Miracle-dz/UniFAR-FTUs huggingface dataset:
The Pastoral Origin of Semiotically Functional Tonal Organization of Music

This paper presents a new line of inquiry into when and how music as a semiotic system was born. Eleven principal expressive aspects of music each contains specific structural patterns whose configuration signifies a certain affective state. This distinguishes the tonal organization of music from the phonetic and prosodic organization of natural languages and animal communication. The question of music’s origin can therefore be answered by establishing the point in human history at which all eleven expressive aspects might have been abstracted from the instinct-driven primate calls and used to express human psycho-emotional states. Etic analysis of acoustic parameters is the prime means of cross-examination of the typical patterns of expression of the basic emotions in human music versus animal vocal communication. A new method of such analysis is proposed here. Formation of such expressive aspects as meter, tempo, melodic intervals, and articulation can be explained by the influence of bipedal locomotion, breathing cycle, and heartbeat, long before Homo sapiens. However, two aspects, rhythm and melodic contour, most crucial for music as we know it, lack proxies in the Paleolithic lifestyle. The available ethnographic and developmental data leads one to believe that rhythmic and directional patterns of melody became involved in conveying emotion-related information in the process of frequent switching from one call-type to another within the limited repertory of calls. Such calls are usually adopted for the ongoing caretaking of human youngsters and domestic animals. The efficacy of rhythm and pitch contour in affective communication must have been spontaneously discovered in new important cultural activities. The most likely scenario for music to have become fully semiotically functional and to have spread wide enough to avoid extinctions is the formation of cross-specific communication between humans and domesticated animals during the Neolithic demographic explosion and the subsequent cultural revolution. Changes in distance during such communication must have promoted the integration between different expressive aspects and generated the basic musical grammar. The model of such communication can be found in the surviving tradition of Scandinavian pastoral music - kulning. This article discusses the most likely ways in which such music evolved.
The Effect of Aqueous Extract of Aillum Sativum (Garlic) on Gram Negative Uropathogenic Bacteria Isolated from Hospitalized Children

This study was aimed to evaluate the antibacterial activity of garlic aqueous extract against Gram negative uropathogenic bacteria. Aqueous extract of garlic showed antibacterial activity against pseudomonas , proteus and klebseilla but has no activity against E.coli which represent the main causative agent of UTIs in Iraqi hospitalized children. Ciprofloxacin is the most effective antibiotic against uropathogenic E.coli that reflect high antibiotic resistance . plasmid profile for two more resistant E.coli isolates showed that each isolate has a different number and size of plasmids
Exposure of the Opportunistic Marine Pathogen Photobacterium damselae subsp. damselae to Human Body Temperature Is a Stressful Condition That Shapes the Transcriptome, Viability, Cell Morphology, and Virulence

Photobacterium damselae subsp. damselae (Pdd), an important pathogen for marine animals, is also an opportunistic human pathogen that can cause fatal necrotizing fasciitis. The regulatory changes triggered by the temperature shift experienced by this marine pathogen upon entering the human body, are completely unknown. Here we report an RNA-seq approach combined with phenotypical assays to study the response of Pdd to cultivation at 37°C in comparison to 25°C. We found that cultivation of a Pdd highly virulent strain for fish and mice, RM-71, at 37°C, initially enhanced bacterial growth in comparison to 25°C as evidenced by the increase in optical density. However, cells were found to undergo a progressive loss of viability after 6 h cultivation at 37°C, and no viable cells could be detected from 30 h cultures at 37°C. In contrast, at 25°C, viable cell counts achieved the highest values at 30 h cultivation. Cells grown at 25°C showed normal rod morphology by scanning electron microscopy analysis whereas cells grown at 37°C exhibited chain-like structures and aberrant long shapes suggesting a defect in daughter cell separation and in septum formation. Cells grown at 37°C also exhibited reduced tolerance to benzylpenicillin. Using a RNA-seq approach we discovered that growth at 37°C triggered a heat-shock response, whereas genes involved in motility and virulence were repressed including iron acquisition systems, the type two secretion system, and damselysin toxin, a major virulence factor of Pdd. Human isolates did not exhibit advantage growing at 37°C compared to fish isolates, and comparative genomics did not reveal gene markers specific of human isolates, suggesting that any Pdd genotype existing in the marine environment might potentially cause disease in humans. Altogether, these data indicate that the potential of Pdd to cause disease in humans is an accidental condition rather than a selected trait, and that human body temperature constitutes a stressful condition for Pdd. This study provides the first transcriptome profile of Pdd exposed at human body temperature, and unveils a number of candidate molecular targets for prevention and control of human infections caused by this pathogen.
Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.
Sacubitril-Valsartan Compared With Enalapril for the Treatment of Heart Failure: A Decision-Analytic Markov Model Simulation in China

