bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of trace metals and potential anthropogenic influences on the historic New York African Burial Ground population: A pXRF technology approach
Authors: Clinton Carter K. , Duncan Candice M. , Shaw Richard K. , Jackson Latifa , Jackson Fatimah L. C. 
Published: December 2019

AbstractThe New York African Burial Ground (NYABG) is the country’s oldest and largest burial site of free and enslaved Africans. Re-discovered in 1991, this site provided evidence of the biological and cultural existence of a 17th and 18th Century historic population viewing their skeletal remains. However, the skeletal remains were reburied in October 2003 and are unavailable for further investigation. The analysis of grave soil samples with modern technology allows for the assessment of trace metal presence. Portable X-ray fluorescence (pXRF) spectrometry provides a semi-quantitative and non-destructive method to identify trace metals of this population and in the surrounding environment. Sixty-five NYABG soil samples were analyzed on a handheld Bruker Tracer III- SD XRF with 40 kV of voltage and a 30μA current. Presence of As, Cu, and Zn can potentially decipher the influence of the local 18th Century pottery factories. Elevated levels of Sr validate the assumed heavy vegetative diets of poor and enslaved Africans of the time. Decreased levels of Ca may be due in part to the proximity of the Collect Pond, the existing water table until the early 19th Century, and Manhattan’s rising sea level causing an elevated water table washing away the leached Ca from human remains. These data help us reconstruct the lives of these early Americans in what became New York City.
SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus
Authors: Cai Weili , Nunziata Schyler , Rascoe John , Stulberg Michael J. 
Published: December 2019

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.
Finding mesopelagic prey in a changing Southern Ocean
Authors: McMahon Clive R. , Hindell Mark A. , Charrassin Jean-Benoit , Corney Stuart , Guinet Christophe , Harcourt Robert , Jonsen Ian , Trebilco Rowan , Williams Guy , Bestley Sophie 
Published: December 2019

AbstractMesopelagic fish and squid occupy ocean depths extending below the photic zone and their vertical migrations represent a massive pathway moving energy and carbon through the water column. Their spatio-temporal distribution is however, difficult to map across remote regions particularly the vast Southern Ocean. This represents a key gap in understanding biogeochemical processes, marine ecosystem structure, and how changing ocean conditions will affect marine predators, which depend upon mesopelagic prey. We infer mesopelagic prey vertical distribution and relative abundance in the Indian sector of the Southern Ocean (20° to 130°E) with a novel approach using predator-derived indices. Fourteen years of southern elephant seal tracking and dive data, from the open ocean between the Antarctic Polar Front and the southern Antarctic Circumpolar Current front, clearly show that the vertical distribution of mesopelagic prey is influenced by the physical hydrographic processes that structure their habitat. Mesopelagic prey have a more restricted vertical migration and higher relative abundance closer to the surface where Circumpolar Deep Water rises to shallower depths. Combining these observations with a future projection of Southern Ocean conditions we show that changes in the coupling of surface and deep waters will potentially redistribute mesopelagic prey. These changes are small overall, but show important spatial variability: prey will increase in relative abundance to the east of the Kerguelen Plateau but decrease to the west. The consequences for deep-diving specialists such as elephant seals and whales over this time scale will likely be minor, but the changes in mesoscale vertical energy flow have implications for predators that forage within the mesopelagic zone as well as the broader pelagic ecosystem.
Analysis of circulating microRNAs aberrantly expressed in alcohol-induced osteonecrosis of femoral head
Authors: Hong Guoju , Han Xiaorui , He Wei , Xu Jiake , Sun Ping , Shen Yingshan , Wei Qiushi , Chen Zhenqiu 
Published: December 2019

