectively); no correlation was found with splenectomy, intracranial MRI/magnetic resonance‐angiography findings, brain tissue iron content or other disease‐related clinical/laboratory/treatment data. FSIQ did not correlate with BPRS scores, although the latter were higher among patients (28·74 ± 3·1 vs. 27·29 ± 4·8, P = 0·01) mainly because of increased depression and anxiety levels. Occupation rate was higher among controls (84·4% vs. 64·9%, P = 0·004) and correlated with higher FSIQ (P = 0·001) and education level (P = 0·001). In conclusion, Italian adult beta‐thalassaemia patients seem to present a characteristic cognitive profile impairment and an increased rate of psychological disorders with possible profound long‐term socio‐economic consequences.
Microstructural Surface Properties of Drifting Seeds—A Model for Non-Toxic Antifouling Solutions

A major challenge in the shipping and marine industry is the biofouling on under water surfaces. So far, biocides have been the main remedy for the prevention of the adhesion of microorganisms that is also influenced by surface topography. In recent years, research projects have explored microstructured surfaces as a non-toxic antifouling strategy. In this study, physical factors of surfaces of seeds of 43 plant species were analyzed with regards to their antifouling effects. After exposure to cold water of the North Sea during the swarming periods of the barnacles larvae, the surface microstructures of seeds without fouling of barnacles were identified and compared with each other, using a scanning electron microscope (SEM). In order to validate the findings, selected microstructured surface structure properties were transferred to technical surfaces with a 2-component silicon system and subjected to the same conditions. The results of the analyses confirmed that drifting seeds with specific microstructural surface structure properties promote biofouling defense of epibionts. These results serve as a starting point for the development of non-toxic antifouling agents based on the interaction of microstructures and geometric shapes.
Technological and textural properties of spent chicken breast, drumstick and thigh meats as affected by marinating with pineapple fruit juice

ABSTRACT 1. This study was conducted to determine the effects of pineapple fruit juice at different marination times (0, 40, 80, 120 and 160 min) on pH, water holding capacity (WHC), cooking loss (CL) and colour (L*, a*, b*, hue angle and chroma) properties of breast, drumstick and thigh meats from spent hens. Textural properties (razor shear force and shear energy) and sensory analyses of the samples were tested. 2. With increasing marination time, there was a decrease in pH and WHC values, and an increase in CL values. However, marination treatment with pineapple fruit juice significantly affected the textural measurement of all the meat muscles compared with the control group. 3. Razor shear force and shear energy were lower when marination was performed for 160 min. Colour analyses showed that marination for 80 min resulted in significantly increased L*, a* and b* values. The samples marinated for longer times were most preferable, according to the tenderness scores assigned by the panellists.
Serotonin spillover onto the axon initial segment of motoneurons induces central fatigue by inhibiting action potential initiation

Motor fatigue induced by physical activity is an everyday experience characterized by a decreased capacity to generate motor force. Factors in both muscles and the central nervous system are involved. The central component of fatigue modulates the ability of motoneurons to activate muscle adequately independently of the muscle physiology. Indirect evidence indicates that central fatigue is caused by serotonin (5-HT), but the cellular mechanisms are unknown. In a slice preparation from the spinal cord of the adult turtle, we found that prolonged stimulation of the raphe-spinal pathway—as during motor exercise—activated 5-HT1A receptors that decreased motoneuronal excitability. Electrophysiological tests combined with pharmacology showed that focal activation of 5-HT1A receptors at the axon initial segment (AIS), but not on other motoneuronal compartments, inhibited the action potential initiation by modulating a Na+ current. Immunohistochemical staining against 5-HT revealed a high-density innervation of 5-HT terminals on the somatodendritic membrane and a complete absence on the AIS. This observation raised the hypothesis that a 5-HT spillover activates receptors at this latter compartment. We tested it by measuring the level of extracellular 5-HT with cyclic voltammetry and found that prolonged stimulations of the raphe-spinal pathway increased the level of 5-HT to a concentration sufficient to activate 5-HT1A receptors. Together our results demonstrate that prolonged release of 5-HT during motor activity spills over from its release sites to the AIS of motoneurons. Here, activated 5-HT1A receptors inhibit firing and, thereby, muscle contraction. Hence, this is a cellular mechanism for central fatigue.
Expression and Functional Analysis of Olfactory Receptors a

