bluuebunny/crossref_metadata_2025_split huggingface dataset:
ACP-MHCNN: an accurate multi-headed deep-convolutional neural network to predict anticancer peptides
Authors: Ahmed Sajid , Muhammod Rafsanjani , Khan Zahid Hossain , Adilina Sheikh , Sharma Alok , Shatabda Swakkhar , Dehzangi Abdollah 
Published: December 2021

AbstractAlthough advancing the therapeutic alternatives for treating deadly cancers has gained much attention globally, still the primary methods such as chemotherapy have significant downsides and low specificity. Most recently, Anticancer peptides (ACPs) have emerged as a potential alternative to therapeutic alternatives with much fewer negative side-effects. However, the identification of ACPs through wet-lab experiments is expensive and time-consuming. Hence, computational methods have emerged as viable alternatives. During the past few years, several computational ACP identification techniques using hand-engineered features have been proposed to solve this problem. In this study, we propose a new multi headed deep convolutional neural network model called ACP-MHCNN, for extracting and combining discriminative features from different information sources in an interactive way. Our model extracts sequence, physicochemical, and evolutionary based features for ACP identification using different numerical peptide representations while restraining parameter overhead. It is evident through rigorous experiments using cross-validation and independent-dataset that ACP-MHCNN outperforms other models for anticancer peptide identification by a substantial margin on our employed benchmarks. ACP-MHCNN outperforms state-of-the-art model by 6.3%, 8.6%, 3.7%, 4.0%, and 0.20 in terms of accuracy, sensitivity, specificity, precision, and MCC respectively. ACP-MHCNN and its relevant codes and datasets are publicly available at:https://github.com/mrzResearchArena/Anticancer-Peptides-CNN. ACP-MHCNN is also publicly available as an online predictor at:https://anticancer.pythonanywhere.com/.
Ecological adaptation and phylogenetic analysis of microsymbionts nodulating Polhillia, Wiborgia and Wiborgiella species in the Cape fynbos, South Africa
Authors: Mpai Tiisetso , Jaiswal Sanjay K. , Cupido Christopher N. , Dakora Felix D. 
Published: December 2021

AbstractPolhillia,WiborgiaandWiborgiellaspecies are shrub legumes endemic to the Cape fynbos of South Africa. They have the ability to fix atmospheric N2when in symbiosis with soil bacteria called ‘rhizobia’. The aim of this study was to assess the morpho-physiological and phylogenetic characteristics of rhizobia associated with the nodulation ofPolhillia,WiborgiaandWiborgiellaspecies growing in the Cape fynbos. The bacterial isolates from root nodules consisted of a mixture of fast and intermediate growers that differed in colony shape and size. The isolates exhibited tolerance to salinity (0.5–3% NaCl) and pH (pH 5–10) and different antibiotic concentrations, and could produce 0.51 to 51.23 µg mL−1of indole-3-acetic acid (IAA), as well as solubilize tri-calcium phosphate. The ERIC-PCR results showed high genomic diversity in the rhizobial population and grouped them into two major clusters. Phylogenetic analysis based on 16S rRNA,atpD,glnII,gyrB,nifHandnodCgene sequences revealed distinct and novel evolutionary lineages related to the genusRhizobiumandMesorhizobium, with some of them being very close toMesorhizobium australicum. However, the phylogenetic analysis ofglnIIandnifHgenes of some isolates showed incongruency.
A lab-on-a-chip approach integrating in-situ characterization and reactive transport modelling diagnostics to unravel (Ba,Sr)SO4 oscillatory zoning
Authors: Poonoosamy Jenna , Mahrous Mohamed , Curti Enzo , Bosbach Dirk , Deissmann Guido , Churakov Sergey V. , Geisler Thorsten , Prasianakis Nikolaos 
Published: December 2021

