Miracle-dz/UniFAR-FTUs huggingface dataset:
A Biotic Index for the Southeastern United States: Derivation and List of Tolerance Values, with Criteria for Assigning Water-Quality Ratings

North Carolina's Division of Environmental Management has a large number of semiquantitative stream macroinvertebrate collections that have been assigned water-quality ratings. These semiquantitative data use abundance values of Rare = 1 Common = 3, and Abundant = 10, allowing the calculation of mean abundance (range = 0-10) for each taxon across five water-quality classes. This information was used to derive tolerance values and classification criteria for a south-eastern biotic index Classification criteria were adjusted for both season and ecoregion, but no corrections were required for stream size. Tolerance values are listed for >500 North Carolina taxa, and are compared with a similar Wisconsin data base.
Food body production in Macaranga triloba (Euphorbiaceae) : a plant investment in anti-herbivore defence via mutualistic ant partners

MARTIN HEIL*, BRIGITTE FIALA*, K. EDUARD LINSENMAIR*, GERHARD ZOTZt, PETRA MENKEt and ULRICH MASCHWITZt *Lehrstuhlfar Zoologie III, Theodor-Boveri-Institut, Biozentrum, Am Hubland, D-97074 Wurzburg, tLehrstuhl far Botanik II, Julius-von-Sachs-Institut, Mittlerer Dallenbergweg 64, D-97082 Wurzburg, and tZoologisches Institut der J. W. Goethe-Universitdt, Siesmayerstr. 70, D-60054 Frankfurt, Germany
Tau phosphorylation by glycogen synthase kinase 3β modulates enzyme acetylcholinesterase expression

In Alzheimer's disease (AD), the enzyme acetylcholinesterase (AChE) co‐localizes with hyperphosphorylated tau (P‐tau) within neurofibrillary tangles. Having demonstrated that AChE expression is increased in the transgenic mouse model of tau Tg‐VLW, here we examined whether modulating phosphorylated tau levels by over‐expressing wild‐type human tau and glycogen synthase kinase‐3β (GSK3β) influences AChE expression. In SH‐SY5Y neuroblastoma cells expressing higher levels of P‐tau, AChE activity and protein increased by (20% ± 2%) and (440% ± 150%), respectively. Western blots and qPCR assays showed that this increment mostly corresponded to the cholinergic ACHE‐T variant, for which the protein and transcript levels increased ~60% and ~23%, respectively. Moreover, in SH‐SY5Y cells differentiated into neurons by exposure to retinoic acid (10 µM), over‐expression of GSK3β and tau provokes an imbalance in cholinergic activity with a decrease in the neurotransmitter acetylcholine in the cell (45 ± 10%). Finally, we obtained cerebrospinal fluid (CSF) from AD patients enrolled on a clinical trial of tideglusib, an irreversible GSK3β inhibitor. In CSF of patients that received a placebo, there was an increase in AChE activity (35 ± 16%) respect to basal levels, probably because of their treatment with AChE inhibitors. However, this increase was not observed in tideglusib‐treated patients. Moreover, CSF levels of P‐tau at the beginning measured by commercially ELISA kits correlated with AChE activity. In conclusion, this study shows that P‐tau can modulate AChE expression and it suggests that AChE may possibly increase in the initial phases of AD.
MiR-520d-5p modulates chondrogenesis and chondrocyte metabolism through targeting HDAC1

MicroRNAs (miRNAs) play an essential role in the chondrogenesis and the progression of osteoarthritis (OA). This study aimed to determine miRNAs associated with chondrogenesis of human mesenchymal stem cells (hMSCs) and chondrocyte metabolism. MiRNAs were screened in hMSCs during chondrogenesis by RNA-seq and qRT-PCR. MiRNA expression was determined in primary human chondrocytes (PHCs), and degraded cartilage samples. MiRNA mimics and inhibitors were transfected to cells to determine the effect of miRNA. Bioinformatic analysis and luciferase reporter assays were applied to determine the target gene of miRNA. The results demonstrated that miR-520d-5p was increased in hMSCs chondrogenesis. The overexpression and knockdown of miR-520d-5p promoted and inhibited chondrogenesis, and regulated chondrocyte metabolism. Histone deacetylase 1 (HDAC1) was decreased in hMSCs chondrogenesis, and HDAC1 was a targeting gene of miR-520d-5p. CI994, HDAC1 inhibitor, elevated cartilage-specific gene expressions and promoted hMSCs chondrogenesis. In IL-1β-treated PHCs, CI994 promoted AGGRECAN expression and suppressed MMP-13 expression, abolishing the effect of IL-1β on PHCs. Taken together, these results suggest that miR-520d-5p promotes hMSCs chondrogenesis and regulates chondrocyte metabolism through targeting HDAC1. This study provides novel understanding of the molecular mechanism of OA progression.
Impact of ALK variants on brain metastasis and treatment response in advanced NSCLC patients with oncogenic ALK fusion

