Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular identification of Trichomonas tenax in the oral environment of domesticated animals in Poland - potential effects of host diversity for human health.

INTRODUCTION The protozoan Trichomonas tenax is considered to be a human specific flagellate of the oral cavity, found in humans with poor oral hygiene and advanced periodontal disease. Morphological variability and great similarity between species occurring in humans and animals, complicate the specific identification of trichomonads, using microscopic examination and other standard parasitological techniques. OBJECTIVE The aim of the study was to search for and identify T. tenax in domesticated animals using molecular methods. The obtained data were assessed in terms of potential effects of a spread of the species deriving from the animals in the human environment. MATERIAL AND METHODS 301 animals: 142 dogs, 57 cats and 102 horses, were examined in terms of their mouth status and occurrence of trichomonads. ITS1-5.8S rRNA-ITS2 region was amplified and sequenced. RESULTS Finally, 7 dogs, 3 cats and 1 horse were diagnosed positive for T. tenax by PCR. In the oral cavity of 9 /11 animals, gingivitis and dental plaque accumulation were diagnosed. 9 /11 sequences of trichomonad isolates showed 100% identity with T. tenax sequence derived from the GenBank. The sequences of 2 isolates differed by substitutions. CONCLUSIONS It was proved that T. tenax, considered so far as a human specific parasite, can also inhabit the oral cavity of dog, cat and horse. To summarize, T. tenax was detected in the mouths of different domesticated animals, indicating that in Poland it can colonize a wider range of hosts than previously known. The owners of 3 dogs showed oral tissue inflammation of different intensity and were also positive for T. tenax; therefore, oral trichomonosis spread from humans to domestic animals and conversely should be taken into consideration.
New Insights Into the Role of Cav2 Protein Family in Calcium Flux Deregulation in Fmr1-KO Neurons

Fragile X syndrome (FXS), the most common form of inherited intellectual disability (ID) and a leading cause of autism, results from the loss of expression of the Fmr1 gene which encodes the RNA-binding protein Fragile X Mental Retardation Protein (FMRP). Among the thousands mRNA targets of FMRP, numerous encode regulators of ion homeostasis. It has also been described that FMRP directly interacts with Ca2+ channels modulating their activity. Collectively these findings suggest that FMRP plays critical roles in Ca2+ homeostasis during nervous system development. We carried out a functional analysis of Ca2+ regulation using a calcium imaging approach in Fmr1-KO cultured neurons and we show that these cells display impaired steady state Ca2+ concentration and an altered entry of Ca2+ after KCl-triggered depolarization. Consistent with these data, we show that the protein product of the Cacna1a gene, the pore-forming subunit of the Cav2.1 channel, is less expressed at the plasma membrane of Fmr1-KO neurons compared to wild-type (WT). Thus, our findings point out the critical role that Cav2.1 plays in the altered Ca2+ flux in Fmr1-KO neurons, impacting Ca2+ homeostasis of these cells. Remarkably, we highlight a new phenotype of cultured Fmr1-KO neurons that can be considered a novel cellular biomarker and is amenable to small molecule screening and identification of new drugs to treat FXS.
European population trends and current conservation status of an endangered steppe-bird species: the Dupont’s lark Chersophilus duponti

Background Steppe-birds face drastic population declines throughout Europe. The Dupont’s lark Chersophilus duponti is an endangered steppe-bird species whose European distribution is restricted to Spain. This scarce passerine bird could be considered an ‘umbrella species’, since its population trends may reveal the conservation status of shrub-steppes. However, trends for the Spanish, and thus European, population of Dupont’s lark are unknown. In this work, we evaluated Dupont’s lark population trends in Europe employing the most recent and largest compiled database to date (92 populations over 12 years). In addition, we assessed the species threat category according to current applicable criteria (approved in March 2017) in the Spanish catalogue of threatened species (SCTS), which have never been applied to the Dupont’s lark nor to any other Spanish species. Finally, we compared the resulting threat categories with the current conservation status at European, national and regional levels. Methods We fitted switching linear trend models (software TRIM—Trends and Indices for Monitoring data) to evaluate population trends at national and regional scale (i.e. per Autonomous Community) during the period 2004–2015. In addition, the average finite annual rate of change (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\overline \lambda $\end{document}λ¯) obtained from the TRIM analysis was employed to estimate the percentage of population size change in a 10-year period. A threat category was assigned following A1 and A2 criteria applicable in the SCTS. Results Trends showed an overall 3.9% annual decline rate for the Spanish population (moderate decline, following TRIM). Regional analyses showed high inter-regional variability. We forecasted a 32.8% average decline over the next 10 years. According to these results, the species should be listed as ‘Vulnerable’ at a national scale (SCTS). At the regional level, the conservation status of the species is of particular concern in Andalusia and Castile-Leon, where the species qualifies for listing as ‘Endangered’. Discussion Our results highlight the concerning conservation status of the European Dupont’s lark population, undergoing a 3.9% annual decline rate. Under this scenario, the implementation of a wide-ranging conservation plan is urgently needed and is vital to ensuring the conservation of this steppe-bird species. The role of administrations in matters of nature protection and the cataloguing of endangered species is crucial to reverse declining population trends of this and other endangered taxa.
Upregulation of microRNA-129-5p inhibits cell invasion, migration and tumor angiogenesis by inhibiting ZIC2 via downregulation of the Hedgehog signaling pathway in cervical cancer

