bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-designing irrigated intensive cereal systems through bundling precision agronomic innovations for transitioning towards agricultural sustainability in North-West India
Authors: Jat H. S. , Sharma P. C. , Datta Ashim , Choudhary Madhu , Kakraliya S. K. , Yadvinder-Singh  , Sidhu Harminder S. , Gerard B. , Jat M. L. 
Published: November 2019

AbstractA study was conducted to design productive, profitable, irrigation water¸ nitrogen and energy use efficient intensive cereal systems (rice-wheat; RW and maize-wheat; MW) in North-West India. Bundling of conservation agriculture (CA) with sub-surface drip irrigation termed as CA+ were compared with CA alone and conventional tillage based and flood irrigated RW rotation (farmer’s practice; ScI). In contrast to conventional till RW rotation which consumed 1889 mm ha−1 irrigation water (2-yr mean), CA+ system saved 58.4 and 95.5% irrigation water in RW and MW rotations, respectively. CA+ practices saved 45.8 and 22.7% of irrigation water in rice and maize, respectively compared to CA with flood irrigation. On a system basis, CA+ practices saved 46.7 and 44.7% irrigation water under RW (ScV) and MW (ScVI) systems compared to their respective CA-based systems with flood irrigation (ScIII and ScIV). CA+ in RW system recorded 11.2% higher crop productivity and improved irrigation water productivity by 145% and profitability by 29.2% compared to farmers’ practice. Substitution of rice with maize (MW system; ScVI) recorded 19.7% higher productivity, saved 84.5% of irrigation water and increased net returns by 48.9% compared to farmer’s practice. CA+ RW and MW system improved energy productivity by 75 and 169% and partial factor productivity of N by 44.6 and 49.6%, respectively compared to ScI. The sub-surface drip irrigation system saved the fertilizer N by 20% under CA systems. CA+ in RW and MW systems recorded ~13 and 5% (2-yr mean) higher profitability with 80% subsidy on installing sub-surface drip irrigation system and similar profitability without subsidy scenario compared with their respective flood irrigated CA-based systems.
An exploration of ambigrammatic sequences in narnaviruses
Authors: DeRisi Joseph L. , Huber Greg , Kistler Amy , Retallack Hanna , Wilkinson Michael , Yllanes David 
Published: November 2019

AbstractNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.
Supreme activity of gramicidin S against resistant, persistent and biofilm cells of staphylococci and enterococci
Authors: Berditsch Marina , Afonin Sergii , Reuster Jennifer , Lux Hannah , Schkolin Kristina , Babii Oleg , Radchenko Dmytro S. , Abdullah Issah , William Nicola , Middel Volker , Strähle Uwe , Nelson Andrew , Valko Klara , Ulrich Anne S. 
Published: November 2019

AbstractThree promising antibacterial peptides were studied with regard to their ability to inhibit the growth and kill the cells of clinical strains of Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium. The multifunctional gramicidin S (GS) was the most potent, compared to the membranotropic temporin L (TL), being more effective than the innate-defence regulator IDR-1018 (IDR). These activities, compared across 16 strains as minimal bactericidal and minimal inhibitory concentrations (MIC), are independent of bacterial resistance pattern, phenotype variations and/or biofilm-forming potency. For S. aureus strains, complete killing is accomplished by all peptides at 5 × MIC. For E. faecalis strains, only GS exhibits a rapid bactericidal effect at 5 × MIC, while TL and IDR require higher concentrations. The biofilm-preventing activities of all peptides against the six strains with the largest biofilm biomass were compared. GS demonstrates the lowest minimal biofilm inhibiting concentrations, whereas TL and IDR are consistently less effective. In mature biofilms, only GS completely kills the cells of all studied strains. We compare the physicochemical properties, membranolytic activities, model pharmacokinetics and eukaryotic toxicities of the peptides and explain the bactericidal, antipersister and antibiofilm activities of GS by its elevated stability, pronounced cell-penetration ability and effective utilization of multiple modes of antibacterial action.
Whole blood RNA signatures in leprosy patients identify reversal reactions before clinical onset: a prospective, multicenter study
Authors: Tió-Coma Maria , van Hooij Anouk , Bobosha Kidist , van der Ploeg-van Schip Jolien J. , Banu Sayera , Khadge Saraswoti , Thapa Pratibha , Kunwar Chhatra B. , Goulart Isabela M. , Bekele Yonas , Hagge Deanna A. , Moraes Milton O. , Teles Rosane M. B. , Pinheiro Roberta Olmo , van Zwet Erik W. , Goeman Jelle J. , Aseffa Abraham , Haks Mariëlle C. , Ottenhoff Tom H. M. , Modlin Robert L. , Geluk Annemieke 
Published: November 2019

