bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neogene Retroarc Foreland Basin Evolution, Sediment Provenance, and Magmatism in Response to Flat Slab Subduction, Western Argentina
Authors: Capaldi Tomas N. , Horton Brian K. , McKenzie N. Ryan , Mackaman‐Lofland Chelsea , Stockli Daniel F. , Ortiz Gustavo , Alvarado Patricia 
Published: June 2020

AbstractUnderstanding the effects of flat slab subduction on mountain building, arc magmatism, and basin evolution is fundamental to convergent‐margin tectonics, with implications for potential feedbacks among geodynamic, magmatic, and surface processes. New stratigraphic and geochronological constraints on Cenozoic sedimentation and magmatism in the southern Central Andes of Argentina (31°S) reveal shifts in volcanism, foreland/hinterland basin development, sediment accumulation, and provenance as the retroarc region was structurally partitioned during slab flattening. Detrital zircon U‐Pb age distributions from the western (Calingasta basin), central (Talacasto and Albarracín basins), and eastern (Bermejo foreland basin) segments of the retroarc basin system preserve syndepositional volcanism and orogenic unroofing of multiple tectonic provinces. Initial shortening‐related exhumation of the Principal Cordillera at 24–17 Ma was recorded by the accumulation of distal eolian deposits bearing Oligocene–Eocene zircons from the Andean magmatic arc. The Calingasta basin chronicled volcanism and basement shortening in the Frontal Cordillera at ~17–11 Ma, as marked by an upward coarsening succession of fluvial to alluvial fan deposits with a sustained zircon U‐Pb age component that matches pervasive Permian‐Triassic bedrock in the hinterland. An ~450 km eastward inboard sweep of volcanism at 11 Ma coincided with the inception of flat slab subduction, and subsequent thin‐skinned shortening in the Precordillera fold‐thrust belt that exhumed wedge‐top deposits and induced cratonward (eastward) advance of flexural subsidence into the Bermejo foreland basin. This foreland basin was structurally partitioned as basement uplifts of the Sierras Pampeanas transformed a fluvial megafan sediment routing network into smaller isolated alluvial fan systems fed by adjacent basement blocks.
Papuan mitochondrial genomes and the settlement of Sahul
Authors: Pedro Nicole , Brucato Nicolas , Fernandes Veronica , André Mathilde , Saag Lauri , Pomat William , Besse Céline , Boland Anne , Deleuze Jean-François , Clarkson Chris , Sudoyo Herawati , Metspalu Mait , Stoneking Mark , Cox Murray P. , Leavesley Matthew , Pereira Luisa , Ricaut François-Xavier 
Published: June 2020

AbstractNew Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuan mitochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50–65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania.
Investigation of cell mechanics using single-beam acoustic tweezers as a versatile tool for the diagnosis and treatment of highly invasive breast cancer cell lines: an in vitro study
Authors: Lim Hae Gyun , Liu Hsiao-Chuan , Yoon Chi Woo , Jung Hayong , Kim Min Gon , Yoon Changhan , Kim Hyung Ham , Shung K. Kirk 
Published: June 2020

AbstractAdvancements in diagnostic systems for metastatic cancer over the last few decades have played a significant role in providing patients with effective treatment by evaluating the characteristics of cancer cells. Despite the progress made in cancer prognosis, we still rely on the visual analysis of tissues or cells from histopathologists, where the subjectivity of traditional manual interpretation persists. This paper presents the development of a dual diagnosis and treatment tool using an in vitro acoustic tweezers platform with a 50 MHz ultrasonic transducer for label-free trapping and bursting of human breast cancer cells. For cancer cell detection and classification, the mechanical properties of a single cancer cell were quantified by single-beam acoustic tweezers (SBAT), a noncontact assessment tool using a focused acoustic beam. Cell-mimicking phantoms and agarose hydrogel spheres (AHSs) served to standardize the biomechanical characteristics of the cells. Based on the analytical comparison of deformability levels between the cells and the AHSs, the mechanical properties of the cells could be indirectly measured by interpolating the Young’s moduli of the AHSs. As a result, the calculated Young’s moduli, i.e., 1.527 kPa for MDA-MB-231 (highly invasive breast cancer cells), 2.650 kPa for MCF-7 (weakly invasive breast cancer cells), and 2.772 kPa for SKBR-3 (weakly invasive breast cancer cells), indicate that highly invasive cancer cells exhibited a lower Young’s moduli than weakly invasive cells, which indicates a higher deformability of highly invasive cancer cells, leading to a higher metastasis rate. Single-cell treatment may also be carried out by bursting a highly invasive cell with high-intensity, focused ultrasound.
Infrared neural stimulation and inhibition using an implantable silicon photonic microdevice
Authors: Horváth Ágoston Csaba , Borbély Sándor , Boros Örs Csanád , Komáromi Lili , Koppa Pál , Barthó Péter , Fekete Zoltán 
Published: June 2020