Objectives Heart failure with reduced ejection fraction (HFrEF) is a major health concern globally due to high mortality rates, frequent hospitalization and considerable medical expenditure. The prevalence of HFrEF is steadily rising in Asian countries, and populous, developing countries like China are facing a significant socio-economic burden as a result. Sacubitril-valsartan (Sac-Val) is currently a class I recommendation for treating HFrEF in major guidelines, although it has not been pharmaco-economically evaluated in China. To this end, we compared the cost-effectiveness of Sac-Val and enalapril based on the negotiated prices in order to fully assess the expected costs and benefits of the clinical use of Sac-Val in China. Method A Markov model was constructed to estimate long-term clinical and economic outcomes of Sac-Val versus enalapril for HFrEF patients in China over a 10-year horizon. Primary model outcomes were total costs and quality-adjusted life years (QALYs), and the incremental cost-effectiveness ratio (ICER). Results Treatment with Sac-Val resulted in 4.67 QALYs at the cost of $4,684.25, while enalapril yielded 4.40 QALYs at the cost of $4,014.47. Compared to enalapril, Sac-Val was associated with a gain of 0.27 QALYs, resulting in an ICER of $ 2,480.67 per QALY. Deterministic sensitivity analysis showed robust results. Probabilistic sensitivity analysis suggested that Sac-Val has a 99.99% probability of being cost-effective at the willingness-to-pay threshold of $10,276. Conclusion From Chinese patients’ perspective, Sac-Val is a cost-effective treatment option for HFrEF in China compared to enalapril. Our findings can aid clinicians plan the Sac-Val regimen, as well as decision makers to discuss the value and position of novel angiotensin receptor neprilysin inhibitors (ARNIs) in future.
TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon

Tick saliva contains a complex mixture of peptides and non-peptides that counteract their hosts' hemostasis, immunity, and tissue-repair reactions. Recent transcriptomic studies have revealed over one thousand different transcripts coding for secreted polypeptides in a single tick species. Not only do these gene products belong to many expanded families, such as the lipocalins, metalloproteases, Antigen-5, cystatins, and apyrases, but also families that are found exclusively in ticks, such as the evasins, Isac, DAP36, and many others. Phylogenetic analysis of the deduced protein sequences indicate that the salivary genes exhibit an increased rate of evolution due to a lower evolutionary constraint and/or positive selection, allowing for a large diversity of tick salivary proteins. Thus, for each new tick species that has its salivary transcriptome sequenced and assembled, a formidable task of annotation of these transcripts awaits. Currently, as of November 2019, there are over 287 thousand coding sequences deposited at the National Center for Biotechnology Information (NCBI) that are derived from tick salivary gland mRNA. Here, from these 287 thousand sequences we identified 45,264 potential secretory proteins which possess a signal peptide and no transmembrane domains on the mature peptide. By using the psiblast tools, position-specific matrices were constructed and assembled into the TickSialoFam (TSF) database. The TSF is a rpsblastable database that can help with the annotation of tick sialotranscriptomes. The TSA database identified 136 tick salivary secreted protein families, as well as 80 families of endosomal-related products, mostly having a protein modification function. As the number of sequences increases, and new annotation details become available, new releases of the TSF database may become available.
Maintenance vs. Manipulation in Auditory Verbal Working Memory in the Elderly: New Insights Based on Temporal Dynamics of Information Processing in the Millisecond Time Range

Working memory (WM) is a limited-capacity cognitive system that allows the storage and use of a limited amount of information for a short period of time. Two WM processes can be distinguished: maintenance (i.e., storing, monitoring, and matching information) and manipulation (i.e., reordering and updating information). A number of studies have reported an age-related decline in WM, but the mechanisms underlying this deterioration need to be investigated. Previous research, including studies conducted in our laboratory, revealed that age-related cognitive deficits are related to decreased millisecond timing, i.e., the ability to perceive and organize incoming events in time. The aim of the current study was: (1) to identify in the elderly the brain network involved in the maintenance and manipulation WM processes; and (2) to use an fMRI task to investigate the relation between the brain activity associated with these two processes and the efficiency of temporal information processing (TIP) on a millisecond level reflected by psychophysical indices. Subjects were 41 normal healthy elderly people aged from 62 to 78 years. They performed: (1) an auditory verbal n-back task for assessing WM efficiency in an MRI scanner; and (2) a psychophysical auditory temporal-order judgment (TOJ) task for assessing temporal resolution in the millisecond domain outside the scanner. The n-back task comprised three conditions (0-, 1-, and 2-back), which allowed maintenance (1- vs. 0-back comparisons) and manipulation (2- vs. 1-back comparisons) processes to be distinguished. Results revealed the involvement of a similar brain network in the elderly to that found in previous studies. However, during maintenance processes, we found relatively limited and focused activations, which were significantly extended during manipulation. A novel result of our study, never reported before, is an indication of significant moderate correlations between the efficiency of WM and TIP. These correlations were found only for manipulation but not for maintenance. Our results confirmed the hypothesis that manipulation in the elderly is a dynamic process requiring skilled millisecond timing with high temporal resolution. We conclude that millisecond timing contributes to WM manipulation in the elderly, but not to maintenance.
A Rare Case of Pituitary Melanoma Metastasis: A Dramatic and Prolonged Response to Dabrafenib-Trametinib Therapy

