Miracle-dz/UniFAR-FTUs huggingface dataset:
Application Realtime-PCR for the Detection of Urogenital Infections in Vietnamese Men

Introduction Sexually Transmitted Diseases (STDs) are a group of infectious diseases that have a negative influence on human health, especially reproductive health. Despite the crucial progress in terms of diagnosis, treatment and prevention (e.g. vaccination), they remain the most widespread and hazardous infectious diseases [1,2]. According to the World Health Organization (WHO), about one million STDs are acquired every day worldwide. In developing countries in Africa and Asia, STDs are one of the five most common diseases [3]. Urogenital infections are also a worldwide shared problem that represents the most common reason for a woman to decide to visit to gynaecologist or urologist [4].
Inhibitory Effects of Nisin Combined with Plant-derived Antimicrobials on Pathogenic Bacteria and the Interaction with Complex Food Systems

This study aimed to evaluate the synergistic effects of nisin combined with cinnamaldehyde (Nis+Cin) and nisin combined with carvacrol (Nis+Car) on food-borne bacteria. The minimum inhibitory concentrations for Nis, Cin and Car ranged from 2,500 to 10,000 IU/mL, 0.78-6.25 mg/mL and 0.78-3.13 mg/mL, respectively. Nis+Cin displayed a total synergism against all test bacteria, showing a marked release of bacterial intracellular constituents. In a food model, high protein concentration, low starch and oil concentration as well as low pH, positively influenced the antimicrobial activity . Moreover, in sandwich spread, Nis+Cin enhanced the inhibition of S. typhimurium at the greatest level by reducing cell numbers by more than 4 log CFU/g from 6 days of storage. These results suggest that the dose used for each antimicrobial compound can be minimized by combination, thereby decreasing the possibility of antimicrobial resistance and also reducing food processing costs.
NeuroRoots, a bio-inspired, seamless Brain Machine Interface device for long-term recording

Minimally invasive electrodes of cellular scale that approach a bio-integrative level of neural recording could enable the development of scalable brain machine interfaces that stably interface with the same neural populations over long period of time. In this paper, we designed and created NeuroRoots, a bio-mimetic multi-channel implant sharing similar dimension (10µm wide, 1.5µm thick), mechanical flexibility and spatial distribution as axon bundles in the brain. A simple approach of delivery is reported based on the assembly and controllable immobilization of the electrode onto a 35µm microwire shuttle by using capillarity and surface-tension in aqueous solution. Once implanted into targeted regions of the brain, the microwire was retracted leaving NeuroRoots in the biological tissue with minimal surgical footprint and perturbation of existing neural architectures within the tissue. NeuroRoots was implanted using a platform compatible with commercially available electrophysiology rigs and with measurements of interests in behavioral experiments in adult rats freely moving into maze. We demonstrated that NeuroRoots electrodes reliably detected action potentials for at least 7 weeks and the signal amplitude and shape remained relatively constant during long-term implantation. This research represents a step forward in the direction of developing the next generation of seamless brain-machine interface to study and modulate the activities of specific sub-populations of neurons, and to develop therapies for a plethora of neurological diseases.
A model for physiological transmembrane transport derived from thermodynamical principles

A generic formulation for both passive and active transmembrane transport is derived from basic thermodynamical principles. The derivation takes into account the energy required for the motion of molecules across membranes, and includes the possibility of modeling asymmetric flow. Transmembrane currents can then be described by the generic model in the case of electrogenic flow. As it is desirable in new models, it is possible to derive other well known expressions for transmembrane currents as particular cases of the generic formulation. For instance, the conductance-based formulation for current turns out to be a linear approximation of the generic current. Also, under suitable assumptions, other formulas for current based on electrodiffusion, like the constant field approximation by Goldman, can also be recovered from the generic formulation. The applicability of the generic formulations is illustrated first with fits to existing data, and after, with models of transmembrane potential dynamics for pacemaking cardiocytes and neurons. The generic formulations presented here provide a common ground for the biophysical study of physiological phenomena that depend on transmembrane transport.
The phylogeny of Coleopterida (Hexapoda) – morphological characters and molecular phylogenies