AbstractSerum miRNAs are potential biomarkers for predicting the progress of bone diseases, but little is known about miRNAs in alcohol-induced osteonecrosis of femoral head (AIONFH). This study evaluated disease-prevention value of specific serum miRNA expression profiles in AIONFH. MiRNA PCR Panel was taken to explore specific miRNAs in serum of AIONFH cases. The top differentially miRNAs were further validated by RT-qPCR assay in serum and bone tissues of two independent cohorts. Their biofunction and target genes were predicted by bioinformatics databases. Target genes related with angiogenesis and osteogenesis were quantified by RT-qPCR in necrotic bone tissue. Our findings demonstrated that multiple miRNAs were evaluated to be differentially expressed with high dignostic values. MiR-127-3p, miR-628-3p, and miR-1 were downregulated, whereas miR-885-5p, miR-483-3p, and miR-483-5p were upregulated in serum and bone samples from the AIONFH patients compared to those from the normal control individuals (p < 0.01). The predicted target genes of the indicated miRNAs quantified by qRT-PCR, including IGF2, PDGFA, RUNX2, PTEN, and VEGF, were presumed to be altered in necrotic bone tissue of AIONFH patients. The presence of five altered miRNAs in AIONFH patients may serve as non-invasive biomarkers and potential therapeutic targets for the early diagnosis of AIONFH.
In Vivo Mapping of the Choriocapillaris in High myopia: a Widefield Swept Source Optical Coherence Tomography Angiography
Authors: Mastropasqua Rodolfo , Viggiano Pasquale , Borrelli Enrico , Evangelista Federica , Libertini Daniele , Di Antonio Luca , Toto Lisa 
Published: December 2019

AbstractTo report variation of choriocapillaris (CC) flow in widefield in high in myopic subjects compared with an age-matched normal control group using ultra widefield optical coherence tomography angiography (UW-OCTA). This is a Prospective, cross-sectional study. Thirty high myopia subjects and fifty healthy subjects were enrolled. Healthy and high myopia subjects were imaged with the SS-OCTA system (PLEX Elite 9000, Carl Zeiss Meditec Inc., Dublin, CA, USA). For each eye, five 12 × 12-mm OCTA volume scans were acquired. The en face CC images were then exported to imageJ and a semi-automated algorithm was used for subsequent quantitative analysis. The main outcome was a quantitative analysis of the CC. This analysis was performed in three different regions: (i) peripapillary, (ii) macular, and (iii) periphery. In addition, CC variables were further investigated in distinct fields within these three different regions. Thirty myopic eyes (32 subjects; myopic group) and fifty eyes (50 subjects; control group) without elevated myopia were included in the analysis. Mean ± SD age was 26.9 ± 2.9 years [median: 27 years; range: 20.0–40.0 years]. Mean ± SD axial length was 26.6 ± 0.6 mm [median: 26.2 mm; range: 26.1 to 28.0 mm]. Mean ± SD axial length was 26.6 ± 0.6 mm [median: 26.2 mm; range: 26.1 to 28.0 mm] in the myopic group and 23.9 ± 1.1 mm [median: 23.9 mm; range: 21.8 to 25.9 mm] in the control group. The total signal void area was significantly greater in myopic eyes compared with control group. The peripapillary region exhibited the greatest total signal void area (p < 0.0001 vs macular region, p < 0.0001 vs peripheral region). Within the macular region, the foveal area exhibited a greater total signal void area in comparison with both the parafoveal area (p < 0.0001) and the perifoveal area (p < 0.0001). In conclusion we report quantitative mapping of the choriocapillaris in myopic eyes compared with an age-matched normal control group. The CC perfusion appears to have a wide topographical variation.
A cellular defense memory imprinted by early life toxic stress
Authors: Gecse Eszter , Gilányi Beatrix , Csaba Márton , Hajdú Gábor , Sőti Csaba 
Published: December 2019