AbstractBrain is one of the most temperature sensitive organs. Besides the fundamental role of temperature in cellular metabolism, thermal response of neuronal populations is also significant during the evolution of various neurodegenerative diseases. For such critical environmental factor, thorough mapping of cellular response to variations in temperature is desired in the living brain. So far, limited efforts have been made to create complex devices that are able to modulate temperature, and concurrently record multiple features of the stimulated region. In our work, the in vivo application of a multimodal photonic neural probe is demonstrated. Optical, thermal, and electrophysiological functions are monolithically integrated in a single device. The system facilitates spatial and temporal control of temperature distribution at high precision in the deep brain tissue through an embedded infrared waveguide, while it provides recording of the artefact-free electrical response of individual cells at multiple locations along the probe shaft. Spatial distribution of the optically induced temperature changes is evaluated through in vitro measurements and a validated multi-physical model. The operation of the multimodal microdevice is demonstrated in the rat neocortex and in the hippocampus to increase or suppress firing rate of stimulated neurons in a reversible manner using continuous wave infrared light (λ = 1550 nm). Our approach is envisioned to be a promising candidate as an advanced experimental toolset to reveal thermally evoked responses in the deep neural tissue.
Autophagosome biogenesis and human health
Authors: Kawabata Tsuyoshi , Yoshimori Tamotsu 
Published: June 2020

AbstractAutophagy degrades the cytoplasmic contents engulfed by autophagosomes. Besides providing energy and building blocks during starvation via random degradation, autophagy selectively targets cytotoxic components to prevent a wide range of diseases. This preventive activity of autophagy is supported by many studies using animal models and reports identifying several mutations in autophagy-related genes that are associated with human genetic disorders, which have been published in the past decade. Here, we summarize the molecular mechanisms of autophagosome biogenesis involving the proteins responsible for these genetic disorders, demonstrating a role for autophagy in human health. These findings will help elucidate the underlying mechanisms of autophagy-related diseases and develop future medications.
De novo 2q36.3q37.1 deletion encompassing TRIP12 and NPPC yields distinct phenotypes
Authors: Kondo Yuto , Aoyama Kohei , Suzuki Hisato , Hattori Ayako , Hori Ikumi , Ito Koichi , Yoshida Aya , Koroki Mari , Ueda Kentaro , Kosaki Kenjiro , Saitoh Shinji 
Published: June 2020

AbstractWe report a patient with developmental delay, extremely short stature, small hands, dysmorphic facial features, hearing loss, and epilepsy carrying a de novo 2.76-Mb deletion of 2q36.3q37.1, including TRIP12 and NPPC. TRIP12 haploinsufficiency causes developmental delay with isolated dysmorphic facial features, whereas NPPC haploinsufficiency causes short stature and small hands. This is the first report of a unique phenotype, which is secondary to a microdeletion encompassing TRIP12 and NPPC.
Implication of JAK1/STAT3/SOCS3 Pathway in Aging of Cerebellum of Male Rat: Histological and Molecular study
Authors: Mohamed Enas Ahmed , Sayed Walaa Mohamed 
Published: June 2020