AbstractThe co-precipitation of sulphate minerals such as celestine and barite is widely studied because their formation is ubiquitous in natural and anthropogenic systems. Co-precipitation in porous media results in crystallization of solid solutions yielding characteristics such as oscillatory zoning that are rarely observed in bulk solution or in batch experiments. In the past, the precipitation of compositionally-zoned (Ba,Sr)SO4 crystals was observed post-mortem in macroscopic silica gel counter-diffusion experiments. Their formation was originally explained by the difference in the solubility products of the end-members combined with diffusion-limited transport of solutes to the mineral-fluid interface, while a later study favored the idea of kinetically controlled reactions. With recent advances combining in-operando microfluidic experiments and reactive transport modelling, it is now possible to verify hypotheses on the driving forces of transport-coupled geochemical processes. We developed a “lab on a chip” experiment that enabled the systematic study of the nucleation and growth of oscillatory-zoned (Ba,Sr)SO4 crystals in a microfluidic reactor. The compositions of the solid solutions were determined by in-situ Raman spectroscopy. Our investigation shows (1) that the composition of the nucleating phases can be approximated using classical nucleation theory, (2) that the oscillatory zoning is not solely controlled by the limited diffusional transport of solutes, and (3) that nucleation kinetics plays a major role in the switch between different stoichiometric compositions. The zoning phenomena is governed by the complex interplay between the diffusion of reactants and the crystallization kinetics as well as other factors, e.g. surface tension and lattice mismatch.
Oxytocin enhances neural approach towards social and non-social stimuli of high personal relevance
Authors: Alaerts Kaat , Taillieu Aymara , Daniels Nicky , Soriano Javier R. , Prinsen Jellina 
Published: December 2021

AbstractOxytocin (OT) plays a pivotal role in a variety of complex social behaviors by modulating approach-avoidance motivational tendencies, but recently, its social specificity has been challenged. Here, a randomized, double-blind, placebo-controlled study was conducted with forty young adult men, investigating the effect of a single-dose of OT (24 IU) on behavioral and neural approach-avoidance. Frontal alpha asymmetry, indexing neurophysiological approach-avoidance, was obtained from electroencephalographic recordings while participants were presented with a series of pictures, individually rated in terms of personal relevance (i.e., high versus low positive/negative emotional evocativeness) and categorized as social or non-social. Additionally, participants could prolong (approach) or shorten (avoid) the viewing-time of each picture, providing a measure of behavioral approach-avoidance. Intranasal OT enhanced both behavioral and neural approach (increased viewing-time), particularly towards negatively valenced pictures of both social and non-social nature, thus challenging the notion that OT’s effects are specific to social stimuli. Neurally, OT specifically amplified approach-related motivational salience of stimuli that were self-rated to have high personal relevance, but irrespective of their social nature or rated affective valence (positive/negative). Together, these findings provide support to the General Approach-Avoidance Hypothesis of OT, suggesting a role of OT in amplifying the motivational salience of environmental stimuli with high (personal) relevance, but irrespective of their social/non-social nature.Clinical Trial Number: The study design was registered at ClinicalTrials.gov (NCT04443647; 23/06/2020; https://clinicaltrials.gov/ct2/show/NCT04443647).
Genetic and immunologic features of recurrent stage I lung adenocarcinoma
Authors: Kratz Johannes R. , Li Jack Z. , Tsui Jessica , Lee Jen C. , Ding Vivianne W. , Rao Arjun A. , Mann Michael J. , Chan Vincent , Combes Alexis J. , Krummel Matthew F. , Jablons David M. 
Published: December 2021

AbstractAlthough surgery for early-stage lung cancer offers the best chance of cure, recurrence still occurs between 30 and 50% of the time. Why patients frequently recur after complete resection of early-stage lung cancer remains unclear. Using a large cohort of stage I lung adenocarcinoma patients, distinct genetic, genomic, epigenetic, and immunologic profiles of recurrent tumors were analyzed using a novel recurrence classifier. To characterize the tumor immune microenvironment of recurrent stage I tumors, unique tumor-infiltrating immune population markers were identified using single cell RNA-seq on a separate cohort of patients undergoing stage I lung adenocarcinoma resection and applied to a large study cohort using digital cytometry. Recurrent stage I lung adenocarcinomas demonstrated higher mutation and lower methylation burden than non-recurrent tumors, as well as widespread activation of known cancer and cell cycle pathways. Simultaneously, recurrent tumors displayed downregulation of immune response pathways including antigen presentation and Th1/Th2 activation. Recurrent tumors were depleted in adaptive immune populations, and depletion of adaptive immune populations and low cytolytic activity were prognostic of stage I recurrence. Genomic instability and impaired adaptive immune responses are key features of stage I lung adenocarcinoma immunosurveillance escape and recurrence after surgery.
Cut-off value of D. pteronyssinus specific IgE in double negative patients Der p 1 and Der p 2 and its clinical repercussion
Authors: Letrán Antonio , García Ignacio , Espinazo-Romeu Marisa , Moreno-Aguilar Carmen , Moreno Francisco 
Published: December 2021