AbstractStress exposure early in life is implicated in various behavioural and somatic diseases. Experiences during the critical perinatal period form permanent, imprinted memories promoting adult survival. Although imprinting is widely recognized to dictate behaviour, whether it actuates specific transcriptional responses at the cellular level is unknown. Here we report that in response to early life stresses, Caenorhabditis elegans nematodes form an imprinted cellular defense memory. We show that exposing newly-born worms to toxic antimycin A and paraquat, respectively, stimulates the expression of toxin-specific cytoprotective reporters. Toxin exposure also induces avoidance of the toxin-containing bacterial lawn. In contrast, adult worms do not exhibit aversive behaviour towards stress-associated bacterial sensory cues. However, the mere re-encounter with the same cues reactivates the previously induced cytoprotective reporters. Learned adult defenses require memory formation during the L1 larval stage and do not appear to confer increased protection against the toxin. Thus, exposure of C. elegans to toxic stresses in the critical period elicits adaptive behavioural and cytoprotective responses, which do not form imprinted aversive behaviour, but imprint a cytoprotective memory. Our findings identify a novel form of imprinting and suggest that imprinted molecular defenses might underlie various pathophysiological alterations related to early life stress.
Metasurface-based ultra-lightweight high-gain off-axis flat parabolic reflectarray for microwave beam collimation/focusing
Authors: Silva Sinhara R. , Rahman Abdur , de Melo Kort-Kamp Wilton , Rushton Jeremiah J. , Singleton John , Taylor Antoinette J. , Dalvit Diego A. R. , Chen Hou-Tong , Azad Abul K. 
Published: December 2019

AbstractUltra-lightweight deployable antennas with high-gain are pivotal communication components for small satellites, which are intrinsically constrained in size, weight, and power. In this work, we design and demonstrate metasurface-based ultra-lightweight flat off-axis reflectarrays for microwave beam collimation and focusing, similar to a parabolic dish-antenna. Our ultra-thin reflectarrays employ resonators of variable sizes to cover the full 2π phase range, and are arranged on the metasurface to realize a two-dimensional parabolic focusing phase distribution. We demonstrate a 30° off-axis focusing reflector that exhibits a measured gain of 27.5 dB at the central operating frequency of 11.8 GHz and a 3 dB directionality <$$\pm $$±1.6°. Furthermore, we carry out full-wave simulations of the reflectarray, showing high gain of the beam focusing/collimation functionality, in good agreement with measurements. The demonstrated reflectarrays will enable low-cost, lightweight, and high-gain deployable transceivers for small-satellite platforms.
The effects of ship wakes in the Venice Lagoon and implications for the sustainability of shipping in coastal waters
Authors: Scarpa Gian Marco , Zaggia Luca , Manfè Giorgia , Lorenzetti Giuliano , Parnell Kevin , Soomere Tarmo , Rapaglia John , Molinaroli Emanuela 
Published: December 2019

AbstractWe analyse the impact of ship traffic in the vicinity of navigation channels in a wide shallow waterbody. The crucial hydrodynamic driver in this situation is the depression (Bernoulli) wake that may be transferred into a long-living solitary wave of depression over the shoals. The analysis considers navigation channels in the Venice Lagoon using a new large dataset of approximately 600 measured wake events associated to specific ships whose data are provided by the AIS system. Since the development of the modern industrial port and the opening of the Malamocco–Marghera channel in the late 1960s, growing pressure on the lagoon caused by ship traffic has raised concerns about its physical integrity and habitat survival. The transit of large vessels has been shown to have serious impacts on the shallow water areas adjacent to waterways. Depression wakes created by such vessels can reach significant dimensions (water level dropdown of up to 2.45 m at the channel margin), causing unusually large retreat rates of several sections of the shoreline and which may adversely affect the lagoon morphology. The wakes are analysed in relation to ship and morphological parameters. A formulation is proposed to predict wake amplitude on the basis of ship characteristics and motion.
A modular cGAN classification framework: Application to colorectal tumor detection
Authors: Tavolara Thomas E. , Niazi M. Khalid Khan , Arole Vidya , Chen Wei , Frankel Wendy , Gurcan Metin N. 
Published: December 2019