Background To investigate the impact of ALK variants on the features of brain metastases (BM), the outcome of chemotherapy and targeted therapy using crizotinib, as well as the progression pattern in patients with ALK fusion. Methods Patients with ALK fusion were retrospectively collected from January 2013 to July 2017 in Shanghai Pulmonary Hospital. ALK rearrangements were identified via ARMS-PCR. ALK variants were identified via Sanger Sequencing. Results A total of 135 patients and 41 with brain metastasis were identified. Radiological features showed that the patients with ALK variant 1 had a larger BM size compared with patients with ALK non-variant 1 (median tumor size: 16.89 vs. 11.01 mm, P=0.031). Similar time to treatment failure (TTF) was observed in patients with ALK variant 1 and non-variant 1 who received first-line crizotinib (median TTF: 15.7 vs. 13.8 months, HR =0.75, P=0.34). Patients with ALK variant 1 who had baseline BM had significantly shorter TTF than non-variant 1 with baseline BM when treated with first-line crizotinib (median TTF: 9.1 vs. 14.9 months, HR =2.68, P=0.037). In patients treated with chemotherapy, ALK variant 1 was associated with inferior TTF (median TTF: 5.6 vs. 8.1 months, HR =1.66, P=0.039). Progression pattern was similar between ALK variant 1 and non-variant 1. Conclusions Patients with ALK variant 1 and baseline BM had inferior TTF on first-line crizotinib treatment and presented with more aggressive radiological features. Patients with ALK non-variant 1 had better clinical outcome on first-line chemotherapy.
Role of creatine and creatine kinase in UCP1-independent adipocyte thermogenesis.

During recent years, creatine kinase (CK) and its substrates phosphocreatine and creatine emerged as important players in uncoupling protein 1-independent, ATP-dependent non-shivering thermogenesis in beige/brown adipocytes. The exact thermogenic mechanism, that is facilitated by the CK system, however, still remains elusive. A futile creatine-cycling mechanism functioning via a hypothetical phosphocreatine phosphatase has been proposed. However, the molecular basis of such cycling remained elusive, so far. Here, we tend to argue for an alternative mechanism based on the classical CK/phosphocreatine shuttle and phosphocreatine-driven futile Ca2+-cycling at the endoplasmic reticulum.
Roles of lipid rafts in botulinum neurotoxin serotype A activity and differentiation of neuroblastoma cells

Botulinum neurotoxin serotype A (BoNT/A), one of seven serotypes of botulinum neurotoxin, is taken up by neurons of the peripheral nervous system. Within the neurons it catalyzes cleavage of the synaptosomal-associated protein having a mass of 25kDa, SNAP-25, thereby blocking neurotransmission. BoNT/A has been shown to interact with SV2, as well as gangliosides that are often found in lipid rafts. Lipid rafts are microdomains that can be found on the outer leaflet of the plasma membrane and are enriched in cholesterol and glycosphingolipids. To determine whether lipid rafts were needed for BoNT/A activity, those associated with the plasma membranes of murine N2a neuroblastoma cells were disrupted using either the cyclic oligomer methyl-βcyclodextrin or the polyene filipin. Disruption of cholesterol containing lipid rafts by either reagent did not prevent the action of BoNT/A on murine neuroblastoma N2a cells, in fact activity was enhanced. While our results indicate that disruption of lipid rafts enhances BoNT/A activity, disruption of clathrin-dependent endocytosis appeared to be inhibitory. In addition to disruption of lipid rafts enhancing BoNT/A activity, it also induced neuritogenesis of N2a cells. Therefore, studies were performed to determine the type of process formation induced by disruption of lipid rafts by either MβCD or filipin. Because ganglioside composition has been shown to change during neuronal differentiation, the question of whether process expression was accompanied by changes in ganglioside content or subcellular distribution was addressed. The results indicate that the processes formed were axonal in nature and their expression was accompanied by changes in both ganglioside content and subcellular localization.
Keratinocytes Communicate with Sensory Neurons via Synaptic‐like Contacts

