Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxynema aestuarii sp. nov. (Microcoleaceae) isolated from an Indian mangrove forest

Taxonomic characterization by a polyphasic approach was carried out on two cyanobacteria, AP17 and AP24 isolated from soil biofilms of two separate islands, Lothian and Sagar respectively, of the Indian Sundarbans. The strains were studied morphologically by light microscopy, scanning and transmission electron microscopy. Growth responses to various salinities were recorded. Molecular data included sequencing and phylogenetic study of the 16S rRNA gene as well as analysis of the 14 regions of the 16S-23S ITS regions. Morphologically the strains were found to be non-heterocytous, having attenuated trichomes with a narrow, bent terminal cell without any crosswalls. Strains under investigation shared 99–100% 16S rRNA gene sequence similarity with Oxynema thaianum CCALA960, the type species of the novel Oxynema genus, recently separated from the Phormidium-Group I genus. However, cross walls in the apical portion of AP17 and AP24 were totally absent while the same was present in CCALA960. Additionally, optimal growth of AP17 and AP24 was recorded in 5–8% salinity and salinity above 14% inhibited growth of both strains, which were isolated from an intertidal environment; whereas O. thaianum CCALA960 which was found in a hypersaline environment could grow at 40% salinity. Insertion of 9 nucleotides in the D2 with spacer region, insertion of 2 nucleotides in the pre Box B spacer region, deletion of 2 nucleotides in the post Box B spacer region, deletion of 8 nucleotides in the D4 region, deletion of 8 nucleotides in V3 region and insertion of 2 nucleotides in the D5 region of the ITS sequences of AP17 and AP24 were observed in comparison to the analogous regions of CCALA960. Structural details of Box B helices of AP17 and AP24 revealed that although their lengths were identical with the reference, their sequences were completely different from CCALA960. Four nucleotide substitutions were observed in different positions in the Box B helix of O. thaianum CCALA960. Secondary structures of the V3 regions of AP17 and AP24 (containing 51 nucleotides) showed a small terminal bulge and a bigger bilateral bulge while the analogous structure of O. thaianum CCALA 960 (comprising of 59 nucleotides) showed one additional bilateral bulge in comparison to AP17 and AP24. Therefore, based on morphological, ecological and molecular differences in comparison to O. thaianum CCALA960, isolates AP17 and AP24 should be considered as a second novel species in the Oxynema genus, for which the name Oxynema aestuarii sp. nov. is proposed.
Phytochemical Profiles, Antioxidant and Antibacterial Activities of Grape (Vitis vinifera L.) Seeds and Skin from Organic and Conventional Vineyards

The therapeutic benefits of extracts obtained from different red grape fractions were thoroughly studied, however, data regarding the comparison of phytochemical extracts prepared from the same varieties coming from organic versus conventional management systems are rather lacking. The present study aimed at comparing some of the phytochemical characteristics and antimicrobial activity of hydroalcoholic (50% v/v) extracts obtained from four varieties of red grapes cultivated respectively in organic and conventional vineyards. Total flavonoid content, total phenolic compounds, and antioxidant activity were determined by molecular absorption spectroscopy. Antimicrobial activity of the studied extracts was evaluated against common bacterial strains isolated from different habitats according to specific lab procedures. The analyses were performed in solid broths by applying the disk diffusion method, which allowed for the simultaneous determination of the spectrum of the sensitivity of the tested bacteria as well as the values of the minimum inhibition concentration (MIC). It was found that favorable antagonistic activities against the tested bacteria strains were exhibited by the hydroalcoholic extracts from the seeds of the organic varieties, respectively the skin of the conventional varieties.
Stem cell and niche regulation in human short bowel syndrome

Loss of functional small bowel surface area following surgical resection for disorders such as Crohn’s disease, intestinal ischemic injury, radiation enteritis, and in children, necrotizing enterocolitis, atresia, and gastroschisis, may result in short bowel syndrome, with attendant high morbidity, mortality, and health care costs in the United States. Following resection, the remaining small bowel epithelium mounts an adaptive response, resulting in increased crypt cell proliferation, increased villus height, increased crypt depth, and enhanced nutrient and electrolyte absorption. Although these morphologic and functional changes are well described in animal models, the adaptive response in humans is less well understood. Clinically the response is unpredictable and often inadequate. Here we address the hypotheses that human intestinal stem cell populations are expanded and that the stem cell niche is regulated following massive gut resection in short bowel syndrome (SBS). We use intestinal enteroid cultures from patients with SBS to show that the magnitude and phenotype of the adaptive stem cell response are both regulated by stromal niche cells, including intestinal subepithelial myofibroblasts, which are activated by intestinal resection to enhance epithelial stem and proliferative cell responses. Our data suggest that myofibroblast regulation of bone morphogenetic protein signaling pathways plays a role in the gut adaptive response after resection.
Incidence and Prevalence of Type 1 Diabetes Mellitus among Korean Children and Adolescents between 2007 and 2017: An Epidemiologic Study Based on a National Database