AbstractAutomatic identification of tissue structures in the analysis of digital tissue biopsies remains an ongoing problem in digital pathology. Common barriers include lack of reliable ground truth due to inter- and intra- reader variability, class imbalances, and inflexibility of discriminative models. To overcome these barriers, we are developing a framework that benefits from a reliable immunohistochemistry ground truth during labeling, overcomes class imbalances through single task learning, and accommodates any number of classes through a minimally supervised, modular model-per-class paradigm. This study explores an initial application of this framework, based on conditional generative adversarial networks, to automatically identify tumor from non-tumor regions in colorectal H&E slides. The average precision, sensitivity, and F1 score during validation was 95.13 ± 4.44%, 93.05 ± 3.46%, and 94.02 ± 3.23% and for an external test dataset was 98.75 ± 2.43%, 88.53 ± 5.39%, and 93.31 ± 3.07%, respectively. With accurate identification of tumor regions, we plan to further develop our framework to establish a tumor front, from which tumor buds can be detected in a restricted region. This model will be integrated into a larger system which will quantitatively determine the prognostic significance of tumor budding.
Growth Hormone Effects on Bone Loss-Induced by Mild Traumatic Brain Injury and/or Hind Limb Unloading
Authors: Kesavan Chandrasekhar , Bajwa Nikita M. , Watt Heather , Mohan Subburaman 
Published: December 2019

AbstractGrowth hormone (GH) deficiency and loss of physical activity are common features in traumatic brain injury (TBI) patients that may contribute to bone loss. Therefore, we tested the hypothesis that GH treatment will rescue the hind limb unloading (UL)-induced skeletal deficit in TBI mice. Mild TBI was induced once per day for four consecutive days. UL (right hind limb) and treatment (3 mg/day GH or vehicle) began two weeks after the first TBI episode and lasted for four weeks. GH treatment increased femur BMD and lean body mass but decreased the % fat measured by DXA in the Control group. Micro-CT analysis revealed that the TBI, UL and TBI-UL groups showed reduced tibia trabecular (Tb) bone mass by 15%, 70%, and 75%, respectively compared to Control mice and that GH treatment significantly increased Tb. bone mass in all four groups. Vertebra also showed reduced Tb. bone mass in TBI, UL and TBI-UL groups. GH treatment increased vertebral Tb. bone mass in Control and UL groups but not in the TBI or TBI-UL group. GH treatment increased serum IGF-I levels similarly in TBI, UL and TBI-UL groups at day 14, suggesting the GH effect on liver IGF-I production was unaffected by skeletal UL. In contrast, GH effect on expression of ALP, IGFBP5 and axin2 in bone were compromised by UL. In conclusion, skeletal UL caused a greater Tb. bone deficit than mild TBI alone and that GH anabolic effects in the TBI and UL groups vary depending on the skeletal site.
High polymorphism detected by massively parallel sequencing of autosomal STRs using old blood samples from a Chinese Han population
Authors: Dai Wenshen , Pan Yajiao , Sun Xiaochen , Wu Riga , Li Luo , Yang Dongming 
Published: December 2019

AbstractThe development of massively parallel sequencing (MPS) has quickly changed forensic short tandem repeat (STR) genotyping. By providing detailed sequence information, MPS technology may be used as an alternative or additional method to overcome the limitations of capillary electrophoresis-based STR profiling. Most current NGS processes are labour-intensive with regard to library preparation and require high-quality DNA template. In this study, a 16-plex STR typing system (SeqType®R16) was used to achieve direct library preparation without DNA extraction and adaptor ligation. The efficiency of this system was tested in 601 individuals, including 593 old blood samples from the Chinese Han population and eight positive controls. It took approximately 4 hours for library preparation, including blood direct multiplex PCR (1.5 hours), mixing of the product (15 minutes), single tube purification (2 hours) and quantification (15 minutes). The results showed that MPS presented a broader allele range and higher discrimination power. Except for FGA and D19S433, the allele number almost doubled or more than doubled at all complex STR loci and simple STR loci, including D13S317, D16S539, D5S818, and D7S820. The range of discrimination power increased from 0.8008–0.9572 to 0.8401–0.9753, and the culminated matching probability decreased from 1.7 × 10−15 to 1.1 × 10−17.
One-step artificial antigen presenting cell-based vaccines induce potent effector CD8 T cell responses
Authors: Su Qingtai , Igyártó Botond Z. 
Published: December 2019