Coleopterida (Coleoptera + Strepsiptera) has been established as the sister group of Neuropterida (Megaloptera + Neuroptera + Raphidioptera) based on recent phylogenetic analyses of DNA sequence data obtained from genomes and transcriptomes. However, within the resulting clade (Neuropteroidea) the proposed sister‐group relationship between the highly specialized endoparasitic Strepsiptera and the megadiverse Coleoptera still lacks convincing morphological support. Furthermore, relationships among the four suborders of Coleoptera remain controversial, with morphological characters strongly conflicting with results suggested by molecular evidence. A large morphological dataset comprising external and internal features of adults and immature stages is presented here and analysed phylogenetically. Our study is focused on deep splits in Coleopterida and on reconstructing character evolution on the phenotypic level. Parsimony analyses clearly support a sister‐group relationship between Strepsiptera and monophyletic Coleoptera. Presumptive synapomorphies are characters linked with posteromotorism, but also features of the head and prothorax. We recover Archostemata as sister group of the remaining extant Coleoptera, and Polyphaga as sister group of the species‐poor suborder Myxophaga. The most important character complex of Coleoptera is heavy sclerotization without exposed membranes and a simplification of the thoracic muscle apparatus. Non‐archostematan beetles are characterized by further simplifications of the thoracic locomotor apparatus. This trend reaches its peak in Myxophaga and Polyphaga, and these suborders also share apomorphies of the larval legs. A pattern with Polyphaga as sister to all other suborders and a clade Myxophaga + Archostemata (as in recent molecular phylogenetic studies) requires ten additional steps with our dataset. This scenario implies that various simplifications of the thoracic exoskeleton and musculature have taken place several times independently, and also that a complex feeding apparatus suitable for saprophagy and sporophagy was ancestral in Coleoptera, with secondary reduction (or modification) in Archostemata and Adephaga. The coleopteran subordinal relationships remain a challenge, with morphological and molecular data suggesting distinctly different patterns. The earliest evolution of Coleopterida is not documented in the fossil record. The exploration of potential stem‐group fossils is a high priority, as is the study of species from the Permian–Triassic transition zone, which are apparently important in the context of evaluating the relationships among beetle suborders.
Connect-seq to superimpose molecular on anatomical neural circuit maps

Significance Single-cell transcriptomics has emerged as a powerful means to define the molecular heterogeneity of brain neurons. However, which of the neurons with known transcriptomes interact with each other in specific neural circuits is largely unknown. Here, we devised a strategy, termed “Connect-seq,” which combines retrograde viral tracing and single-cell transcriptomics to determine the molecular identities of individual upstream neurons in a defined circuit. Using Connect-seq, we uncovered a large variety of signaling molecules expressed in neurons upstream of hypothalamic neurons that control physiological responses to stress. Information obtained by Connect-seq can be used to overlay molecular maps on anatomical neural circuit maps and generate molecular tools for probing the functions of individual circuit components. The mouse brain contains about 75 million neurons interconnected in a vast array of neural circuits. The identities and functions of individual neuronal components of most circuits are undefined. Here we describe a method, termed “Connect-seq,” which combines retrograde viral tracing and single-cell transcriptomics to uncover the molecular identities of upstream neurons in a specific circuit and the signaling molecules they use to communicate. Connect-seq can generate a molecular map that can be superimposed on a neuroanatomical map to permit molecular and genetic interrogation of how the neuronal components of a circuit control its function. Application of this method to hypothalamic neurons controlling physiological responses to fear and stress reveals subsets of upstream neurons that express diverse constellations of signaling molecules and can be distinguished by their anatomical locations.
Formation of local immunity in infants on different types of feeding

Rational feeding from the early days of life programs the health, growth and development of the child over the following years. By the age of 6 months children on artificial feeding are reliably more likely to form excess body weight. The nature of nutrition depends on the condition of the overall and local immune protection of the child. Application of non-invasive methods for determining sIgA (in oral fluid (saliva), in coprofiltrate) allows to assess local immunity in infancy age. Breastfed infants receive sIgA with mother’s milk and have additional protection against the pathogens of respiratory and intestinal infections. The level of sIgA in the mother’s breast milk can be determined to assess the condition of children’s immunity. Children on breastfeeding experience acute respiratory diseases less often compared to children fed with adapted milk formula.
Evaluation of Multislice-CT compared with Ultrasound Abdomen and Pelvis in Diagnosis of Acute Appendicitis in Female of Reproductive Age