Introduction: Pituitary metastases (PM) are rare events and to date only very few cases of melanoma PM have been described in literature up to now. Case Presentation: We describe the clinical history of a 33-year-old male patient who underwent surgical excision of an inter-scapular melanoma in 2008. The subsequent follow-up was negative for ~10 years. In September 2018, due to the onset of a severe headache, the patient underwent a brain magnetic resonance imaging, which showed an expansive mass in the saddle and suprasellar region with a maximum diameter of 17 mm. Pituitary function tests and visual field were normal. Worsening of the headache and the appearance of a left eye ptosis led the patient to surgical removal of the lesion in October 2018. The histological examination unexpectedly showed metastasis of the melanoma. Post-operative hormonal assessment showed secondary hypothyroidism and hypoadrenalism, which were both promptly treated, and a mild hypogonadism. Three months after surgery, a sellar MRI showed a persistent, increased pituitary mass (3 cm of diameter); fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) detected an increased radiopharmaceutical uptake in the sellar region. Due to the persistence of the disease and the evidence of a BRAF V600E mutation, in February 2019, the patient underwent a combined treatment with dabrafenib (a BRAF inhibitor) and trametinib (mitogen-activated extracellular signal-regulate kinase inhibitor). Sellar MRI performed 6 months later showed no evidence of mass in the sellar region. The patient was in a good clinical condition and did not complain of headaches or other symptoms; there were no significant side-effects from the anticancer therapy. After 13 months of treatment, the patient showed no recurrence of the disease on morphological imaging. Anticancer therapy was confirmed, replacement therapies with hydrocortisone and levothyroxine continued and the pituitary-gonadal axis was restored. Conclusion: This is a very interesting case, both for the rarity of the pituitary melanoma metastasis and for the singular therapeutic course carried out by the patient. This is the first case of a pituitary melanoma metastasis with BRAF mutation, successfully treated with the combination of dabrafenib and trametinib after incomplete surgical removal.
Changes of Dynamic Functional Connectivity Associated With Maturity in Late Preterm Infants

Objective: To investigate the changes of dynamic functional connectivity (DFC) in late preterm infants, and assess whether these changes are associated with the indicators measuring the maturity of neonates. Methods: Resting-state fMRI (rs-fMRI) data of eligible neonates was acquired with a 3.0-T MRI scanner in the Department of Radiology, Daping Hospital, Army Medical University (Chongqing, China). After the selection of functional connectivity networks obtained by independent component analysis (ICA), a sliding-window approach was used to cluster all the windows into different states. Then the differences of temporal properties of DFC between groups were compared, and the association between these temporal properties and the degree of maturity was also explored in each state. Results: Eventually, 34 late preterm and 37 term neonates were included in the final analysis. Based on their data, 5 components were located in 5 networks: default-mode (DMN), dorsal attention (DAN), auditory (AUD), sensorimotor (SMN), and visual (VN). Then four reoccurring state patterns of functional connectivity were identified with the k-means clustering method. The late preterm group dwelled significantly longer in State III (late preterm: 33.57 ± 37.64 s, term: 18.50 ± 11.71 s; P = 0.03), which was characterized by general weaker connectivity between networks. Also, the correlation analysis shows the degree of maturity is negatively correlated to the dwell time and fractional windows in State III. Conclusion: Our findings suggested that compared with term infants, late preterm infants preferred to stay in a state with general weak connectivity between networks, but this preference declined as maturity increased.
Use of Habitat by the Semiaquatic Lizard, Norops aquaticus

Abstract We assessed use of habitat by the semiaquatic lizard Norops aquaticus along the Río Java at the Las Cruces Biological Station, Costa Rica. We surveyed the river for lizards and determined characteristics of their perches relative to edge of the water. Individuals preferentially positioned themselves near eddies. Demographic classes differed in height of perches above the river, with adult males using the highest perches. Males were most likely to perch directly above water. In addition, males and juveniles tended to be in exposed areas, whereas females selected cover. Behavior of N. aquaticus on land is dependent on characteristics of rivers.
Obituary: Stanley Marion Garn (1922–2007)