AbstractAging causes morphological and functional changes in the cerebellum. This work aimed to demonstrate the implication of JAK1/STAT3/SOCS3 on aging–induced changes of rat cerebellum. Thirty male rats were divided into: adult (12 months), early senile (24 months) and late senile (32 months) groups. Immunohistochemical reaction of the cerebellum to GFAP and caspase-3 was assessed and the expression of JAK1, STAT3, SOCS3 proteins was also evaluated. TNFα as well as the activities of malondialdehyde (MDA) and reduced glutathione (GSH) in cerebellar tissue were also measured. The cerebellum of late senile rats revealed more degenerative changes than early senile rats in the form of increase in GFAP and caspase-3 immunoreaction. Additionally, there was decrease in JAK1and STAT3 expression in early and late senile rats and increase in SOCS3 when compare early and late senile groups with adult one. Enhancement of TNFα was noticed with aging as well as significant decrease in GSH and increase in MDA in early senile group. Moreover, late senile group revealed significant decrease in GSH and increase in MDA. It could be concluded that aging resulting in variable changes of the cerebellum as detected by morphological changes, immunohistochemical reactions of caspase-3 and GFAP and expression of JAK1/STAT3/SOCS3 proteins. Additionally, inflammatory marker TNFα and the activity of oxidative/antioxidative stress markers; malondialdehyde (MDA) and reduced glutathione (GSH) were also affected with aging.
Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation Experiments
Authors: Luechtefeld Thomas , Lin Nole , Paller Channing , Kuhns Katherine , Laterra John J. , Bressler Joseph P. 
Published: June 2020

AbstractThis paper examines the effect of TET1 expression on survival in glioma patients using open-access data from the Genomic Data Commons. A neural network-based survival model was built on expression data from a selection of genes most affected by TET1 knockdown with a median cross-validated survival concordance of 82.5%. A synthetic experiment was then conducted that linked two separately trained neural networks: a multitask model estimating cancer hallmark gene expression from TET1 expression, and a survival neural network. This experiment quantified the mediation of the TET1 survival effect through eight cancer hallmarks: apoptosis, cell cycle, cell death, cell motility, DNA repair, immune response, two phosphorylation pathways, and a randomized gene sets. Immune response, DNA repair, and apoptosis displayed greater mediation than the randomized gene set. Cell motility was inversely associated with only 12.5% mediated concordance. We propose the neural network linkage mediation experiment as an approach to collecting evidence of hazard mediation relationships with prognostic capacity useful for designing interventions.
Quantitative analysis of metal artifact reduction using the auto-edge counting method in cone-beam computed tomography
Authors: Kim Young Hyun , Lee Chena , Han Sang-Sun , Jeon Kug Jin , Choi Yoon Joo , Lee Ari 
Published: June 2020

AbstractThe metal artifact reduction (MAR) algorithm is used in most CBCT unit to reduce artifact from various dental materials. The performance of MAR program of a CBCT unit according to the dental material type under different imaging mode was evaluated as introducing automatic quantification of the amount of artifact reduced. Four customized phantoms with different dental prostheses (amalgam, gold, porcelain-fused-metal, zirconia) underwent CBCT scanning with and without the MAR option. The imaging was performed under varied scanning conditions; 0.2 and 0.3 mm3 voxel sizes; 70 and 100 kVp. The amount of artifacts reduced by each prosthesis and scanning mode automatically counted using canny edge detection in MATLAB, and statistical analysis was performed. The overall artifact reduction ratio was ranged from 17.3% to 55.4%. The artifact caused by the gold crown was most effectively reduced compared to the other prostheses (p < 0.05, Welch’s ANOVA analysis). MAR showed higher performance in smaller voxel size mode for all prostheses (p < 0.05, independent t-test). Automatic quantification efficiently evaluated MAR performance in CBCT image. The impact of MAR was different according to the prostheses type and imaging mode, suggesting that thoughtful consideration is required when selecting the imaging mode of CBCT.
The Southern Ocean with the largest uptake of anthropogenic nitrogen into the ocean interior
Authors: Pan Xianliang L. , Li Bofeng F. , Watanabe Yutaka W. 
Published: June 2020