AbstractAccessibility to more precise diagnostic techniques such as component resolved diagnostics (CRD), provides us with an important advance in diagnostic aspects as well as treatment. The subject of this study aims to better understand the profiles of sensitization to Der p 1, Der p 2 and Der p 23 and to know to what extent their use could help us in optimizing the decision-making for their treatment with Specific Immunotherapy. Cross-sectional study of subjects older than 5 years, diagnosed with allergy to HDM using skin prick test and sIgE, with symptoms of rhinitis and/or asthma. Total and specific IgE was determined to D. pteronyssinus, nDer p 1, rDer p 2 and rDer p 23 using ImmunoCAP. 240 patients were recruited (97.1% rhinitis and 46.25% rhinitis and asthma). Four different phenotypes were observed: positive or negative for sIgE nDer p 1 and/or IgE rDer p 2. 17% of these patients sIgE were double negative for Der p 1 and Der p 2 (increasing with age and with significantly lower sIgE levels than the rest of the groups). Using ROC curves, value less than 2.18 KUA/L for D. pteronyssinus sIgE gave us a sensitivity and specificity of 0.882 and 0.985, respectively, to double negative IgE nDer p 1 and IgE rDer p 2 group. Despite positive SPT and sIgE to D. pteronyssinus, 17% of the studied population is IgE nDer p 1 and IgE rDer p 2 double negative, with a cut-off value of 2.18 KU/L, which is very relevant for taking of decisions in prescription of AIT. The double positive population sIgE nDer p 1 and IgE rDer p 2 is associated with asthma compared to the other groups and this does not seem to be influenced by IgE rDer p 23.
Single neonatal irradiation induces long-term gene expression changes in the thyroid gland, which may be involved in the tumorigenesis
Authors: Fujimoto Nariaki , Matsuu-Matsuyama Mutsumi , Nakashima Masahiro 
Published: December 2021

AbstractExposure to ionizing radiation in childhood has been recognized as a risk factor for thyroid cancer. We previously demonstrated that neonatal X-irradiation induced specific deformation of the thyroid follicles. Here, we further analyzed this model to understand the possible relationship with thyroid carcinogenesis. Wistar rats were subjected to cervical X-irradiation at different ages of 1–8 weeks old and at different doses of 1.5–12 Gy. For tumor promotion, rats were fed with an iodine-deficient diet (IDD). In cervically X-irradiated neonatal rats, the size of thyroid follicles decreased, accompanied by an increase in the number of TUNEL-positive cells. Fas and Lgals3 mRNA levels increased, while Mct8 and Lat4 expressions decreased. The co-administration of IDD induced the proliferation and the upregulation in Lgals3 expression, resulting in thyroid adenoma development at 28 weeks post-exposure. Our data demonstrated that single neonatal X-irradiation induced continuous apoptotic activity in the thyroid with the long-term alternation in Fas, Mct8, Lat4, and Lgals3 mRNA expressions. Some of these changes were similar to those induced by IDD, suggesting that neonatal X-irradiation may partially act as a thyroid tumor promoter. These radiation-induced thyroidal changes may be enhanced by the combined treatment with IDD, resulting in the early development of thyroid adenoma.
DNA barcoding of medicinal orchids in Asia
Authors: Raskoti Bhakta Bahadur , Ale Rita 
Published: December 2021

AbstractGrowing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2,matK,rbcL,trnH-psbAand their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matKexhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
In-vitro propagation and phytochemical profiling of a highly medicinal and endemic plant species of the Himalayan region (Saussurea costus)
Authors: Khan Ajmal , Shah Azhar Hussain , Ali Niaz 
Published: December 2021