ABSTRACT Recently, some studies have placed additional research focus on microRNAs (miRNAs) in a bid to discover novel therapeutic approaches for cervical cancer (CC), which is one of the most common female reproductive tract malignancies with high rates of morbidity and mortality. Hence, the aim of the present study was to evaluate the ability of miR-129-5p to influence cell angiogenesis, invasion and migration by targeting ZIC2 through the Hedgehog signaling pathway in CC. Both CC and adjacent normal tissues were extracted from 87 eligible participating patients with CC. Measurements of the levels of miR-129-5p, mRNA and protein levels of ZIC2, sonic Hedgehog (Shh), Gli1, and Gli2 and levels of CXCL1, VEGF and Ang2 were determined accordingly. An angiogenesis assay was performed to evaluate cell angiogenesis in vitro, while a scratch test and transwell assay were adopted for cell invasion and migration determination. Lastly, tumor formation within nude mice was performed in order to analyze angiogenesis and tumor growth among the nude mice in vivo. The findings revealed that upregulation of miR-129-5p resulted in the decrease in the mRNA and protein levels of ZIC2, Shh, Gli1, Gli2, as well as reduced levels of CXCL1, VEGF and Ang2. Moreover, up-regulation of miR-129-5p was determined to inhibit CC cell angiogenesis ability in vitro, in addition to the processes of cell migration, and invasion. Finally, up-regulation of miR-129-5p was observed to inhibit the tumor growth and angiogenesis ability of nude mice in vivo. The results of the present study provided evidence suggesting that overexpressed miR-129-5p prevents angiogenesis and inhibits cell migration and invasion by means of negatively targeting ZIC2 through suppression of the Hedgehog signaling pathway in CC. Thus, highlighting the promise of miR-129-5p as a novel target for treating CC is promising.
Hierarchy-Based Image Embeddings for Semantic Image Retrieval

Deep neural networks trained for classification have been found to learn powerful image representations, which are also often used for other tasks such as comparing images w.r. t. their visual similarity. However, visual similarity does not imply semantic similarity. In order to learn semantically discriminative features, we propose to map images onto class embeddings whose pair-wise dot products correspond to a measure of semantic similarity between classes. Such an embedding does not only improve image retrieval results, but could also facilitate integrating semantics for other tasks, e.g., novelty detection or few-shot learning. We introduce a deterministic algorithm for computing the class centroids directly based on prior world-knowledge encoded in a hierarchy of classes such as WordNet. Experiments on CIFAR-100, NABirds, and ImageNet show that our learned semantic image embeddings improve the semantic consistency of image retrieval results by a large margin.
Otellerde Nepotizm (Akraba Kayırmacılığı) ve İşten Ayrılma Niyeti İlişkisi: Kariyer Düzleşmesinin Aracılık Etkisi

Bu calisma, otel calisanlarinda nepotizm(akraba kayirmaciligi), kariyer duzlesmesi ve isten ayrilma niyeti arasindaki iliskiyi belirlemeyi amaclamaktadir. Bu kapsamda, nepotizm, kariyer duzlesmesi ve isten ayrilma niyeti olceklerini kapsayan bir anket formu olusturulmustur. Anketler, kolayda ornekleme yontemi ile 03 Ekim 2016 ve 02 Şubat 2017 tarihleri arasinda, Istanbul ve Antalya’da faaliyet gosteren sekiz 4 ve 5 yildizli otel isletmesinde uygulanmistir. Toplam 236 adet kullanilabilir anket toplanmistir. Arastirmanin sonucu, nepotizmin, isten ayrilma niyeti uzerinde istatistiksel olarak anlamli ve pozitif bir etkisinin oldugunu gostermistir. Ayrica, kariyer duzlesmesinin bu iliski uzerinde araci bir etkisinin oldugu bulunmustur. Bu calismanin en onemli kisiti, calismanin, Istanbul ve Antalya’da sekiz otel isletmesinde yapilmis olmasindan dolayi genellenememesidir
Epigenetic modifications in chronic myeloid leukemia cells through ruxolitinib treatment