Appendicitis is the commonest causes of the acute abdominal pain and most frequent causes for an urgent abdominal surgical operation. Recently, it is clarified that the appendix may have an immune-protective function and working as a lymphoid organ especially in young age. Other theories claimed that appendix work as storage for "good" colonic bacteria. Moreover, others theories claimed that it is a just developmental remnant and without function. The present investigation was done between March 2016 and July 2019, and including 60 female patients in reproductive age who clinically suspected as acute appendicitis with Alvarado score. Then, the female patients were divided to 2 groups; Group A, including 30 patients, the primary diagnosis based on Alvarado score with pelvic-bdominal sonography and group B, including 30 patients, the primary diagnosis of acute appendicitis depend up on Alvarado score and multislicepelviabdominal CT. All patients in the 2 groups were complaining from acute rtlower abdominal pain with Alvarado score more than 3. All patients in the 2 groups diagnosed of acute appendicitis were managed by open appendicectomy. Postoperative final results were depended on the histopathological evaluations of the samples. Multislice-pelvi-abdominal CT play an important role in diagnosis of acute appendicitis in female patients and it is more sensitive and specific than the modified Alvarado score plus US abdomen and pelvis. CT abdomen and pelvis rule out other pelvic pathology, and so lowering the high rates of -veappendicectomy and increase accuracy of final diagnosis of acute appendicitis.
Effect of water acidification on some morphological, digestive and production traits in broiler chickens

The objective of the study was to determine the effect of acidifier added to drinking water on growth rate, performance index, flock uniformity, weight of edible giblets and immune organs, fermentation process in the caecum and excretion of dry matter and crude protein in broiler chicks. One hundred one day old broiler chicks were assigned in two equal groups. Birds of the test group were supplied with drinking water with the addition of acidifying preparation (in amount of 2 mL/L during the whole experiment). Acidification of drinking water had positive effect on growth rate during finisher phase (P<0.05) and reduction of crude protein in faeces (P<0.001). Although not statistically significant, water acidification increased flock body weight uniformity. No significant effect of water acidification were observed on performance index, weight of edible giblets and immune organs, pH and concentration of short chain fatty acids in caecum content as well as content of dry matter in faeces.
Beware the Jaccard: the choice of metric is important and non-trivial in genomic colocalisation analysis

Background The generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation, and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of metrics have been proposed for this problem in other fields like ecology. However, while several of these metrics have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated. Results We show that the choice of metric may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly affected by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less affected by dataset size, but one should be aware of increased variance for small datasets. Availability All results on simulated and real data can be inspected and reproduced at: https://hyperbrowser.uio. no/sim-measure
Assembly Defects Abrogate Proofreading by Initiation Factors and License the Entry of Premature Ribosomes into the Translation Cycle

Numerous quality control steps are deployed by the translational machinery to ensure faithful decoding of genetic message to synthesize proteins. However, what transpires to quality control mechanism during protein synthesis when the ribosomes are produced with assembly defects remains enigmatic. In E. coli, we show that ribosomes with assembly defects evade the proofreading steps during translation initiation and participate in the translation cycle. Such ribosomes show severely compromised decoding capabilities that give rise to errors in initiation and elongation. Tracing the genesis, we discovered that the assembly defects compromise the binding of initiation factors, thus licensing the rapid transitioning of 30S (pre) initiation complex to 70S initiation complex by tempering the proofreading mechanism. Overall, our work highlights that a mass balance deficit between premature ribosomes and initiation factors steers the entry of premature ribosomes into the translation cycle.
ECG Biometric Recognition: Unlinkability, Irreversibility, and Security

Security is a primary concern in Internet-of-Things (IoT) applications, and biometric recognition is considered to be a promising solution. In this article, we propose a novel electrocardiogram (ECG)-based biometric recognition scheme that can potentially strengthen the security of IoT-based patient monitoring systems. A biometric system is designed to operate in either verification or identification mode, and we concentrate on applying the proposed approach to the latter due to its difficulty and popularity in existing studies. Through the concept of “subspace oversampling,” we are able to create distinct and irreversible templates for an enrollee to avoid the cross-matching problem and privacy invasion. With the help of “subspace matching,” the identity of unknown subjects can be determined using only their beat bundles without any additional information required for template construction. Moreover, the proposed scheme includes a method for unregistered subject exclusion to avoid falsely linking an initially unidentifiable subject to someone in the database, further strengthening its security. The performance of the proposed scheme was evaluated using the ECGs of 287 subjects from the Physikalisch Technische Bundesanstalt data set. The experimental results demonstrated the linkability of the constructed templates as low as 0.0938, and beat bundles reconstructed from the templates of a given subject were more likely to be identified as those from another user. An identification rate of 99.02% was obtained even when the proposed exclusion scheme was incorporated; meanwhile, the corresponding false-positive identification error rate was 0.44% under a dictionary attack with real ECGs.
A parakeet specimen held at National Museums Scotland is a unique skin of the extinct Réunion ParakeetPsittacula eques eques: a reply to Cheke and Jansen ()