Stanley Marion Garn, 84, Professor Emeritus of Nutrition in the School of Public Health, Professor Emeritus of Anthropology in the College of Literature, Science and Arts, and Emeritus Fellow in the Center for Human Growth and Development, died August 31, 2007 in Ann Arbor, Michigan of complications from peripheral vascular disease. Born October 27, 1922 in New London, Connecticut, Stanley Garn (Fig. 1) was a prolific author and researcher, authority on human biology, and a key figure in physical anthropology of the 20th century. He served as president of the American Association of Physical Anthropologists 1965–1967. He was elected to the U.S. National Academy of Sciences in 1976, and in 1988, the AAPA honored him with the Charles R. Darwin Lifetime Achievement Award. In 2002, The Human Biology Council selected him for their Franz Boas award.
KINETICS OF SILICIC ACID UPTAKE AND RATES OF SILICA DISSOLUTION IN THE MARINE DIATOM THALASSIOSIRA PSEUDONANA 1, 2

Tracer techniques using the stable isotope 30Si were used to measure rates of silicic acid uptake and silica dissolution in silicon replete and silicon depleted populations of 2 clones of the marine diatom Thalassiosira pseudonana Hasle & Heimdal. Uptake kinetics were describable using the Michaelis‐Menten equation for enzyme kinetics, and no threshold concentration for uptake was evident. The maximum specific uptake rate of the estuarine clone 3H (0.062–0.092 · h−1) was higher than that of the Sargasso Sea clone 13‐1 (0.028–0.031 · h−1), but half‐saturation constants for uptake by the 2 clones were not measurably different (0.8–2.3 μM for 3H; 1.4–1.5 μM for 13‐1). There was little or no light dependence of uptake in populations grown under optimal light conditions prior to the experiment. Exponentially growing populations released silicic acid to the medium by dissolution of cellular silica at rates ranging from 6.5 to 15% of the maximum uptake rate.
Metabolically assessed fibre recruitment

The effect of hamstring fatigue on knee extension torque was examined at different knee angles for seven male subjects. Before and after a dynamic flexion fatigue protocol (180°·s, until dynamic torque had declined by 50%), maximal voluntary contraction (MVC) extension torque was measured at four knee flexion angles (90°, 70°, 50° and 30°). Maximal torque generating capacity (MTGC) and voluntary activation (VA) of the quadriceps muscle were determined using electrical stimulation. Average rectified EMG (EMGar) of the biceps femoris was determined. Mean dynamic flexion torque declined by 48 ± 11%. Extensor MVC torque, MTGC, VA and EMGar at the four knee angles were unaffected by the hamstring fatigue protocol. Only at 50° knee angle was VA significantly lower, 15.7%, after fatigue (P<0.05). In addition, EMGar before fatigue was not significantly influenced by knee angle. It was concluded that a fatigued hamstring muscle did not increase the MVC extension torque and knee angle did not change coactivation. Three possible mechanisms may explain the results: a potential difference in recruited fibre populations in antagonist activity compared with the fibres which were fatigued in the protocol, a smaller loss in isometric torque generating capacity of the hamstring muscle than was expected from the dynamic measurements and/or a reduction in VA.
Automatic Determination of the Number of Clusters for Semi-Supervised Relational Fuzzy Clustering

Semi-supervised clustering relies on both labeled and unlabeled data to steer the clustering process towards optimal categorization and escape from local minima. In this paper, we propose a novel fuzzy relational semi-supervised clustering algorithm based on an adaptive local distance measure (SSRF-CA). The proposed clustering algorithm utilizes side-information and formulates it as a set of constraints to supervise the learning task. These constraints are expressed using reward and penalty terms, which are integrated into a novel objective function. In particular, we formulate the clustering task as an optimization problem through the minimization of the proposed objective function. Solving this optimization problem provides the optimal values of different objective function parameters and yields the proposed semi-supervised clustering algorithm. Along with its ability to perform data clustering and learn the underlying dissimilarity measure between the data instances, our algorithm determines the optimal number of clusters in an unsupervised manner. Moreover, the proposed SSRF-CA is designed to handle relational data. This makes it appropriate for applications where only pairwise similarity (or dissimilarity) information between data instances is available. In this paper, we proved the ability of the proposed algorithm to learn the appropriate local distance measures and the optimal number of clusters while partitioning the data using various synthetic and real-world benchmark datasets that contain varying numbers of clusters with diverse shapes. The experimental results revealed that the proposed SSRF-CA accomplished the best performance among other state-of-the-art algorithms and conﬁrmed the outperformance of our clustering approach.