Chronic myeloid leukemia is a clonal malignancy of hematopoietic stem cell that is characterized by the occurrence of t(9;22)(q34;q11.2) translocation, named Philadelphia chromosome. Ruxolitinib is a powerful Janus tyrosine kinase 1 and 2 inhibitor that is used for myelofibrosis treatment. DNA‐histone connection mediates a wide range of genes that code methylation, demethylation, acetylation, deacetylation, ubiquitination, and phosphorylation enzymes. Epigenetic modifications regulate chromatin compactness, which plays pivotal roles in critical biological processes including the transcriptional activity and cell proliferation as well as various pathological mechanisms, including CML. This study is aimed to determine the alterations of the expression levels of epigenetic modification–related genes after ruxolitinib treatment. Total RNA was isolated from K‐562 cells treated with the IC50 value of ruxolitinib and untreated K‐562 control cells. A reverse transcription procedure was performed for complementary DNA synthesis, and gene expressions were detected by real‐time polymerase chain reaction compared with the untreated cells. Ruxolitinib treatment caused a significant alteration in the expression levels of epigenetic regulation‐related genes in K‐562 cells. Our novel results suggested that ruxolitinib has inhibitor effects on epigenetic modification–regulator genes.
Engineered titanium implants for localized drug delivery: recent advances and perspectives of Titania nanotubes arrays

ABSTRACT Introduction: Therapeutics delivery to bones to treat skeletal diseases or prevent postsurgical infections is challenging due to complex and solid bone structure that limits blood supply and diffusion of therapeutics administered by systemic routes to reach effective concentration. Titanium (Ti) and their alloys are employed as mainstream implant materials in orthopedics and dentistry; having superior mechanical/biocompatibility properties which could provide an alternative solution to address this problem. Areas covered: This review presents an overview of recent development of Ti drug-releasing implants, with emphasis on nanoengineered Titania nanotubes (TNTs) structures, for solving key problems to improve implants osseointegration, overcome inflammation and infection together with providing localized drug delivery (LDD) for bone diseases including cancer. Critical analysis of the advantages/disadvantages of developed concepts is discussed, their drug loading/releasing performances and specific applications. Expert opinion: LDD to bones can address many disorders and postsurgical conditions such as inflammation, implants rejection and infection. To this end, TNTs-Ti implants represent a potential promise for the development of new generation of multifunctional implants with drug release functions. Even this concept is extensively explored recently, there is a strong need for more preclinical studies using animal models to confirm the long-term safety and stability of TNTs-Ti implants for real-life medical applications.
Effect of Precipitation Temperature on the Properties of Cellulose Ultrafiltration Membranes Prepared via Immersion Precipitation with Ionic Liquid as Solvent

Supported cellulose ultrafiltration membranes are cast from a cellulose-ionic liquid solution by the immersion precipitation technique. The effects of coagulation bath temperature and polymer concentration in the casting solution on the membrane morphology, wettability, pure water flux, molecular weight cut-off, and fouling resistance are studied. Scanning electron microscopy, contact angle measurements, atomic force microscopy, and filtration experiments are carried out in order to characterise the obtained ultrafiltration cellulose membranes. The results show the effect of coagulation bath temperature and polymer concentration on the surface morphology and properties of cellulose ultrafiltration membranes. Optimisation of the two parameters leads to the creation of dense membranes with good pure water fluxes and proven fouling resistance towards humic acid water solutions.
Inflammation, a Double-Edge Sword for Cancer and Other Age-Related Diseases

Increasing evidence from diverse sources during the past several years has indicated that long-term, low level, chronic inflammation mediates several chronic diseases including cancer, arthritis, obesity, diabetes, cardiovascular diseases, and neurological diseases. The inflammatory molecules and transcription factors, adhesion molecules, AP-1, chemokines, C-reactive protein (CRP), cyclooxygenase (COX)-2, interleukins (ILs), 5-lipooxygenase (5-LOX), matrix metalloproteinases (MMPs), nuclear factor (NF)-kB, signal transducer and activator of transcription 3 (STAT3), tumor necrosis factor (TNF), and vascular endothelial growth factor (VEGF) are molecular links between inflammation and chronic diseases. Thus, suppression of inflammatory molecules could be potential strategy for the prevention and therapy of chronic diseases. The currently available drugs against chronic diseases are highly expensive, minimally effective and produce several side effects when taken for long period of time. The focus of this review is to discuss the potential of nutraceuticals derived from “Mother Nature” such as apigenin, catechins, curcumin, ellagic acid, emodin, epigallocatechin gallate, escin, fisetin, flavopiridol, genistein, isoliquiritigenin, kaempferol, mangostin, morin, myricetin, naringenin, resveratrol, silymarin, vitexin, and xanthohumol in suppression of these inflammatory pathways. Thus, these nutraceuticals offer potential in preventing or delaying the onset of chronic diseases. We provide evidence for the potential of these nutraceuticals from pre-clinical and clinical studies.
Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication

