bluuebunny/crossref_metadata_2025_split huggingface dataset:
FQSqueezer: k-mer-based compression of sequencing data
Authors: Deorowicz Sebastian 
Published: January 2020

AbstractThe amount of data produced by modern sequencing instruments that needs to be stored is huge. Therefore it is not surprising that a lot of work has been done in the field of specialized data compression of FASTQ files. The existing algorithms are, however, still imperfect and the best tools produce quite large archives. We present FQSqueezer, a novel compression algorithm for sequencing data able to process single- and paired-end reads of variable lengths. It is based on the ideas from the famous prediction by partial matching and dynamic Markov coder algorithms known from the general-purpose-compressors world. The compression ratios are often tens of percent better than offered by the state-of-the-art tools. The drawbacks of the proposed method are large memory and time requirements.
Quantitation of deoxynucleoside triphosphates by click reactions
Authors: Huang Chang-Yu , Yagüe-Capilla Miriam , González-Pacanowska Dolores , Chang Zee-Fen 
Published: January 2020

AbstractThe levels of the four deoxynucleoside triphosphates (dNTPs) are under strict control in the cell, as improper or imbalanced dNTP pools may lead to growth defects and oncogenesis. Upon treatment of cancer cells with therapeutic agents, changes in the canonical dNTPs levels may provide critical information for evaluating drug response and mode of action. The radioisotope-labeling enzymatic assay has been commonly used for quantitation of cellular dNTP levels. However, the disadvantage of this method is the handling of biohazard materials. Here, we described the use of click chemistry to replace radioisotope-labeling in template-dependent DNA polymerization for quantitation of the four canonical dNTPs. Specific oligomers were designed for dCTP, dTTP, dATP and dGTP measurement, and the incorporation of 5-ethynyl-dUTP or C8-alkyne-dCTP during the polymerization reaction allowed for fluorophore conjugation on immobilized oligonucleotides. The four reactions gave a linear correlation coefficient >0.99 in the range of the concentration of dNTPs present in 106 cells, with little interference of cellular rNTPs. We present evidence indicating that data generated by this methodology is comparable to radioisotope-labeling data. Furthermore, the design and utilization of a robust microplate assay based on this technology evidenced the modulation of dNTPs in response to different chemotherapeutic agents in cancer cells.
Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome
Authors: Sundin Johanna , Aziz Imran , Nordlander Sofia , Polster Annikka , Hu Yue O. O. , Hugerth Luisa W. , Pennhag Alexandra A. L. , Engstrand Lars , Törnblom Hans , Simrén Magnus , Öhman Lena 
Published: January 2020

AbstractAltered bacterial composition and small intestinal bacterial overgrowth (SIBO) may be associated with irritable bowel syndrome (IBS). This study aimed to determine the fecal and mucosa-associated bacterial composition along the gastrointestinal (GI) tract and to assess SIBO in IBS. Bacterial composition of feces, and mucosa of the duodenum and sigmoid colon was determined by 16S rRNA-amplicon-sequencing. SIBO was evaluated by bacterial culture of duodenal aspirate, glucose and lactulose breath tests. Mucosal antibacterial gene expression was assessed by PCR Array. The bacterial profiles of feces and the mucosa of sigmoid colon, but not duodenum, differed between IBS patients (n = 17) and HS (n = 20). The IBS specific bacterial profiles were linked to the colonic antibacterial gene expression. Fecal bacterial profile differed between IBS subtypes, while the mucosa-associated bacterial profile was associated with IBS symptom severity and breath tests results at baseline (H2 and/or CH4 ≥ 15 ppm). The prevalence of SIBO was similar between IBS patients and HS. This study demonstrates that alterations in the bacterial composition of the sigmoid colon of IBS patients were linked to symptoms and immune activation. While breath tests reflected the mucosa-associated bacterial composition, there was no evidence for high prevalence of SIBO or small intestinal bacterial alterations in IBS.
Latency and interval therapy affect the evolution in metastatic colorectal cancer
Authors: Nikbakht Hamid , Jessa Selin , Sukhai Mahadeo A. , Arseneault Madeleine , Zhang Tong , Letourneau Louis , Thomas Mariam , Bourgey Mathieu , Roehrl Michael H. A. , Eveleigh Robert , Chen Eric X. , Krzyzanowska Monika , Moore Malcolm J. , Giesler Amanda , Yu Celeste , Bedard Philippe L. , Kamel-Reid Suzanne , Majewski Jacek , Siu Lillian L. , Riazalhosseini Yasser , Graham Donna M. 
Published: January 2020