ABSTRACT: The olfactory system recognizes and discriminates myriads of odorants of diverse molecular structure. This task is supposed to be accomplished by a large array of seven‐transmembrane domain receptors encoded by a multigene family. Although circumstantial evidence suggests that the identified genes encode odorant receptors, unequivocal proof requires demonstration that the resulting proteins should be able to interact with odorous molecules and couple via G proteins onto second messenger cascades. This goal can be achieved by heterologous expression of receptor proteins in surrogate eucaryotic cells, although the task is complicated by the diversity of putative odorous ligands and the large size of the receptor family. Employing the baculovirus/Sf9 cell system it was found that receptor proteins can be expressed at high levels. Stimulating receptor‐expressing Sf9 cells with a mixture of numerous odorous compounds elicited a significant and dose‐dependent second messenger response, which was never observed in control cells. Assaying a large panel of odorous compounds, including representatives of different odor classes and compounds of different chemical classes revealed that distinct receptor subtypes respond to certain odorants but not to others. Graded responses to only a subset of odorants indicate that the heterologous expressed receptor types have a selective but relatively broad ligand specificity. The easily manipulated bacterial system was employed to produce olfactory receptor proteins in large quantities. It was solubilized from inclusion bodies and upon reconstitution in liposomes displayed specific interaction with odor ligands.
Quantitative in vivo imaging of neuronal glucose concentrations with a genetically encoded fluorescence lifetime sensor

Glucose is an essential source of energy for the brain. Recently, the development of genetically encoded fluorescent biosensors has allowed real time visualization of glucose dynamics from individual neurons and astrocytes. A major difficulty for this approach, even for ratiometric sensors, is the lack of a practical method to convert such measurements into actual concentrations in ex vivo brain tissue or in vivo. Fluorescence lifetime imaging provides a strategy to overcome this. In a previous study, we reported the lifetime glucose sensor iGlucoSnFR‐TS (then called SweetieTS) for monitoring changes in neuronal glucose levels in response to stimulation. This genetically encoded sensor was generated by combining the Thermus thermophilus glucose‐binding protein with a circularly permuted variant of the monomeric fluorescent protein T‐Sapphire. Here, we provide more details on iGlucoSnFR‐TS design and characterization, as well as pH and temperature sensitivities. For accurate estimation of glucose concentrations, the sensor must be calibrated at the same temperature as the experiments. We find that when the extracellular glucose concentration is in the range 2–10 mM, the intracellular glucose concentration in hippocampal neurons from acute brain slices is ~20% of the nominal external glucose concentration (~0.4–2 mM). We also measured the cytosolic neuronal glucose concentration in vivo, finding a range of ~0.7–2.5 mM in cortical neurons from awake mice.
Bioeconomy for Sustainable Development

Bioeconomy is an emerging paradigm under which the creation, development, and revitalization of economic systems based on a sustainable use of renewable biological resources in a balanced way is rapidly spreading globally. Bioeconomy is building bridges between biotechnology and economy as well as between science, industry, and society. Biotechnology, from its ancient origins up to the present is at the core of the scientific and innovative foundation of bioeconomy policies developed in numerous countries. The challenges and perspectives of bioeconomies are immense, from resource‐efficient large‐scale manufacturing of products such as chemicals, materials, food, pharmaceuticals, polymers, flavors, and fragrances to the production of new biomaterials and bioenergy in a sustainable and economic way for a growing world population. Key success factors for different countries working on the bioeconomy vary widely from high‐tech bioeconomies, emerging diversified or diversified bioeconomies to advanced and basic primary sector bioeconomies. Despite the large variety of bioeconomies, several common elements are identified, which are simultaneously needed altogether.
Effect of Stroke on Joint Control during Reach-to-Grasp: A Preliminary Study

Abstract We investigated changes in control of inter-segmental dynamics underlying upper extremity dyscoordination caused by stroke. Individuals with stroke and healthy individuals performed a natural reach-to-grasp movement. Kinetic analysis revealed that both groups rotated the shoulder by muscle torque and used interaction torque to rotate the elbow. However, individuals with stroke used interaction torque less than healthy individuals, actively suppressing a substantial portion of it. This resulted in inefficient use of active control and dyscoordination of the upper extremity. The degree of interaction torque suppression and inefficiency of active control at the elbow positively correlated with stroke severity. The increased interaction torque suppression can be a strategy used by individuals with stroke to compensate for deficient feedforward control of this torque.
A QoS‐aware exception handling method in scientific workflow execution