The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
BanditSum: Extractive Summarization as a Contextual Bandit

In this work, we propose a novel method for training neural networks to perform single-document extractive summarization without heuristically-generated extractive labels. We call our approach BanditSum as it treats extractive summarization as a contextual bandit (CB) problem, where the model receives a document to summarize (the context), and chooses a sequence of sentences to include in the summary (the action). A policy gradient reinforcement learning algorithm is used to train the model to select sequences of sentences that maximize ROUGE score. We perform a series of experiments demonstrating that BanditSum is able to achieve ROUGE scores that are better than or comparable to the state-of-the-art for extractive summarization, and converges using significantly fewer update steps than competing approaches. In addition, we show empirically that BanditSum performs significantly better than competing approaches when good summary sentences appear late in the source document.
The role of inflammation on the functionality of intracortical microelectrodes

Objective. Neuroinflammation has long been associated with the performance decline of intracortical microelectrodes (IMEs). Consequently, several strategies, including the use of anti-inflammatories, have been employed to mitigate the inflammation surrounding IMEs. However, these strategies have had limited success towards achieving a chronically viable cortical neural interface, questioning the efficacy of anti-inflammatory approach. Approach. Herein, we conducted a systematic study in rats implanted with functional devices by modulating inflammation via systemic injection of lipopolysaccharide (LPS), dexamethasone (DEX), a combination of both, or none to assess the degree of inflammation on device functionality. We hypothesized that implanted rats treated with LPS will have a negative impact, and rats treated with DEX will have a positive impact on functionality IMEs and histological outcome. Main results. Contrary to our hypothesis, we did not observe adverse effects in recording metrics among different groups with LPS and/or DEX treatment despite alterations in initial pro-inflammatory markers. We also did not observe any functional benefit of anti-inflammatory treatment. Regardless of the treatment conditions, the recording quality degraded at chronic time points. In end-point histology, implanted rats that received LPS had significantly lower NeuN density and higher levels of CD68 surrounding the implant site, indicative of the pro-inflammatory effect of LPS, which, however, contradicted with the recorded results. Significance. Collectively, our results suggest that acute inflammatory events may not be the key driver for functional degradation of IMEs. Future intervention strategies geared towards improving the functional longevity of intracortical devices may benefit using multi-modal approaches rather than a single approach, such as controlling the initial inflammatory response.
The Availability and Nutritional Adequacy of Gluten-Free Bread and Pasta

Management of coeliac disease (CD) requires the removal of gluten from the diet. Evidence of the availability, cost, and nutritional adequacy of gluten-free (GF) bread and pasta products is limited. GF flours are exempt from UK legislation that requires micronutrient fortification of white wheat flour. This study surveyed the number and cost of bread and pasta products available and evaluated the back-of-pack nutritional information, the ingredient content, and the presence of fortification nutrients of GF bread and pasta, compared to standard gluten-containing equivalent products. Product information was collected from four supermarket websites. Standard products were significantly cheaper, with more products available than GF (p < 0.05). GF bread products were significantly higher in fat and fiber (p < 0.05). All GF products were lower in protein than standard products (p < 0.01). Only 5% of GF breads were fortified with all four mandatory fortification nutrients (calcium, iron, nicotinic acid or nicotamide and thiamin), 28% of GF breads were fortified with calcium and iron only. This lack of fortification may increase the risk of micronutrient deficiency in coeliac sufferers. It is recommended that fortification legislation is extended to include all GF products, in addition to increased regulation of the nutritional content of GF foods.
Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis

Abstract DNA replication is coupled to growth by an unknown mechanism. Here, we investigated this coupling by analyzing growth and replication in 15 mutants of central carbon metabolism (CCM) cultivated in three rich media. In about one-fourth of the condition tested, defects in replication resulting from changes in initiation or elongation were detected. This uncovered 11 CCM genes important for replication and showed that some of these genes have an effect in one, two or three media. Additional results presented here and elsewhere (Jannière, L., Canceill, D., Suski, C., et al. (2007), PLoS One, 2, e447. ) showed that, in the LB medium, the CCM genes important for DNA elongation (gapA and ackA) are genetically linked to the lagging strand polymerase DnaE while those important for initiation (pgk and pykA) are genetically linked to the replication enzymes DnaC (helicase), DnaG (primase) and DnaE. Our work thus shows that the coupling between growth and replication involves multiple, medium-dependent links between CCM and replication. They also suggest that changes in CCM may affect initiation by altering the functional recruitment of DnaC, DnaG and DnaE at the chromosomal origin, and may affect elongation by altering the activity of DnaE at the replication fork. The underlying mechanism is discussed.