AbstractEarly diagnosis of leprosy is challenging, particularly its inflammatory reactions, the major cause of irreversible neuropathy in leprosy. Current diagnostics cannot identify which patients are at risk of developing reactions. This study assessed blood RNA expression levels as potential biomarkers for leprosy. Prospective cohorts of newly diagnosed leprosy patients, including reactions, and healthy controls were recruited in Bangladesh, Brazil, Ethiopia and Nepal. RNA expression in 1,090 whole blood samples was determined for 103 target genes for innate and adaptive immune profiling by dual color Reverse-Transcription Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) followed by cluster analysis. We identified transcriptomic biomarkers associated with leprosy disease, different leprosy phenotypes as well as high exposure toMycobacterium lepraewhich respectively allow improved diagnosis and classification of leprosy patients and detection of infection. Importantly, a transcriptomic signature of risk for reversal reactions consisting of five genes (CCL2, CD8A, IL2, IL15andMARCO) was identified based on cross-sectional comparison of RNA expression. In addition, intra-individual longitudinal analyses of leprosy patients before, during and after treatment of reversal reactions, indicated that several IFN-induced genes increased significantly at onset of reaction whereasIL15decreased. This multi-site study, situated in four leprosy endemic areas, demonstrates the potential of host transcriptomic biomarkers as correlates of risk for leprosy. Importantly, a prospective five-gene signature for reversal reactions could predict reversal reactions at least 2 weeks before onset. Thus, transcriptomic biomarkers provide promise for early detection of these acute inflammatory episodes and thereby help prevent permanent neuropathy and disability in leprosy patients.
IFN-α as a time-sensitive biomarker during Oropouche virus infection in early and late seroconverters
Authors: de Oliveira Euzébio , Azevedo Raimunda do Socorro Silva , Coelho-dos-Reis Jordana Grazziela , Antonelli Lis Ribeiro do Valle , Ferreira Milene Silveira , Campi-Azevedo Ana Carolina , Costa-Silva Matheus Fernandes , Martins Lívia Carício , Chiang Jannifer Oliveira , Teixeira-Carvalho Andréa , Martins-Filho Olindo Assis , Vasconcelos Pedro Fernando Costa 
Published: November 2019

AbstractIn the present study, patients with acute OROV fever were classified as early seroconverters (IgM/IgG positive at baseline) or late seroconverters (IgM/IgG negative at baseline) and the timeline kinetics of the production of chemokines and cytokines were assessed at 1–3, 4–7, 8–10 and ≥11 days after patients have reported the first symptoms. Regardless immunoglobulin profile, all OROV fever patients presented higher levels of CXCL8, and IFN-α and lower levels of TNF and IL-10 at baseline as compared to healthy donors (HD). Lower levels of CCL2, CXCL10, and IFN-γ and higher levels of CCL2, CXCL10, IL-6, and IL-17A were detected in early and late seroconverters, respectively, as compared to HD. While early seroconverters presented the increasing levels of CCL2 along the timeline, late seroconverters displayed decreasing levels of CCL2, CXCL10, and IL-6 following days of disease onset. Noteworthy was that IFN-α was revealed as universal biomarker of human OROV fever, while CXCL8 & IL-5 and CXCL10 & IL-17 were consistently observed in early and late seroconverters, respectively. Thus, our results suggest that the production of IFN-α, CXCL10, and IL-17 precede the seroconversion bringing novel insights on the immunological events triggered by the OROV disease.
Glucose lowering by SGLT2-inhibitor empagliflozin accelerates atherosclerosis regression in hyperglycemic STZ-diabetic mice
Authors: Pennig Jan , Scherrer Philipp , Gissler Mark Colin , Anto-Michel Nathaly , Hoppe Natalie , Füner Lisa , Härdtner Carmen , Stachon Peter , Wolf Dennis , Hilgendorf Ingo , Mullick Adam , Bode Christoph , Zirlik Andreas , Goldberg Ira J. , Willecke Florian 
Published: November 2019