AbstractThe oceanic external nitrogen (Nex) deposition to the global ocean is expected to rise significantly owing to human activities. The Southern Ocean (SO) is an important pathway, which brings external influences into the ocean interior. It touches the borders of several developing countries that emit a large amount of anthropogenic nitrogen. To comprehend the dynamics of Nexin the SO, we developed a new method to assess the change in the oceanic uptake of Nex(ΔNex) in the entire SO. We obtained the spatiotemporal distribution of ΔNexin the SO by applying this method to a high-resolution grid data constructed using ship-based observations. During the 1990s to the 2010s, Nexincreased significantly by 67 ± 1 Tg-N year−1in the SO. By comparing this value with the rate of Nexdeposition to the ocean, the SO has received ~70% of Nexdeposition to the global ocean, indicating that it is the largest uptake region of anthropogenic nitrogen into the ocean interior.
Antibiotic stewardship in the PICU: Impact of ward rounds led by paediatric infectious diseases specialists on antibiotic consumption
Authors: Renk Hanna , Sarmisak Eva , Spott Corinna , Kumpf Matthias , Hofbeck Michael , Hölzl Florian 
Published: June 2020

AbstractAntimicrobial stewardship programmes (ASP) are aimed at optimising antimicrobial utilization. However, only few studies have focused on paediatric intensive care units (PICU), where inappropriate antibiotic use occurs frequently. We assessed the effect and safety of a once weekly paediatric infectious disease (PID) ward round with prospective audit and feedback on antibiotic consumption in a multidisciplinary PICU. This study was conducted within 6-months periods before and after the implementation of a weekly PID-ward round. Antimicrobial management and two main recommendations per patient were discussed and documented. The primary outcome was antimicrobial utilization, measured by days of therapy (DoT) and length of therapy (LoT) per 1000 patient days (PD) for all PICU stays. Secondary outcomes included PICU mean length of stay, total mortality, infection-related mortality and cost of therapy. 1964 PD were analyzed during the pre- and 1866 PD during the post-implementation phase. Adherence to the recommendations was 79%. An 18% reduction of DoT/1000 PD was observed in the post-implementation period (p = 0.005). LoT/1000 PD decreased by 11% (p = 0.09). Meropenem and vancomycin usage were reduced by 49% (p = 0.07) and 56% (p = 0.03), respectively. We conclude, that a once weekly PID-ward round with prospective audit and feedback is safe and effective and reduces antibiotic consumption in PICUs.
Identification and tissue-specific expression of rutin biosynthetic pathway genes in Capparis spinosa elicited with salicylic acid and methyl jasmonate
Authors: Kianersi Farzad , Abdollahi Mohammad Reza , Mirzaie-asl Asghar , Dastan Dara , Rasheed Faiza 
Published: June 2020

AbstractCapparis spinosa is an edible medicinal plant which is considered as an excellent source of rutin. Rutin is a glycoside of the flavonoid quercetin that has been reported to have a beneficial role in controlling various diseases such as hypertension, arteriosclerosis, diabetes, and obesity. In this study, the partial cDNA of four genes involved in the rutin biosynthetic pathway including 4-coumaroyl CoA ligase (4CL), flavonoid 3′-hydroxylase (F3′H), flavonol synthase (FLS) and flavonol-3-O-glucoside L-rhamnosyltransferase (RT) were identified in C.spinosa plants for the first time. The protein sequences of these genes shared high similarity with the same proteins in other plant species. Subsequently, the expression patterns of these genes as well as rutin accumulation in C.spinosa leaves treated with different concentrations of salicylic acid (SA) and methyl jasmonate (MeJA) and also in different tissues of Caper plants treated with 100 mgL−1 SA and 150 μM MeJA were evaluated. The expression of all four genes was clearly up-regulated and rutin contents increased in response to MeJA and SA treatments after 24 h. The highest rutin contents (5.30 mgg−1 DW and 13.27 mgg−1 DW), as well as the highest expression levels of all four genes, were obtained using 100 mgL−1 SA and 150 μM MeJA, respectively. Among the different tissues, the highest rutin content was observed in young leaves treated with 150 μM MeJA, which corresponded to the expression of related genes, especially RT, as a key gene in the rutin biosynthetic pathway. These results suggest that rutin content in various tissues of C. spinosa can be enhanced to a significant extent by MeJA and SA treatments and the gene expression patterns of rutin-biosynthesis-related genes are regulated by these elicitors.
Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
Authors: Langó Tamás , Pataki Zoltán Gergő , Turiák Lilla , Ács András , Varga Julia Kornélia , Várady György , Kucsma Nóra , Drahos László , Tusnády Gábor E. 
Published: June 2020

AbstractTransmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structures, the parallel development of various bioinformatics and experimental methods was necessary for their topological characterization. The combination of these methods is a powerful approach in the determination of TMP topology as in the Constrained Consensus TOPology prediction. To support the prediction, we previously developed a high-throughput topology characterization method based on primary amino group-labelling that is still limited in identifying all TMPs and their extracellular segments on the surface of a particular cell type. In order to generate more topology information, a new step, a partial proteolysis of the cell surface has been introduced to our method. This step results in new primary amino groups in the proteins that can be biotinylated with a membrane-impermeable agent while the cells still remain intact. Pre-digestion also promotes the emergence of modified peptides that are more suitable for MS/MS analysis. The modified sites can be utilized as extracellular constraints in topology predictions and may contribute to the refined topology of these proteins.
MBR-UV/Cl2 system in treating polluted surface water with typical PPCP contamination
Authors: Liu Dan , Song Kang , Xie Guojun , Li Lu 
Published: June 2020

AbstractThis study proposed the membrane bioreactor–ultraviolet/chlorine (MBR-UV/Cl2) process for treating polluted surface water with pharmaceutical personal care product (PPCP) contamination. Results showed that MBR-UV/Cl2 effectively removed the organic matters and ammonia at approximately 80% and 95%. MBR-UV/Cl2 was used in the removal of sulfadiazine(SDZ), sulfamethoxazole(SMZ), tetracycline(TC), oxytetracycline(OTC), ciprofloxacin(CIP), ofloxacin(OFX), erythromycin(ERY), roxithromycin(ROX), ibuprofen(IBU) and, naproxen(NAX) at 12.18%, 95.61%, 50.50%, 52.97%, 33.56%, 47.71%, 87.57%, 93.38%, 93.80%, and 71.46% in which their UV/Cl2 contribution was 12.18%, 95.61%, 29.04%, 38.14%, 25.94%, 7.20%, 80.28%, 33.79%, 73.08%, and 23.05%, respectively. The removal of 10 typical PPCPs using UV/Cl2 obtained higher contributions than those of the MBR process, except OTC, ROX, and IBU. The UV/Cl2 process with 3-min hydraulic retention time and chlorine concentration at 3 mg/L effectively removed the trace of PPCPs. MBR-UV/Cl2 has the potential to be developed as an effective technology in treating polluted surface water with PPCP contamination.
Mitochondrial genetic variation reveals phylogeographic structure and cryptic diversity in Trioza erytreae
Authors: Ajene Inusa , Khamis Fathiya M. , Pietersen Gerhard , van Asch Barbara 
Published: June 2020

AbstractTrioza erytreaeis the main vector for ‘Candidatus Liberibacter africanus’, the causative agent of African Citrus Greening disease. The insect is widespread in Africa, and has recently disseminated to Southwestern Europe. This study aimed at generating reference mitogenome sequences forT. erytreae, as a background for future genetic diversity surveys. Complete mitochondrial sequences of three specimens collected in Ethiopia, Uganda and South Africa were recovered using Ion Torrent technology. The mitogenomes ofT. erytreaefrom Uganda and Ethiopia were highly similar, and distinct from that found in South Africa. The phylogeographic structure ofT. erytreaewas assessed using genetic clustering and pairwise distances, based on a dataset of publicCOIsequences recorded asT. erytreae. The dataset revealed ten haplotypes with strong phylogeographic structure in Africa and Europe. Three haplotypes found in Kenya onClausena anisatabelonged to pairs separated by distances as high as 11.2%, and were basal to all other sequences. These results indicate that not all sequences identified asT. erytreaebelong to the same species, and that some degree of specificity with different plant hosts is likely to exist. This study provides new baseline information on the diversity ofT. erytreae, with potential implications for the epidemiology of African Citrus Greening disease.