AbstractWhile comparison of primary tumor and metastases has highlighted genomic heterogeneity in colorectal cancer (CRC), previous studies have focused on a single metastatic site or limited genomic testing. Combining data from whole exome and ultra-deep targeted sequencing, we explored possible evolutionary trajectories beyond the status of these mutations, particularly among patient-matched metastatic tumors. Our findings confirm the persistence of known clinically-relevant mutations (e.g., those of RAS family of oncogenes) in CRC primary and metastases, yet reveal that latency and interval systemic therapy affect the course of evolutionary events within metastatic lesions. Specifically, our analysis of patient-matched primary and multiple metastatic lesions, developed over time, showed a similar genetic composition for liver metastatic tumors, which were 21-months apart. This genetic makeup was different from those identified in lung metastases developed before manifestation of the second liver metastasis. These results underscore the role of latency in the evolutionary path of metastatic CRC and may have implications for future treatment options.
Differential interaction of Or proteins with the PSY enzymes in saffron
Authors: Ahrazem Oussama , López Alberto José , Argandoña Javier , Castillo Raquel , Rubio-Moraga Ángela , Gómez-Gómez Lourdes 
Published: January 2020

AbstractColored apocarotenoids accumulate at high concentrations in few plant species, where display a role in attraction of pollinators and seed dispersers. Among these apocarotenoids, crocins accumulate at high concentrations in the stigma of saffron and are responsible for the organoleptic and medicinal properties of this spice. Phytoene synthase and Orange protein are key for carotenoid biosynthesis and accumulation. We previously isolated four phytoene synthase genes from saffron with differential roles in carotenoid and apocarotenoid biosynthesis. However, the implications of Orange genes in the regulation of apocarotenoid accumulation are unknown. Here, we have identified two Orange genes from saffron, with different expression patterns. CsOr-a was mainly expressed in vegetative tissues and was induced by light and repressed by heat stress. Both CsOr-a and CsOr-b were expressed in stigmas but showed a different profile during the development of this tissue. The interactions of CsOr-a and CsOr-b were tested with all the four phytoene synthase proteins from saffron and with CsCCD2. None interactions were detected with CCD2 neither with the phytoene synthase 2, involved in apocarotenoid biosynthesis in saffron. The obtained results provide evidence of different mechanisms regulating the phytoene synthase enzymes in saffron by Orange for carotenoid and apocarotenoid accumulation in saffron.
Components of partial resistance to Plasmopara viticola enable complete phenotypic characterization of grapevine varieties
Authors: Bove Federica , Rossi Vittorio 
Published: January 2020

AbstractSix components of partial resistance (RCs) were studied in 15 grapevine varieties with partial resistance to Plasmopara viticola: (i) infection frequency (IFR, proportion of inoculation sites showing sporulation), (ii) latent period (LP50, degree-days between inoculation and appearance of 50% of the final number of sporulating lesions), (iii) lesion size (LS, area of single lesions in mm2), (iv) production of sporangia (SPOR, number of sporangia produced per lesion, and SPOR’, number of sporangia produced per mm2 of lesion), (v) infectious period (IP, number of sporulation events on a lesion), and (vi) infectivity of sporangia (INF, infection efficiency of sporangia produced on resistant varieties). Artificial inoculation monocycle experiments were conducted for a 3-year period on leaves collected at leaf development, flowering, and fruit development. Compared to the susceptible variety ‘Merlot’, the partially resistant varieties showed reduced IFR, longer LP, smaller LS, fewer SPOR and SPOR’, shorter IP, and lower INF. At leaf development, IFR, SPOR, and INF were higher and LP was shorter than at flowering and fruit development. RCs analysis through monocyclic experiments provides reliable assessments of the resistance response of grapevine accessions. The workload required for routine assessment in breeding programs could be reduced by measuring IFR and SPOR, while producing robust results.
Brain mechanisms in motor control during reaching movements: Transition of functional connectivity according to movement states
Authors: Yeom Hong Gi , Kim June Sic , Chung Chun Kee 
Published: January 2020

AbstractUnderstanding how the brain controls movements is a critical issue in neuroscience. The role of brain changes rapidly according to movement states. To elucidate the motor control mechanism of brain, it is essential to investigate the changes in brain network in motor-related regions according to movement states. Therefore, the objective of this study was to investigate the brain network transitions according to movement states. We measured whole brain magnetoencephalography (MEG) signals and extracted source signals in 24 motor-related areas. Functional connectivity and centralities were calculated according to time flow. Our results showed that brain networks differed between states of motor planning and movement. Connectivities between most motor-related areas were increased in the motor-planning state. In contrast, only connectivities with cerebellum and basal ganglia were increased while those of other motor-related areas were decreased during movement. Our results indicate that most processes involved in motor control are completed before movement. Further, brain developed network related to feedback rather than motor decision during movements. Our findings also suggest that neural signals during motor planning might be more predictive than neural signals during movement. They facilitate accurate prediction of movement for brain-machine interfaces and provide insight into brain mechanisms in motor control.
Comparative Proteomics Reveal Me31B’s Interactome Dynamics, Expression Regulation, and Assembly Mechanism into Germ Granules during Drosophila Germline Development
Authors: McCambridge Aidan , Solanki Dhruv , Olchawa Nicholas , Govani Neal , Trinidad Jonathan C. , Gao Ming 
Published: January 2020