AbstractEfficient protocols for callus induction and micro propagation ofSaussurea costus(Falc.) Lipsch were developed and phytochemical diversity of wild and in-vitro propagated material was investigated. Brown and red compact callus was formed with frequency of 80–95%, 78–90%, 70–95% and 65–80% from seeds, leaf, petiole and root explants, respectively. MS media supplemented with BAP (2.0 mgL−1), NAA (1.0 mgL−1) and GA3 (0.25 mgL−1) best suited for multiple shoot buds initiation (82%), while maximum shoot length was formed on media with BAP (1.5 mgL−1), NAA (0.25 mgL−1) and Kinetin (0.5 mgL−1). Full strength media with IAA (0.5 mgL−1) along with IBA (0.5 mgL−1) resulted in early roots initiation. Similarly, maximum rooting (87.57%) and lateral roots formation (up to 6.76) was recorded on full strength media supplemented with BAP (0.5 mgL−1), IAA (0.5 mgL−1) and IBA (0.5 mgL−1). Survival rate of acclimatized plantlets in autoclaved garden soil, farmyard soil, and sand (2:1:1) was 87%. Phytochemical analysis revealed variations in biochemical contents i.e. maximum sugar (808.32 µM/ml), proline (48.14 mg/g), ascorbic acid (373.801 mM/g) and phenolic compounds (642.72 mgL−1) were recorded from callus cultured on different stress media. Nonetheless, highest flavenoids (59.892 mg/g) and anthocyanin contents (32.39 mg/kg) were observed in in-vitro propagated plants. GC–MS analysis of the callus ethyl acetate extracts revealed 24 different phytochemicals. The variability in secondary metabolites of both wild and propagated plants/callus is reported for the first time for this species. This study may provide a baseline for the conservation and sustainable utilization ofS. costuswith implications for isolation of unique and pharmacologically active compounds from callus or regenerated plantlets.
Post-translational modifications by SIRT3 de-2-hydroxyisobutyrylase activity regulate glycolysis and enable nephrogenesis
Authors: Perico Luca , Morigi Marina , Pezzotta Anna , Corna Daniela , Brizi Valerio , Conti Sara , Zanchi Cristina , Sangalli Fabio , Trionfini Piera , Buttò Sara , Xinaris Christodoulos , Tomasoni Susanna , Zoja Carlamaria , Remuzzi Giuseppe , Benigni Ariela , Imberti Barbara 
Published: December 2021

AbstractAbnormal kidney development leads to lower nephron number, predisposing to renal diseases in adulthood. In embryonic kidneys, nephron endowment is dictated by the availability of nephron progenitors, whose self-renewal and differentiation require a relatively repressed chromatin state. More recently, NAD+-dependent deacetylase sirtuins (SIRTs) have emerged as possible regulators that link epigenetic processes to the metabolism. Here, we discovered a novel role for the NAD+-dependent deacylase SIRT3 in kidney development. In the embryonic kidney, SIRT3 was highly expressed only as a short isoform, with nuclear and extra-nuclear localisation. The nuclear SIRT3 did not act as deacetylase but exerted de-2-hydroxyisobutyrylase activity on lysine residues of histone proteins. Extra-nuclear SIRT3 regulated lysine 2-hydroxyisobutyrylation (Khib) levels of phosphofructokinase (PFK) andSirt3deficiency increased PFK Khib levels, inducing a glycolysis boost. This altered Khib landscape inSirt3−/−metanephroi was associated with decreased nephron progenitors, impaired nephrogenesis and a reduced number of nephrons. These data describe an unprecedented role of SIRT3 in controlling early renal development through the regulation of epigenetics and metabolic processes.
Quantitative mismatch between empirical temperature-size rule slopes and predictions based on oxygen limitation
Authors: Einum Sigurd , Bech Claus , Kielland Øystein Nordeide 
Published: December 2021