AbstractDiabetes worsens atherosclerosis progression and leads to a defect in repair of arteries after cholesterol reduction, a process termed regression. Empagliflozin reduces blood glucose levels via inhibition of the sodium glucose cotransporter 2 (SGLT-2) in the kidney and has been shown to lead to a marked reduction in cardiovascular events in humans. To determine whether glucose lowering by empagliflozin accelerates atherosclerosis regression in a mouse model, male C57BL/6J mice were treated intraperitoneally with LDLR- and SRB1- antisense oligonucleotides and fed a high cholesterol diet for 16 weeks to induce severe hypercholesterolemia and atherosclerosis progression. At week 14 all mice were rendered diabetic by streptozotocin (STZ) injections. At week 16 a baseline group was sacrificed and displayed substantial atherosclerosis of the aortic root. In the remaining mice, plasma cholesterol was lowered by switching to chow diet and treatment with LDLR sense oligonucleotides to induce atherosclerosis regression. These mice then received either empagliflozin or vehicle for three weeks. Atherosclerotic plaques in the empagliflozin treated mice were significantly smaller, showed decreased lipid and CD68+ macrophage content, as well as greater collagen content. Proliferation of plaque resident macrophages and leukocyte adhesion to the vascular wall were significantly decreased in empagliflozin-treated mice. In summary, plasma glucose lowering by empagliflozin improves plaque regression in diabetic mice.
Isolation and comparative genomics of Mycobacterium tuberculosis isolates from cattle and their attendants in South India
Authors: Palaniyandi Kannan , Kumar Narender , Veerasamy Maroudam , Kabir Refaya Ahmed , Dolla Chandrakumar , Balaji Subramanyam , Baskaran Dhanaraj , Thiruvengadam Kannan , Rajendran Ananthi , Narayanan Sujatha , Raj Dhinakar , Swaminathan Soumya , Peacock Sharon J. 
Published: November 2019

AbstractThe major human pathogen Mycobacterium tuberculosis is rarely reported to cause disease in other animals. Cases in livestock are thought to occur through contact with infected handlers, but previous studies evaluating putative livestock-human transmission used typing techniques with limited resolution. Here, we undertook cross-sectional surveillance for tuberculosis in 271 livestock handlers and 167 cattle on three farms in Chennai, India and defined the relatedness of cultured isolates using whole genome sequencing. Humans and livestock were screened for active mycobacterial infection, and opportunistic post-mortem examination was performed on comparative intradermal test-positive cattle that died. Four cattle and 6 handlers on two farms were culture-positive for M. tuberculosis; M. bovis was not isolated. All 10 isolates (one from each case) belonged to Lineage 1. Pairwise genome comparisons of single nucleotide polymorphism (SNP) differences ranged from 1 to 600 SNPs, but 3 isolate pairs were less than 5 SNPs different. Two pairs were from handlers and the third pair were from two cattle on the same farm. The minimum pairwise SNP difference between a cattle and human isolate was >250 SNPs. Our study confirms the presence of M. tuberculosis infection in cattle in India, sequencing of which characterised relatedness between human and cattle-derived isolates.
Multi-layered core-sheath fiber membranes for controlled drug release in the local treatment of brain tumor
Authors: Han Daewoo , Serra Riccardo , Gorelick Noah , Fatima Umailla , Eberhart Charles G. , Brem Henry , Tyler Betty , Steckl Andrew J. 
Published: November 2019

AbstractInterstitial chemotherapy plays a pivotal role in the treatment of glioblastoma multiforme (GBM), an aggressive form of primary brain cancer, by enhancing drug biodistribution to the tumor and avoiding systemic toxicities. The use of new polymer structures that extend the release of cytotoxic agents may therefore increase survival and prevent recurrence. A novel core-sheath fiber loaded with the drug carmustine (BCNU) was evaluated in an in vivo brain tumor model. Three-dimensional discs were formed from coaxially electrospun fiber membranes and in vitro BCNU release kinetics were measured. In vivo survival was assessed following implantation of discs made of compressed core-sheath fibers (NanoMesh) either concurrently with or five days after intracranial implantation of 9L gliosarcoma. Co-implantation of NanoMesh and 9L gliosarcoma resulted in statistically significant long-term survival (>150 days). Empty control NanoMesh confirmed the safety of these novel implants. Similarly, Day 5 studies showed significant median, overall, and long-term survival rates, suggesting optimal control of tumor growth, confirmed with histological and immunohistochemical analyses. Local chemotherapy by means of biodegradable NanoMesh implants is a new treatment paradigm for the treatment for brain tumors. Drug delivery with coaxial core-sheath structures benefits from high drug loading, controlled long-term release kinetics, and slow polymer degradation. This represents a promising evolution for the current treatment of GBM.
HDAC4 and 5 repression of TBX5 is relieved by protein kinase D1
Authors: Ghosh Tushar K. , Aparicio-Sánchez José J. , Buxton Sarah , Brook J. David 
Published: November 2019