Background The incidence of type 1 diabetes mellitus (T1DM) among children is high in Europe and the USA and relatively low in Asia, including Korea. The present study aimed to investigate the incidence and prevalence of childhood-onset T1DM in Korea and examine trends in incidence. Methods This study was conducted using the national registry data provided by the Health Insurance Review and Assessment Service in Korea from 2007 to 2017. We included children aged 0 to 14 years who were newly registered with a T1DM diagnosis each year (code E10). Results A total of 29,013 children were registered. The overall incidence of T1DM was 4.45 per 100,000 persons (girls, 4.93; boys, 4.01). The overall incidence of childhood-onset T1DM in Korea increased from 3.70 in 2008 to 4.77 in 2016 (P=0.002). The incidence of T1DM increased from 3.07 in 2008 to 4.89 in 2016 (P<0.001) among boys. Although the incidence of the disease increased significantly among boys aged 5–9 and 10–14 years, it remained constant among girls (4.39 in 2008, 4.64 in 2016). The overall prevalence of childhood-onset T1DM in Korea increased from 32.85 in 2007 to 41.03 per 100,000 persons in 2017 (girls, 35.54 to 43.88; boys, 32.85 to 41.03). Conclusion We calculated relatively accurate incidence and prevalence of childhood-onset T1DM from a nation-based registry. The incidence increased by 3% to 4% every year from 2007 to 2017. The increasing trend is noteworthy compared with previous reports.
Recognition and Grasping of Disorderly Stacked Wood Planks Using a Local Image Patch and Point Pair Feature Method

Considering the difficult problem of robot recognition and grasping in the scenario of disorderly stacked wooden planks, a recognition and positioning method based on local image features and point pair geometric features is proposed here and we define a local patch point pair feature. First, we used self-developed scanning equipment to collect images of wood boards and a robot to drive a RGB-D camera to collect images of disorderly stacked wooden planks. The image patches cut from these images were input to a convolutional autoencoder to train and obtain a local texture feature descriptor that is robust to changes in perspective. Then, the small image patches around the point pairs of the plank model are extracted, and input into the trained encoder to obtain the feature vector of the image patch, combining the point pair geometric feature information to form a feature description code expressing the characteristics of the plank. After that, the robot drives the RGB-D camera to collect the local image patches of the point pairs in the area to be grasped in the scene of the stacked wooden planks, also obtaining the feature description code of the wooden planks to be grasped. Finally, through the process of point pair feature matching, pose voting and clustering, the pose of the plank to be grasped is determined. The robot grasping experiment here shows that both the recognition rate and grasping success rate of planks are high, reaching 95.3% and 93.8%, respectively. Compared with the traditional point pair feature method (PPF) and other methods, the method present here has obvious advantages and can be applied to stacked wood plank grasping environments.
Effects of Netarsudil on Actin-Driven Cellular Functions in Normal and Glaucomatous Trabecular Meshwork Cells: A Live Imaging Study

The actin cytoskeleton of trabecular meshwork (TM) cells is a therapeutic target for lowering intraocular pressure (IOP) in glaucoma patients. Netarsudil (the active ingredient in RhopressaTM) is a Rho-associated protein kinase inhibitor that induces disassembly of actin stress fibers. Here, we used live cell imaging of SiR-actin-labeled normal (NTM) and glaucomatous TM (GTM) cells to investigate actin dynamics during actin-driven biological processes with and without netarsudil treatment. Actin stress fibers were thicker in GTM than NTM cells and took longer (>120 min) to disassemble following addition of 1 µM netarsudil. Actin-rich extracellular vesicles (EVs) were derived by two mechanisms: exocytosis of intracellular-derived vesicles, and cleavage of filopodial tips, which detached the filopodia from the substratum, allowing them to retract to the cell body. While some phagocytosis was noted in untreated TM cells, netarsudil potently stimulated phagocytic uptake of EVs. Netarsudil treatment induced lateral fusion of tunneling nanotubes (TNTs) that connected adjacent TM cells; TNTs are important for TM cellular communication. Together, our results suggest that netarsudil may clear outflow channels in TM tissue by inducing phagocytosis and/or by modulating TM communication via EVs and TNTs. These cellular functions likely work together to regulate IOP in normal and glaucomatous TM.
Bioglass incorporated methacrylated collagen bioactive ink for 3D printing of bone tissue