AbstractIn ectotherms, adult body size commonly declines with increasing environmental temperature, a pattern known as the temperature-size rule. One influential hypothesis explaining this observation is that the challenge of obtaining sufficient oxygen to support metabolism becomes greater with increasing body size, and more so at high temperatures. Yet, previous models based on this hypothesis do not account for phenotypic plasticity in the physiology of organisms that counteracts oxygen limitation at high temperature. Here, we model the predicted strength of the temperature-size response using estimates of how both the oxygen supply and demand is affected by temperature when allowing for phenotypic plasticity in the aquatic ectotherm Daphnia magna. Our predictions remain highly inconsistent with empirical temperature-size responses, with the prior being close to one order of magnitude stronger than the latter. These results fail to provide quantitative support for the hypothesis that oxygen limitation drives temperature-size clines in aquatic ectotherms. Future studies into the role of oxygen limitation should address how the strength of the temperature-size response may be shaped by evolution under fluctuating temperature regimes. Finally, our results caution against applying deterministic models based on the oxygen limitation hypothesis when predicting future changes in ectotherm size distributions under climate change.
The PRY/SPRY domain of pyrin/TRIM20 interacts with β2-microglobulin to promote inflammasome formation
Authors: Samukawa Sei , Yoshimi Ryusuke , Kirino Yohei , Nakajima Hideaki 
Published: December 2021

AbstractPyrin/TRIM20 is expressed in the neutrophils and monocytes/macrophages and regulates caspase-1 activation and interleukin-1β maturation. Although the mutations in the PRY/SPRY domain of pyrin cause familial Mediterranean fever (FMF), the mechanism of how mutated pyrin provokes excessive inflammation in FMF patients is not well understood. The present study investigated the role of pyrin/TRIM20 in inflammation and the pathogenesis of FMF. β2-Microglobulin (β2MG) was identified as the novel pyrin ligand binding to the PRY/SPRY domain by yeast two-hybrid screenings and co-immunoprecipitation analysis. β2MG was co-localized with pyrin not only in the HEK293 cells overexpressing these proteins but also in the monosodium urate-stimulated human neutrophils in the speck-like structures. The pyrin–β2MG interaction triggered the binding of pyrin and proline–serine–threonine phosphatase interacting protein 1 (PSTPIP1) and then the subsequent recruitment of apoptosis-associated speck-like protein containing caspase recruitment domain (ASC). Caspase-1 p20 subunit, produced by pyrin inflammasome, also interacted with the pyrin PRY/SPRY domain and inhibited the pyrin–β2MG interaction. FMF-associated pyrin mutation M694V did not affect pyrin–β2MG interaction but weakened this inhibition. Our findings suggest that β2MG functions as the pyrin ligand inducing pyrin inflammasome formation and that the FMF-associated pyrin mutations weakened negative feedback of caspase-1 p20 subunit.
Validation of reference genes for quantitative real-time PCR in chemical exposed and at different age’s brackish water flea Diaphanosoma celebensis
Authors: Lee Young-Mi , Cho Hayoung , Kim Ryeo-Ok , In Soyeon , Kim Se-Joo , Won Eun-Ji 
Published: December 2021

AbstractReal-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), a primary approach for evaluating gene expression, requires an appropriate normalization strategy to confirm relative gene expression levels by comparison, and rule out variations that might occur in analytical procedures. The best option is to use a reference gene whose expression level is stable across various experimental conditions to compare the mRNA levels of a target gene. However, there is limited information on how the reference gene is differentially expressed at different ages (growth) in small invertebrates with notable changes such as molting. In this study, expression profiles of nine candidate reference genes from the brackish water flea, Diaphanosoma celebensis, were evaluated under diverse exposure to toxicants and according to growth. As a result, four different algorithms showed similar stabilities of genes for chemical exposures in the case of limited conditions using the same developmental stage (H2A was stable, whereas Act was fairly unstable in adults), while the results according to age showed a significantly different pattern in suite of candidate reference genes. This affected the results of genes EcRA and GST, which are involved in development and detoxification mechanisms, respectively. Our finding is the first step towards establishing a standardized real-time qRT-PCR analysis of this environmentally important invertebrate that has potential for aquatic ecotoxicology, particularly in estuarine environments.