AbstractTBX5 is a T-box family transcription factor that regulates heart and forelimb development in vertebrates and functional deficiencies in this protein result in Holt-Oram syndrome. Recently, we have shown that acetylation of TBX5 potentiates its activity and is important for heart and limb development. Here we report that class II histone deacetylases HDAC4 and HDAC5 associate with TBX5 and repress its role in cardiac gene transcription. Both HDAC4 and HDAC5 deacetylate TBX5, which promotes its relocation to the cytoplasm and HDAC4 antagonizes the physical association and functional cooperation between TBX5 and MEF2C. We also show that protein kinase D1 (PRKD1) relieves the HDAC4/5-mediated repression of TBX5. Thus, this study reveals a novel interaction of HDAC4/5 and PRKD1 in the regulation of TBX5 transcriptional activity.
Surgical-orthodontic treatment for class II asymmetry: outcome and influencing factors
Authors: Chen Yun-Fang , Liao Yu-Fang , Chen Ying-An , Chen Yu-Ray 
Published: November 2019

AbstractThe study aimed to evaluate the treatment outcome of bimaxillary surgery for class II asymmetry and find the influencing factors for residual asymmetry. Cone-beam computed tomographic images of 30 adults who had bimaxillary surgery were acquired, and midline and contour landmarks of soft tissue and teeth were identified to assess treatment changes and outcome of facial asymmetry. The postoperative positional asymmetry of each osteotomy segment was also measured. After surgery, the facial midline asymmetry of the mandible, chin, and lower incisors improved significantly (all p < 0.01). However, the residual chin deviation remained as high as 2.64 ± 1.80 mm, and the influencing factors were residual shift asymmetry of the mandible (p < 0.001), chin (p < 0.001), and ramus (p = 0.001). The facial contour asymmetry was not significantly improved after surgery, and the influencing factors were the initial contour asymmetry (p < 0.001), and the residual ramus roll (p < 0.001) or yaw (p < 0.01) asymmetry. The results showed that bimaxillary surgery significantly improved midline but not contour symmetry. The postoperative midline and contour asymmetry was mainly affected by the residual shift and rotational jaw asymmetry respectively.
Effective Mass of Quasiparticles in Armchair Graphene Nanoribbons
Authors: Fischer Marcelo Macedo , de Sousa Leonardo Evaristo , Luiz e Castro Leonardo , Ribeiro Luiz Antonio , de Sousa Rafael Timóteo , Magela e Silva Geraldo , de Oliveira Neto Pedro Henrique 
Published: November 2019

AbstractArmchair graphene nanoribbons (AGNRs) may present intrinsic semiconducting bandgaps, being of potential interest in developing new organic-based optoelectronic devices. The induction of a bandgap in AGNRs results from quantum confinement effects, which reduce charge mobility. In this sense, quasiparticles’ effective mass becomes relevant for the understanding of charge transport in these systems. In the present work, we theoretically investigate the drift of different quasiparticle species in AGNRs employing a 2D generalization of the Su-Schrieffer-Heeger Hamiltonian. Remarkably, our findings reveal that the effective mass strongly depends on the nanoribbon width and its value can reach 60 times the mass of one electron for narrow lattices. Such underlying property for quasiparticles, within the framework of gap tuning engineering in AGNRs, impact the design of their electronic devices.
A Novel Approach to Sensorimotor Skill Acquisition Utilizing Sensory Substitution: A Driving Simulation Study
Authors: Ueda Sayako , Sakai Hiroyuki , Kumada Takatsune 
Published: November 2019