Pain, temperature, and itch are conventionally thought to be exclusively transduced by the intraepidermal nerve endings. Although recent studies have shown that epidermal keratinocytes also participate in sensory transduction, the mechanism underlying keratinocyte communication with intraepidermal nerve endings remains poorly understood. We sought to demonstrate the synaptic character of the contacts between keratinocytes and sensory neurons and their involvement in sensory communication between keratinocytes and sensory neurons.
Long‐term expansion with germline potential of human primordial germ cell‐like cells in vitro

Human germ cells perpetuate human genetic and epigenetic information. However, the underlying mechanism remains elusive, due to a lack of appropriate experimental systems. Here, we show that human primordial germ cell‐like cells (hPGCLCs) derived from human‐induced pluripotent stem cells (hiPSCs) can be propagated to at least ~106‐fold over a period of 4 months under a defined condition in vitro. During expansion, hPGCLCs maintain an early hPGC‐like transcriptome and preserve their genome‐wide DNA methylation profiles, most likely due to retention of maintenance DNA methyltransferase activity. These characteristics contrast starkly with those of mouse PGCLCs, which, under an analogous condition, show a limited propagation (up to ~50‐fold) and persist only around 1 week, yet undergo cell‐autonomous genome‐wide DNA demethylation. Importantly, upon aggregation culture with mouse embryonic ovarian somatic cells in xenogeneic‐reconstituted ovaries, expanded hPGCLCs initiate genome‐wide DNA demethylation and differentiate into oogonia/gonocyte‐like cells, demonstrating their germline potential. By creating a paradigm for hPGCLC expansion, our study uncovers critical divergences in expansion potential and the mechanism for epigenetic reprogramming between the human and mouse germ cell lineage.
ITS-PCR sequencing approach deciphers molecular phylogeny in chickpea

Abstract Twenty chickpea accessions belonging to ten different countries of the world have been subjected to phylogeny and length variations from nuclear ribosomal DNA (nr DNA). ITS1–5.8S–ITS2 regions of Cicer accessions were used for amplification in two sets, each comprising a reverse and forward ITS primers. Lengths of ITS-1 of C. arietinum and C. reticulatum ranged from 340 to 350 bp whereas that of ITS-2 from 400 to 410 bp. In all the 20 accessions investigated, GC content in ITS-1 ranged from 40 to 55% and in ITS-2 from 42 to 55%. Sequencing of polymerase chain reaction product from ITS-1 showed variability in 278 and 290 bp due to adenine and guanine nucleotide base pairs. BLAST search for ITS-1 region revealed highest homology (99%) with four strains of C. arietinum accessions. Whereas, ITS2 showed 100% homology with C. arietinum and 99% homology with that of C. echinospermum.
Astrocytes are necessary for blood-brain barrier maintenance in the adult mouse brain

In the adult brain, multiple cell types are known to produce factors that regulate blood-brain barrier properties, including astrocytes. Yet several recent studies disputed a role for mature astrocytes at the blood-brain barrier. To determine if astrocytes contribute a non-redundant and necessary function in maintaining the adult blood-brain barrier, we used a mouse model of tamoxifen-inducible astrocyte ablation. In adult mice, tamoxifen induction caused sparse apoptotic astrocyte cell death within 2 hours. Indicative of BBB damage, leakage of the small molecule Cadaverine and the large plasma protein fibrinogen into the brain parenchyma indicative of BBB damage was detected as early as astrocyte ablation was present. Vessels within and close to regions of astrocyte loss had lower expression of the tight junction protein zonula occludens-1 while endothelial glucose transporter 1 expression was undisturbed. Cadaverine leakage persisted for several weeks suggesting a lack of barrier repair. This is consistent with the finding that ablated astrocytes were not replaced. Adjacent astrocytes responded with partial non-proliferative astrogliosis, characterized by morphological changes and delayed phosphorylation of STAT3, which restricted dye leakage to the brain and vessel surface areas lacking coverage by astrocytes one month after ablation. In conclusion, astrocytes are necessary to maintain blood-brain barrier integrity in the adult brain. Blood-brain barrier-regulating factors secreted by other cell types, such as pericytes, are not sufficient to compensate for astrocyte loss. Main Points Mature astrocytes are necessary for maintenance of endothelial tight junctions in the adult brain. Ablated astrocytes are not replaced by proliferation or process extension of neighboring astrocytes resulting in long-term blood-brain barrier damage.
3D Printing of cultured meat products