AbstractThe production and wide use of artificial antigen presenting cells (aAPCs) in the clinic as cancer immunotherapeutics are hindered by the need of identifying immunogenic cancer antigens and production of recombinant patient-specific major histocompatibility complexes (MHC) loaded with these peptides. To overcome these limitations, in this study, we tested the idea of whether peptide-MHCs can directly be captured from cell lysates, including cancer cells using affinity beads, and used to initiate T cell responses. In theory, these affinity beads covered with the unknown peptide-MHC repertoire captured from the cancer cells could interact with a wide range of antigen-specific T cells and promote anti-cancer responses. Indeed, we found that we can successfully pull-down peptide-MHCs from cell lysates and the aAPCs generated using this technique were able to induce antigen-specific cytotoxic effector T cell responses that led to in vitro and in vivo tumor cell killing. In summary, we present here a novel technique to generate patient-specific aAPCs, that might have the potential to revolutionize the field of cancer vaccines, and provide patients with a vaccine in matters of days at minimal costs.
WNT gene polymorphisms and predisposition to apical periodontitis
Authors: de Souza Letícia Chaves , Cavalla Franco , Maili Lorena , Garlet Gustavo P. , Vieira Alexandre R. , Silva Renato M. , Letra Ariadne 
Published: December 2019

AbstractSingle nucleotide polymorphisms (SNPs) in WNT genes may impact gene/protein function and contribute to individual predisposition to apical periodontitis (AP). Here, we investigated the association of SNPs in/nearby WNT3, WNT3A, WNT5A, WNT8A, WNT9B and WNT11 genes with AP using a case-control dataset. Cases were defined as individuals with deep caries and AP (n = 188); controls had deep caries and no AP (n = 230). Genotyping was performed using Taqman chemistry in real time PCR. Data analyses was performed using Fisher Exact tests assuming a Bonferroni correction threshold value of 0.005. Single-SNP association analysis revealed a trend for association with WNT3 rs9890413 genotypes (P = 0.009) under a dominant model and allelic association for WNT3A rs1745420 (P = 0.009). Haplotypes involving WNT3-WNT9B-WNT3A alleles were also significantly associated with AP (P ≤ 0.003). Luciferase reporter assays showed higher transcriptional activity (1.4-fold) with the alternate G allele in rs1745420. Expression of WNT3, WNT3A and WNT5A in AP tissues was significantly higher than in control tissues, and inversely correlated with the expression of SERPINB1, COL1A1 and TIMP1 (P < 0.05). Our results suggest that WNT genes have a role in modulating AP and polymorphisms in these genes may increase susceptibility to AP.
Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery
Authors: Nasta Veronica , Da Vela Stefano , Gourdoupis Spyridon , Ciofi-Baffoni Simone , Svergun Dmitri I. , Banci Lucia 
Published: December 2019

AbstractIn mitochondria, a complex protein machinery is devoted to the maturation of iron-sulfur cluster proteins. Structural information on the last steps of the machinery, which involve ISCA1, ISCA2 and IBA57 proteins, needs to be acquired in order to define how these proteins cooperate each other. We report here the use of an integrative approach, utilizing information from small-angle X-ray scattering (SAXS) and bioinformatics-driven docking prediction, to determine a low-resolution structural model of the human mitochondrial [2Fe-2S]2+ISCA2-IBA57 complex. In the applied experimental conditions, all the data converge to a structural organization of dimer of dimers for the [2Fe-2S]2+ISCA2-IBA57 complex with ISCA2 providing the homodimerization core interface. The [2Fe-2S] cluster is out of the ISCA2 core while being shared with IBA57 in the dimer. The specific interaction pattern identified from the dimeric [2Fe-2S]2+ISCA2-IBA57 structural model allowed us to define the molecular grounds of the pathogenic Arg146Trp mutation of IBA57. This finding suggests that the dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a physiologically relevant species playing a role in mitochondrial [4Fe-4S] protein biogenesis.