AbstractThe aim of this study is to demonstrate the potential of sensory substitution/augmentation (SS/A) techniques for driver assistance systems in a simulated driving environment. Using a group-comparison design, we examined lane-keeping skill acquisition in a driving simulator that can provide information regarding vehicle lateral position by changing the binaural balance of auditory white noise delivered to the driver. Consequently, lane-keeping accuracy was significantly degraded when the lower visual scene (proximal part of the road) was occluded, suggesting it conveyed critical visual information necessary for lane keeping. After 40 minutes of training with auditory cueing of vehicle lateral position, lane-keeping accuracy returned to the baseline (normal driving) level. This indicates that auditory cueing can compensate for the loss of visual information. Taken together, our data suggest that auditory cueing of vehicle lateral position is sufficient for lane-keeping skill acquisition and that SS/A techniques can potentially be used for the development of driver assistance systems, particularly for situations where immediate time-sensitive actions are required in response to rapidly changing sensory information. Although this study is the first to apply SS/A techniques to driver assistance, further studies are however required to establish the generalizability of the findings to real-world settings.
Eye-Hand Span is not an Indicator of but a Strategy for Proficient Sight-Reading in Piano Performance
Authors: Lim Yeoeun , Park Jeong Mi , Rhyu Seung -Yeon , Chung Chun Kee , Kim Youn , Yi Suk Won 
Published: November 2019

AbstractEye-hand span, i.e., the distance between a performer’s fixation and execution of a note, has been regarded as a decisive indicator of performers’ competence in sight-reading. However, integrated perspectives regarding the relationship between eye-hand span and sight-reading variables have been less discussed. The present study explored the process of sight-reading in terms of three domains and their interrelations. The domain indicators included musical complexity and playing tempo (musical domain), eye-hand span (cognitive domain), and performance accuracy (behavioural domain). Thirty professional pianists sight-read four musical pieces with two different complexities and playing tempi. We measured the participants’ eye-hand span, evaluated their performance accuracy, and divided the participants into three groups according to their performance accuracy values. Interestingly, we found that the eye-hand span did not change solely based on the performance accuracy. In contrast, the relationship between the eye-hand span and performance accuracy changed according to the difficulty of the sight-reading task. Our results demonstrate that the eye-hand span is not a decisive indicator of sight-reading proficiency but is a strategy that can vary according to the difficulty of sight-reading tasks. Thus, proficient sight-readers are performers who are skilled at adjusting their eye-hand span instead of always maintaining an extended span.
Paper-Based SERS Platform for One-Step Screening of Tetracycline in Milk
Authors: Marques Ana , Veigas Bruno , Araújo Andreia , Pagará Beatriz , Baptista Pedro Viana , Águas Hugo , Martins Rodrigo , Fortunato Elvira 
Published: November 2019

AbstractThroughout the last decade, the expansion of food testing has been gradually moving towards ordinary high throughput screening methods performed on-site. The demand for point-of-care testing, able to distinguish molecular signatures with high accuracy, sensitivity and specificity has been significantly increasing. This new requirement relies on the on-site detection and monitorization of molecular signatures suitable for the surveillance of food production and processing. The widespread use of antibiotics has contributed to disease control of livestock but has also created problems for the dairy industry and consumers. Its therapeutic and subtherapeutic use has increased the risk of contamination in milk in enough concentrations to cause economic losses to the dairy industry and have a health impact in highly sensitive individuals. This study focuses on the development of a simple Surface-Enhanced Raman Spectroscopy (SERS) method for fast high throughput screening of tetracycline (TET) in milk. For this, we integrate a paper-based low-cost, fully recyclable and highly stable SERS platform, with a minimal sample preparation protocol. A two-microliter sample of milk solutions spiked with TET (from 0.01 to 1000 ppm) is dried on a silver nanoparticle coated cardboard substrate and measured via a Raman spectrophotometer. The SERS substrate showed to be extremely stable with a shelf life of several months. A global spectrum principal component analysis approach was used to test all the detected vibrational modes and their correlation with TET concentration. Peak intensity ratios (455 cm−1/1280 cm−1 and 874 cm−1/1397 cm−1) were found to be correlated with TET concentrations in milk, achieving a sensitivity as low as 0.1 ppm. Results indicate that this SERS method combined with portable Raman spectrometer is a potential tool that can be used on-site for the monitoring of TET residues and other antibiotics.