Abstract Three-dimensional (3D) printing is a fast-developing digital technology with colossal market scope in food and nutrition technology, providing a platform for establishing unique food products with enhanced sensory and nutritional value for a particular end-user. Cultured meat is the concept of producing meat sustainably in laboratory conditions without the sacrifice of animal life and the excessive use of antibiotics. 3D printing could offer unique solutions for the vital issues of cultured meat production; particularly on regulating the protein, fat, and other nutritional content, along with providing realistic texture. This review highlights the immense benefits of 3D printing technology for the scalable and reproducible production of cultured meat products.
A Cut-and-paste Community: Birds of Monsoon Rainforests in Kakadu National Park, Northern Territory

The bird species composition of 88 patches of monsoon rainforest in the Kakadu National Park area of the Northern Territory was examined in the period April-November 1987. The monsoon rainforest avifauna is a 'cut-and-paste' community, comprising species derived from wet tropical rainforests, from Eucalyptus open forests, from mangroves, from paperbark woodlands and habitat generalist species. Its composition may be seasonally unstable, and is re-arranged between monsoon rainforests of differing floristics or environment. For most bird species considered, the distribution was well associated with a division of monsoon rainforests into six groups: coastal, subcoastal, lowland springs, sandstone springs, escarpment and rock outcrop. Escarpment and rock outcrop rainforests were relatively depauperate. Monsoon rainforests are fragmented into small patches. The distribution of many characteristic rainforest birds (e.g. Orange-footed Scrub-fowl, Rainbow Pitta, Grey Whistler), bird species diversity and a Conservation Index were correlated with patch size. Bird species more typical of Eucalyptus open forests were abundant in patches most disturbed by buffalo, pigs, weeds and fire. No species were particularly associated with the edges of monsoon rainforests, but several open forest species occurred more commonly at edges than in the interior of monsoon rainforests (e.g. Barshouldered Dove, White-throated Honeyeater and Doublebarred Finch). Birds occurring in monsoon rainforests are probably highly vagile, a response mainly to the marked seasonality of the environment and the fragmented nature of monsoon rainforests.
Predictions of coronavirus COVID-19 distinct cases in Pakistan through an artificial neural network

Abstract This study presents the main motivation to investigate the COVID-19 pandemic, a major threat to the whole world from the day when it first emerged in China city of Wuhan. Predictions on the number of cases of COVID-19 are crucial in order to prevent and control the outbreak. In this research study, an artificial neural network with rectifying linear unit-based technique is implemented to predict the number of deaths, recovered and confirmed cases of COVID-19 in Pakistan by using previous data of 137 days of COVID-19 cases from the day 25 February 2020 when the first two cases were confirmed, until 10 July 2020. The collected data were divided into training and test data which were used to test the efficiency of the proposed technique. Furthermore, future predictions have been made by the proposed technique for the next 7 days while training the model on whole available data.
The Adapted Resistance Training with Instability Randomized Controlled Trial for Gait Automaticity

Deficits in the cerebellar locomotor region (CLR) have been associated with loss of gait automaticity in individuals with freezing of gait in Parkinson's disease (freezers); however, exercise interventions that restore gait automaticity in freezers are lacking. We evaluated the effects of the adapted resistance training with instability ([ARTI] complex exercises) compared with traditional motor rehabilitation (without complex exercises) on gait automaticity and attentional set‐shifting. We also verified associations between gait automaticity change and CLR activation change previously published.
Establishment of a quality control circle to reduce biofilm formation in flexible endoscopes by improvement of qualified cleaning rate