Scientific workflow is gaining ever‐increasing attention as it integrates a wide range of heterogeneous services to enable and accelerate the scientific discovery processes. However, the exception occurred in a scientific workflow execution often decreases the robustness of a scientific workflow system. For example, if a service engaged in a scientific workflow schedule becomes unavailable during its execution, an exception might be raised and the whole workflow execution may be interrupted unexpectedly. In this situation, it is a challenge to smooth the interrupted workflow execution. In view of this challenge, an exception handling method, named RelaxingMe (constraints Relaxing Method, RelaxingMe) is proposed in this paper. This method aims at relaxing the original QoS constraint values requested by the interrupted task node, in order to find a near‐to‐optimal candidate service to replace the unavailable one. At last, the feasibility of our method is evaluated by an experiment. Copyright © 2011 John Wiley & Sons, Ltd.
Studies of Laboulbeniales on Myrmica ants (IV): host-related diversity and thallus distribution patterns of Rickia wasmannii

Fungal species identities are often based on morphological features, but current molecular phylogenetic and other approaches almost always lead to the discovery of multiple species in single morpho-species. According to the morphological species concept, the ant-parasitic fungus Rickia wasmannii (Ascomycota, Laboulbeniales) is a single species with pan-European distribution and a wide host range. Since its description, it has been reported from ten species of Myrmica (Hymenoptera, Formicidae), of which two belong to the rubra-group and the other eight to the phylogenetically distinct scabrinodis-group. We found evidence for R. wasmannii being a single phylogenetic species using sequence data from two loci. Apparently, the original morphological description (dating back to 1899) represents a single phylogenetic species. Furthermore, the biology and host-parasite interactions of R. wasmannii are not likely to be affected by genetic divergence among different populations of the fungus, implying comparability among studies conducted on members of different ant populations. We found no differences in total thallus number on workers between Myrmica species, but we did observe differences in the pattern of thallus distribution over the body. The locus of infection is the frontal side of the head in Myrmica rubra and M. sabuleti whereas in M. scabrinodis the locus of infection differs between worker ants from Hungary (gaster tergites) and the Netherlands (frontal head). Possible explanations for these observations are differences among host species and among populations of the same species in (i) how ant workers come into contact with the fungus, (ii) grooming efficacy, and (iii) cuticle surface characteristics.
Story Ending Prediction by Transferable BERT

Recent advances, such as GPT and BERT, have shown success in incorporating a pre-trained transformer language model and fine-tuning operation to improve downstream NLP systems. However, this framework still has some fundamental problems in effectively incorporating supervised knowledge from other related tasks. In this study, we investigate a transferable BERT (TransBERT) training framework, which can transfer not only general language knowledge from large-scale unlabeled data but also specific kinds of knowledge from various semantically related supervised tasks, for a target task. Particularly, we propose utilizing three kinds of transfer tasks, including natural language inference, sentiment classification, and next action prediction, to further train BERT based on a pre-trained model. This enables the model to get a better initialization for the target task. We take story ending prediction as the target task to conduct experiments. The final result, an accuracy of 91.8%, dramatically outperforms previous state-of-the-art baseline methods. Several comparative experiments give some helpful suggestions on how to select transfer tasks to improve BERT.
Factors Influencing Patients’ Experiences of Pain Management in the Emergency Department

Background Despite management of acute pain, concerns regarding pain are still prevalent in the emergency department (ED). Purpose This study aimed to explore the factors influencing patients’ pain management in a Jordanian ED. Method Fifteen semistructured interviews (N = 15) with purposively selected patients in the ED. Results The thematic analysis uncovered two related themes. The first theme described the stage of “being on ED bed” which encapsulates two subthemes: “bad pain means, bad diagnosis” and “smiley faces versus grumpy faces. ” The second theme referred to as “being discharged” including two subthemes, namely, “praying for not paying” and “being grateful to God. ” The lack of money to pay for pain management was equally as stressful as pain itself. Patients’ narratives suggest that nursing pain management is a critical time, extending beyond medical management to encompass communication and spirituality. Conclusions The factors influencing the patients’ experience of pain management extend beyond addressing the source of the pain. Consequently, effective communication coupled with respecting patients’ spirituality and socioeconomic concerns is essential to pain management. To enhance patients’ experience of pain management, the ED system should shift toward a patient-centric model.