Bioactive three-dimensional (3D) printed scaffolds are promising candidates for bone tissue engineering (BTE) applications. Here, we introduce a bioactive ink composed of Bioglass 45S5 (BG) and methacrylated collagen (CMA) for 3D printing of biomimetic constructs that resemble the organic and inorganic composition of native bone tissue. A uniform dispersion of BG particles within the collagen network improved stability and reduced swelling of collagen hydrogels. Rheological testing showed significant improvement in the yield stress and percent recovery of 3D printed constructs upon BG incorporation. Further, addition of BG improved the bone bioactivity of 3D printed constructs in stimulated body fluid. BG incorporated CMA (BG-CMA) constructs maintained high cell viability and enhanced alkaline phosphatase activity of human mesenchymal stem cells. In addition, cell-mediated calcium deposition was significantly higher on BG-CMA constructs, compared to CMA alone. In conclusion, 3D printed BG-CMA constructs have significant potential for use in BTE applications.
Emerging roles of long noncoding RNAs in cholangiocarcinoma: Advances and challenges

Cholangiocarcinoma (CCA), a cancer with a relatively low incidence rate, is usually associated with poor prognosis. Current modalities for the diagnosis and treatment of CCA patients are still far from satisfactory. In recent years, numerous long noncoding RNAs (lncRNAs) have been identified as crucial players in the development of various cancers, including CCA. Abnormally expressed lncRNAs in CCA, regulated by some upstream molecules, significantly influence the biological behavior of tumor cells and are involved in tumor development through various mechanisms, including interactions with functional proteins, participation in competing for endogenous RNA (ceRNA) regulatory networks, activation of cancer‐related signaling pathways and epigenetic modification of gene expression. Furthermore, several lncRNAs are closely associated with the clinicopathological features of CCA patients, and are promising biomarkers for diagnosing and prognostication of CCA. Some of these lncRNAs play an important role in chemotherapy drug resistance. In addition, lncRNAs have also been shown to be involved in the inflammation microenvironment of CCA and malignant outcome of CCA risk factors, such as cholestatic liver diseases. In view of the difficulty of diagnosing CCA, more attention should be paid to detectable lncRNAs in the serum or bile. This review summarizes the recent knowledge on lncRNAs in CCA and provides a new outlook on the molecular mechanisms of CCA development from the perspective of lncRNAs. Moreover, we also discussed the limitations of the current studies and differential expression of lncRNAs in different types of CCA.
Virtual Reality as a Portable Alternative to Chromotherapy Rooms for Stress Relief: A Preliminary Study

Chromotherapy rooms are comfortable spaces, used in places like special needs schools, where stimuli are carefully selected to cope with stress. However, these rooms are expensive and require a space that cannot be reutilized. In this article, we propose the use of virtual reality (VR) as an inexpensive and portable alternative to chromotherapy rooms for stress relief. We recreated a chromotherapy room stress relief program using a commercial head mounted display (HD). We assessed the stress level of two groups (test and control) through an EEG biomarker, the relative gamma, while they experienced a relaxation session. First, participants were stressed using the Montreal imaging stress task (MIST). Then, for relaxing, the control group utilized a chromotherapy room while the test group used virtual reality. We performed a hypothesis test to compare the self- perceived stress level at different stages of the experiment and it yielded no significant differences in reducing stress for both groups, during relaxing (p-value: 0.8379, α = 0.05) or any other block. Furthermore, according to participant surveys, the use of virtual reality was deemed immersive, comfortable and pleasant (3.9 out of 5). Our preliminary results validate our approach as an inexpensive and portable alternative to chromotherapy rooms for stress relief.
In vitro-induction of metronidazole-resistant Giardia duodenalis is not associated with nucleotide alterations in the genes involved in pro-drug activation