Objective In recent years, the Emergency Care Research Institute has advised that endoscope cleaning is of considerable importance. In the present study, a quality control circle (QCC) was used to reduce the formation of biofilms in flexible endoscopes within one hospital in Guangdong Province, China. Methods During reprocessing of 235 flexible endoscopes in the urology surgical suite, adenosine triphosphate (ATP) detection was used to monitor the efficacy of biofilm removal. The internal and external parts of flexible endoscopes were used as sampling sites by means of the flushing and smudge methods, respectively. When the two results reached the standard of less than 500 relative light units/piece at the same time, endoscopic biofilm clearance was considered to be qualified. A QCC was established to implement a 10-step plan-do-check-act model. Results The baseline qualified rate (i.e., ATP monitoring pass rate) during reprocessing of 235 flexible endoscopes was 50%. During the study, the qualified rate increased to 85.29% after establishment of the QCC. During reprocessing of 150 flexible endoscopes in the following 6 months, the qualified rate remained at 90%. Conclusion Establishment of the QCC improved the removal of biofilm from flexible endoscopes in the urology surgical suite.
Systematics for types and effects of RNA variations

ABSTRACT Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.
Noncanonical cytoplasmic poly(A) polymerases regulate RNA levels, alternative RNA processing, and synaptic plasticity but not hippocampal-dependent behaviours

ABSTRACT Noncanonical poly(A) polymerases are frequently tethered to mRNA 3ʹ untranslated regions and regulate poly(A) tail length and resulting translation. In the brain, one such poly(A) polymerase is Gld2, which is anchored to mRNA by the RNA-binding protein CPEB1 to control local translation at postsynaptic regions. Depletion of CPEB1 or Gld2 from the mouse hippocampus results in a deficit in long-term potentiation (LTP), but only depletion of CPEB1 alters animal behaviour. To test whether a related enzyme, Gld4, compensates for the lack of Gld2, we separately or simultaneously depleted both proteins from hippocampal area CA1 and again found little change in animal behaviour, but observed a deficit in LTP as well as an increase in long-term depression (LTD), two forms of protein synthesis-dependent synaptic plasticity. RNA-seq data from Gld2, Gld4, and Gld2/Gld4-depleted hippocampus show widespread changes in steady state RNA levels, alternative splicing, and alternative poly(A) site selection. Many of the RNAs subject to these alterations encode proteins that mediate synaptic function, suggesting a molecular foundation for impaired synaptic plasticity.
How do travelers manage jetlag and travel fatigue? A survey of passengers on long-haul flights

ABSTRACT Jetlag and travel fatigue can impair functioning, but it is unknown what strategies are used by travelers to minimize these consequences. Passengers on Qantas Airways flights were invited to take part in online surveys. Long-haul flights of ≥8 h into and out of Australia were targeted, which involved time differences of 1 to 18 h between the origin and destination. Passengers were queried about the use of travel booking choices before the flight, and the use of behavioral strategies before, during, and after flight for reducing jetlag and travel fatigue. Surveys were completed by N = 460 passengers aged 18 to 78 (43% male; mean age 50 y). Selecting a seat location (59%) and choosing a direct flight (52%) were the most common booking strategies. Almost all (99%) employed specific behavioral strategies during flight, with fewer implementing strategies before flight (73%) and after flight (89%). During the journey, 81% consumed or avoided caffeine and alcohol, 68% altered food intake, 68% used comfort/relaxation strategies, 53% light exposure, 35% physical activity, 31% compression stockings, 15% pharmaceutical sleep aids, and 8% melatonin. Surprisingly, only 1 of 460 passengers reported using a jetlag app. Younger travelers were more likely to adopt any strategy before the flight than older travelers (χ 2 2 = 14.90, p =.01), while female travelers appeared more likely than male travelers to use strategies before (77% vs. 68%) and after flight (91% vs. 85%). Reason for travel, flight cabin, leg of journey, and country of residence were not significantly associated with the use of behavioral strategies. Nearly all passengers took measures to improve the experience and consequences of long-haul flying. The results suggest that interventions around food/drink and physical activity may be highly acceptable to passengers for mitigating travel fatigue and that greater public education on evidence-based strategies may be helpful for reducing travel fatigue and jetlag.