AbstractMe31B is a protein component of Drosophila germ granules and plays an important role in germline development by interacting with other proteins and RNAs. To understand the dynamic changes that the Me31B interactome undergoes from oogenesis to early embryogenesis, we characterized the early embryo Me31B interactome and compared it to the known ovary interactome. The two interactomes shared RNA regulation proteins, glycolytic enzymes, and cytoskeleton/motor proteins, but the core germ plasm proteins Vas, Tud, and Aub were significantly decreased in the embryo interactome. Our follow-up on two RNA regulations proteins present in both interactomes, Tral and Cup, revealed that they colocalize with Me31B in nuage granules, P-bodies/sponge bodies, and possibly in germ plasm granules. We further show that Tral and Cup are both needed for maintaining Me31B protein level and mRNA stability, with Tral’s effect being more specific. In addition, we provide evidence that Me31B likely colocalizes and interacts with germ plasm marker Vas in the ovaries and early embryo germ granules. Finally, we show that Me31B’s localization in germ plasm is likely independent of the Osk-Vas-Tud-Aub germ plasm assembly pathway although its proper enrichment in the germ plasm may still rely on certain conserved germ plasm proteins.
Incidence and treatment outcomes of secondary epiretinal membrane following intravitreal injection for diabetic macular edema
Authors: Kang Yong Koo , Park Han Sang , Park Dong Ho , Shin Jae Pil 
Published: January 2020

AbstractThe purpose of this study was to investigate the incidence of secondary epiretinal membrane (ERM) after intravitreal injection and the effect of ERM on visual acuity and central macular thickness (CMT) in patients with diabetic macular edema (DME). We included 147 eyes of 95 patients over 18 years old who were diagnosed with DME from 2012 to 2016, treated with intravitreal injection, and followed-up more than 24 months. Mean CMT in the ERM group was significantly thicker than in the non-ERM group after 9, 12, 18, and 24 months. Secondary ERM developed in 9.5% of patients during follow-up. Compared to other agents, the incidence of secondary ERM was significantly higher after intravitreal injection of dexamethasone implant. Among patients in the ERM group, the mean decrease of CMT between pre-injection and 2 weeks post-injection was significantly less after secondary ERM formation than before ERM formation. Secondary ERM formation was significantly associated with the number of intravitreal injections and the use of dexamethasone implant. Therefore, secondary ERM develops more frequently as the number of intravitreal injections increases and after intravitreal dexamethasone implant injection. The therapeutic effects of intravitreal injections for DME patients decrease after secondary ERM formation.
Exploration of a New Source of Sustainable Nanomaterial from the Koh-e-Suleiman Mountain Range of Pakistan for Industrial Applications
Authors: Nirwan J. S. , Farhaj S. , Chaudhary M. M. , Khizer Z. , Hasan S. S. , Angelis-Dimakis A. , Gill A. , Rasheed H. , Abbas N. , Arshad M. S. , Hussain T. , Shahzad Y. , Yousaf A. M. , Chohan T. A. , Hussain T. , Merchant H. A. , Akram M. R. , Khan T. M. , Ashraf M. , Conway B. R. , Ghori M. U. 
Published: January 2020

AbstractThe present study aimed to explore a new source of montmorillonite and to develop an extraction and purification protocol for its isolation from raw clay samples acquired from the Koh-e-Suleiman mountain range in Pakistan. The process involved the collection of raw clay from the source, identification and quantification of montmorillonite. Granulometric extraction and purification protocols increased the montmorillonite content from 21.8–25.1% in the raw clay to 90.1–93.9% after small-scale extraction and 85.33–89.33% on a larger scale. A techno-economic analysis highlighted the practicality and economic benefits of large-scale extraction for industrial applications. This study highlights the existence of a substantial new source of this valuable clay which is currently used across multiple industries including construction, pottery making, pharmaceuticals, cosmetics and engineering. It is intuitively expected that the large-scale extraction of the material will improve the economic condition of the region by providing employment opportunities to locals and may be a valuable resource for export.
Reduced Expression of Genes Regulating Cohesion Induces Chromosome Instability that May Promote Cancer and Impact Patient Outcomes
Authors: Leylek Tarik R. , Jeusset Lucile M. , Lichtensztejn Zelda , McManus Kirk J. 
Published: January 2020