Giardiasis is an infectious disease caused by Giardia duodenalis. The pro-drug metronidazole (MTZ) is the first-line treatment for giardiasis. Parasite’s proteins as pyruvate:ferredoxin oxidoreductase (PFOR), ferredoxin (Fd), nitroreductase-1 (NR-1) and thioredoxin reductase (TrxR) participate in MTZ activation. Here, we showed Giardia trophozoites long-term exposed to MTZ presented higher IC50 than controls, showing the drug influenced the parasite survival. That reduction in MTZ’s susceptibility does not seem to be related to mutations in the genes pfor, fd, nr-1 or trxr. It points that different mechanism as alterations in other metabolic pathways can account for Giardia resistance to MTZ therapy.
Endovascular Treatment of Stroke Caused by Carotid Artery Dissection

Ischemic stroke due to large vessel occlusion (LVO) is a devastating condition. Most LVOs are embolic in nature. Arterial dissection is responsible for only a small proportion of LVOs, is specific in nature and poses some challenges in treatment. We describe 3 cases where patients with stroke caused by carotid artery dissection were treated with mechanical thrombectomy and extensive stenting with good outcome. We believe that mechanical thrombectomy and stenting is a treatment of choice in these cases.
Association of the functional capacity and violence in the elderly community.

OBJECTIVE To analyze the relationship between the functional capacity of elderly community members and the sociodemographic and violence characteristics. METHODS Cross-sectional, epidemiological, analytical study with 159 elderly people. For data collection, a questionnaire was used for sociodemographic characterization; the Katz, Lawton and Brody scale; a questionnaire adapted from the FIBRA network; and the Conflict Tactics Scales, analyzed using descriptive and inferential statistics using Pearson's chi-square test, Fisher's exact test and multiple logistic regression models. RESULTS It was observed that the sociodemographic variables influence the prevalence of functional dependence for basic activities of daily living and reduction in advanced activities in elderly people with psychological and physical violence. CONCLUSION The dependence of the elderly for basic and intermediate activities is related to characteristics such as advanced age, work exercise and knowing how to read and write. The participants' functional dependence can favor violent outcomes, whether physical or psychological.
A New Species of Eumanota Edwards (Diptera: Mycetophilidae: Manotine) from Colombia: Evidence for a Pseudogondwanan Pattern

ABSTRACT Eumanota wolffae, sp. nov., is described from the high Andean forests of Colombia. This is the first Neotropical species of the clade of non-Manota genera of the mycetophilid subfamily Manotinae—to date known entirely from the Oriental and the northwestern Australasian regions, and in Baltic amber. With the other species of Eumanota Edwards, this species shares, among other features, a largely developed third maxillary palpomere, projecting beyond the base of fourth palpomere, with a wide sensorial pit, a flat inner face, and the last palpomere at least 4× the length of the fourth palpomere. The systematic position of the Colombian species within the Manotinae is addressed. The biogeographic significance of Eumanota in the Neotropical region is discussed, interpreted here as a concurrent incidence of a circumtropical pattern and Gondwanan distributions, in other words, a particular pattern of biogeographic pseudocongruence, referred to here as a “pseudogondwanan pattern. ” This pattern is associated with an early Cenozoic tropical biota over Laurasian terranes that expanded its distribution to the south (in the Americas, Africa, and Australasia), followed by large-scale extinction of Nearctic and Palearctic representatives due to global cooling in the Neogene. A discussion is provided about the correlation between these patterns and evidence of Late Cretaceous-Paleogene tropical floras over Laurasian terranes.
The matrix metalloproteinase inhibitor IPR-179 has antiseizure and antiepileptogenic effects.

Matrix metalloproteinases (MMPs) are synthesized by neurons and glia and released into the extracellular space, where they act as modulators of neuroplasticity and neuroinflammatory agents. Development of epilepsy (epileptogenesis) is associated with increased expression of MMPs and therefore they may represent potential therapeutic drug targets. Using qPCR and immunohistochemistry, we studied the expression of MMPs and their endogenous inhibitors TIMPs, in patients with status epilepticus (SE) or temporal lobe epilepsy (TLE), and in a rat TLE model. Furthermore, we tested the MMP2/9 inhibitor IPR-179 in the rapid kindling rat model and in the intrahippocampal kainic-acid mouse model.In both human and experimental epilepsy, MMP and TIMP expression was persistently dysregulated in the hippocampus compared to controls. IPR-179 treatment reduced seizure severity in the rapid kindling model and reduced the number of spontaneous seizures in the kainic-acid model (during and up to 7 weeks after delivery) without side effects while improving cognitive behavior. Moreover, our data suggest that IPR-179 prevented an MMP2/9-dependent switch-off normally restraining network excitability during the activity period. Since increased MMP expression is a prominent hallmark of the human epileptogenic brain and the MMP inhibitor IPR-179 has antiseizure and antiepileptogenic effects in rodent epilepsy models and attenuates seizure-induced cognitive decline, it deserves further investigation in clinical trials.
Elektrostatische Wechselwirkungen in komplexen Flüssigkeiten und ihre Beschreibung mit Molekulardynamiksimulationen