This is the peer reviewed version of the following article: Jones, C. G. , Jackson, H. A. , McGowan, R. Y. , Hume, J. P., Forshaw, J. M. , Tatayah, V. , Winters, R. and Groombridge, J. J. (2019), A parakeet specimen held at National Museums Scotland is a unique skin of the extinct Reunion Parakeet Psittacula eques eques: a reply to Cheke and Jansen (). Ibis, 161: 230-238. doi:10.1111/ibi.12673, which has been published in final form at doi:10.1111/ibi.12673. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
Evaluation of Antibacterial Activity of Plant Extracts on Antibiotic Resistant Bacteria

It is now common that market is receiving new antibiotics everyday to tackle the problem of drug resistance developed by pathogenic microorganisms. All pharmaceutical companies are reserving substantial part of their annual budget for developing new medicines. Clinical history of the disease is also changing due to development of new bacterial strains. Thus patients have become victim of these new drugs which are mostly tried on trial and error basis. The patients have to bear the side effects of such antibiotics such as suppressed immunity, hypersensitive reactions, stomach upsets, etc.
Novel Network-Based Integrated Analyses of Multi-Omics Data Reveal New Insights into CD8+ T Cell Differentiation and Mouse Embryogenesis

Author(s): Zhang, Kai | Advisor(s): Wang, Wei | Abstract: Advancements in next-generation sequencing technologies have fueled the development of high throughput profiling assays. The sheer volume of data generated by these experiments grants us an unprecedented opportunity to deepen our understanding of complex biological systems, but also raise many computational challenges. With multi-omics data becoming very common in modern biological research, one of the most urgent tasks is to develop novel algorithms to perform integrated data analyses of these data. In the thesis, we developed network-based frameworks to integrate a variety of omics data. We combined the strength of different high throughput assays and analyzed multi-omics data to infer molecular interactions and build regulatory networks. Using network-based approaches, we addressed two important biological problems: identifying protein complexes mediating the formation of chromosome loops and identifying driver TFs in different biological processes. We further conducted computational and biological experiments to validate our findings. Our study provides new insights into the processes of CD8+ T cell development and mouse embryogenesis. The identified driver TFs can be used as the blueprint for future mechanistic study.
Modeling and optimization of essential amino acids effects on productive performance in second-cycle hens

In this study, a model based on a modification of the Gompertz equation was used to estimate the maximum percentage of egg production and digestible requirements of lysine (Lys), methionine + cystine (Met + Cys) and threonine (Thr) of H&N brown laying hens during 16 weeks of production. The productive performance model was adjusted to field data of 23 treatments, which were defined from a composite central design that combines five levels of Lys, Met + Cys, and Thr ranged from 0.636% up to 1.000%; 0.579% up to 0.910%; 0.483% up to 0.760%, respectively. The proposed model showed to be adequate to evaluate the efficiency in the use of digestible amino acids for egg production and can be a useful tool to diagnose the effectiveness of the nutritional requirements in each of the production phases.
Membership Function-Dependent Local Controller Design for T–S Fuzzy Systems

For the conservatism issue of state-feedback control for Takagi–Sugeno (T–S) fuzzy systems, a novel local controller design method and stability analysis approach are proposed in this article. First, based on a membership function piecewise linearization technique, a local linear controller is proposed to form a closed-loop system. Then, a series of system stability conditions are derived using quadratic and piecewise function approaches. Further, with a designed fuzzy local controller and fuzzy Lyapunov function, less conservative stability conditions are obtained. Finally, a simulation example is adopted to make comparisons with existing and proposed methods. The results clearly show the conservatism reduction and excellent performance of the proposed approach.
Floristic-structural relationships between Canga ferruginous tree communities and adjacent vegetation types

Our objective was to evaluate the floristic and structural relationships between Canga tree communities and other vegetation types inserted in the physiognomic units set, in order to test the hypothesis that these communities have unique characteristics due to their specific environmental conditions. For this, we compared the structural and floristic attributes of Canga vegetation with adjacent semideciduous seasonal forest, Savanna and ecotone areas, evaluating the similarity in its behavior. Our results demonstrate the existence of distinct relationships among vegetation types in relation to different perspectives, related to macro-scale environmental attributes and to the phytogeographic context. In general, Canga tree vegetation has its structure associated with open vegetation types, such as the Cerrado (Savanna) and its composition associated with forest vegetation types, constituted by a community with specific ecological characteristics. Our results suggest the presence of ferruginous soils as a factor that contributes to environmental and ecological heterogeneity in vegetation matrices.