AbstractChromosome instability (CIN), or continual changes in chromosome complements, is an enabling feature of cancer; however, the molecular determinants of CIN remain largely unknown. Emerging data now suggest that aberrant sister chromatid cohesion may induce CIN and contribute to cancer. To explore this possibility, we employed clinical and fundamental approaches to systematically assess the impact reduced cohesion gene expression has on CIN and cancer. Ten genes encoding critical functions in cohesion were evaluated and remarkably, each exhibits copy number losses in 12 common cancer types, and reduced expression is associated with worse patient survival. To gain mechanistic insight, we combined siRNA-based silencing with single cell quantitative imaging microscopy to comprehensively assess the impact reduced expression has on CIN in two karyotypically stable cell lines. We show that reduced expression induces CIN phenotypes, namely increases in micronucleus formation and nuclear areas. Subsequent direct tests involving a subset of prioritized genes also revealed significant changes in chromosome numbers with corresponding increases in moderate and severe cohesion defects within mitotic chromosome spreads. Collectively, our clinical and fundamental findings implicate reduced sister chromatid cohesion, resulting from gene copy number losses, as a key pathogenic event in the development and progression of many cancer types.
Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects
Authors: Medvedeva Irina V. , Stokes Matthew E. , Eisinger Dominic , LaBrie Samuel T. , Ai Jing , Trotter Matthew W. B. , Schafer Peter , Yang Robert 
Published: January 2020

AbstractFinding biomarkers that provide shared link between disease severity, drug-induced pharmacodynamic effects and response status in human trials can provide number of values for patient benefits: elucidating current therapeutic mechanism-of-action, and, back-translating to fast-track development of next-generation therapeutics. Both opportunities are predicated on proactive generation of human molecular profiles that capture longitudinal trajectories before and after pharmacological intervention. Here, we present the largest plasma proteomic biomarker dataset available to-date and the corresponding analyses from placebo-controlled Phase III clinical trials of the phosphodiesterase type 4 inhibitor apremilast in psoriasis (PSOR), psoriatic arthritis (PsA), and ankylosing spondylitis (AS) from 526 subjects overall. Using approximately 150 plasma analytes tracked across three time points, we identified IL-17A and KLK-7 as biomarkers for disease severity and apremilast pharmacodynamic effect in psoriasis patients. Combined decline rate of KLK-7, PEDF, MDC and ANGPTL4 by Week 16 represented biomarkers for the responder subgroup, shedding insights into therapeutic mechanisms. In ankylosing spondylitis patients, IL-6 and LRG-1 were identified as biomarkers with concordance to disease severity. Apremilast-induced LRG-1 increase was consistent with the overall lack of efficacy in ankylosing spondylitis. Taken together, these findings expanded the mechanistic knowledge base of apremilast and provided translational foundations to accelerate future efforts including compound differentiation, combination, and repurposing.
Deep neural networks for automated detection of marine mammal species
Authors: Shiu Yu , Palmer K. J. , Roch Marie A. , Fleishman Erica , Liu Xiaobai , Nosal Eva-Marie , Helble Tyler , Cholewiak Danielle , Gillespie Douglas , Klinck Holger 
Published: January 2020

AbstractDeep neural networks have advanced the field of detection and classification and allowed for effective identification of signals in challenging data sets. Numerous time-critical conservation needs may benefit from these methods. We developed and empirically studied a variety of deep neural networks to detect the vocalizations of endangered North Atlantic right whales (Eubalaena glacialis). We compared the performance of these deep architectures to that of traditional detection algorithms for the primary vocalization produced by this species, the upcall. We show that deep-learning architectures are capable of producing false-positive rates that are orders of magnitude lower than alternative algorithms while substantially increasing the ability to detect calls. We demonstrate that a deep neural network trained with recordings from a single geographic region recorded over a span of days is capable of generalizing well to data from multiple years and across the species’ range, and that the low false positives make the output of the algorithm amenable to quality control for verification. The deep neural networks we developed are relatively easy to implement with existing software, and may provide new insights applicable to the conservation of endangered species.
Stochastic nucleation processes and substrate abundance explain time-dependent freezing in supercooled droplets
Authors: Knopf Daniel A. , Alpert Peter A. , Zipori Assaf , Reicher Naama , Rudich Yinon 
Published: January 2020

AbstractAtmospheric immersion freezing (IF), a heterogeneous ice nucleation process where an ice nucleating particle (INP) is immersed in supercooled water, is a dominant ice formation pathway impacting the hydrological cycle and climate. Implementation of IF derived from field and laboratory data in cloud and climate models is difficult due to the high variability in spatio-temporal scales, INP composition, and morphological complexity. We demonstrate that IF can be consistently described by a stochastic nucleation process accounting for uncertainties in the INP surface area. This approach accounts for time-dependent freezing, a wide range of surface areas and challenges phenomenological descriptions typically used to interpret IF. The results have an immediate impact on the current description, interpretation, and experiments of IF and its implementation in models. The findings are in accord with nucleation theory, and thus should hold for any supercooled liquid material that nucleates in contact with a substrate.