Wasser ist eine hochpolare Flussigkeit. Ihre ungewohnlichen elektrostatischen Eigenschaften haben das organische Leben, das sich dort entwickelt hat, gepragt. Daher bestimmen beispielsweise die elektrostatischen Wechselwirkungen zwischen der wassrigen Zellflussigkeit und den darin gelosten Proteinen, den molekularen Funktionstragern der Biologie, sowohl die Struktur als auch die Dynamik dieser Makromolekule. Mikroskopische Simulationsbeschreibungen der in Protein-Losungsmittel Systemen ablaufenden Prozesse mussen deshalb jene Probleme losen, welche durch den sehr langsamen 1/r Abfall der Coulomb Wechselwirkung und die endliche Grose von Simulationsmodellen aufgeworfen werden. Die vorliegende Arbeit fasst eine Reihe von Publikationen zusammen, in denen zunachst mit dem sog. SAMM/RF Algorithmus eine genaue und recheneffiziente Losung fur die angesprochenen methodischen Probleme vorgeschlagen und verifiziert wird [G. Mathias, B. Egwolf, M. Nonella, P. Tavan, J. Chem. Phys. 118, 10847-10860 (2003)]. Bei molekularmechanischen (MM) Molekulardynamik (MD) Simulationen ermoglicht dieser Algorithmus die Beschreibung sehr groser Systeme mit mehr als 10^5 Atomen auf einer Nanosekunden-Zeitskala. Fur flussiges Wasser konnten damit winkelaufgeloste Korrelationsfunktionen, die von mir vorgeschlagen wurden, auch bei grosen Abstanden statistisch genau berechnet werden [G. Mathias, P. Tavan, J. Chem. Phys. 120, 4393-4403 (2004)]. Damit lies sich die dipolare Struktur der Solvatschalen um ein gegebenes Wassermolekul analysieren. Daruber hinaus wurde nachgewiesen, dass sich Wasser ab Distanzen von etwa 15 A° wie ein homogenes Dielektrikum verhalt. Die SAMM/RF Methode wurde ferner zur Beschreibung der langreichweitigen Elektrostatik bei Hybridrechnungen eingesetzt, welche Dichtefunktional Methoden mit MM Kraftfeldern kombinieren, um so Schwingungsspektren biologischer Chromophore in polaren und in komplexen Losungsmitteln quantitativ genau berechnen zu konnen. An den Beispielen des Retinalchromophors im Meta-III Zustand des Rhodopsins [R. Vogel, F. Siebert, G. Mathias, P. Tavan, G. Fan, M. Sheves, Biochemistry 42, 9863-9874 (2003)], der Chinone im bakteriellen Reaktionszentrum [M. Nonella, G. Mathias, M. Eichinger, P. Tavan, J. Phys. Chem. B 107, 316-322 (2003)] und eines Chinonmolekuls in wassriger Losung [M. Nonella, G. Mathias, P. Tavan, J. Phys. Chem. A 107, 8638-8647 (2003)] wird gezeigt, wie elektrostatische Wechselwirkungen eines Molekuls mit seiner Losungsmittelumgebung seine Schwingungsspektren modifizieren.
The recurrence of dense face-centered cubic cesium

At ambient conditions, alkali metal cesium (Cs) owns a body-centered cubic phase, and this phase will transform to a face-centered cubic (fcc) phase at a pressure of 2.3 GPa. Under stronger compression, Cs will transform to oC84, tI4, oC16, and double hexagonal close-packed (dhcp) phases in sequence. Here, using first-principles structure searching prediction and total-energy calculation, we report that the Cs will re-transform to the fcc phase as the post-dhcp phase above 180 GPa. The transition state calculations suggest that the phase transition takes place by overcoming an energy barrier (144 meV/atom at 200 GPa) and finishes within a volume collapse of 0.3%. The electronic states at Fermi level are derived mainly from d electrons and there is a large overlap between inner core electrons, making the high-pressure fcc Cs distinguished from the first one at low pressure. The same phase transition also occurs in potassium and rubidium but with higher pressures.