bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing different nonlinearities in readout systems for optical neuromorphic computing networks
Authors: Ma Chonghuai , Lambrecht Joris , Laporte Floris , Yin Xin , Dambre Joni , Bienstman Peter 
Published: December 2021

AbstractNonlinear activation is a crucial building block of most machine-learning systems. However, unlike in the digital electrical domain, applying a saturating nonlinear function in a neural network in the analog optical domain is not as easy, especially in integrated systems. In this paper, we first investigate in detail the photodetector nonlinearity in two main readout schemes: electrical readout and optical readout. On a 3-bit-delayed XOR task, we show that optical readout trained with backpropagation gives the best performance. Furthermore, we propose an additional saturating nonlinearity coming from a deliberately non-ideal voltage amplifier after the detector. Compared to an all-optical nonlinearity, these two kinds of nonlinearities are extremely easy to obtain at no additional cost, since photodiodes and voltage amplifiers are present in any system. Moreover, not having to design ideal linear amplifiers could relax their design requirements. We show through simulation that for long-distance nonlinear fiber distortion compensation, using only the photodiode nonlinearity in an optical readout delivers BER improvements over three orders of magnitude. Combined with the amplifier saturation nonlinearity, we obtain another three orders of magnitude improvement of the BER.
Analysis of avian Usutu virus infections in Germany from 2011 to 2018 with focus on dsRNA detection to demonstrate viral infections
Authors: Störk Theresa , de le Roi Madeleine , Haverkamp Ann-Kathrin , Jesse Sonja T. , Peters Martin , Fast Christine , Gregor Katharina M. , Könenkamp Laura , Steffen Imke , Ludlow Martin , Beineke Andreas , Hansmann Florian , Wohlsein Peter , Osterhaus Albert D. M. E. , Baumgärtner Wolfgang 
Published: December 2021

AbstractUsutu virus (USUV) is a zoonotic arbovirus causing avian mass mortalities. The first outbreak in North-Western Germany occurred in 2018. This retrospective analysis focused on combining virological and pathological findings in birds and immunohistochemistry. 25 common blackbirds, one great grey owl, and one kingfisher collected from 2011 to 2018 and positive for USUV by qRT-PCR were investigated. Macroscopically, most USUV infected birds showed splenomegaly and hepatomegaly. Histopathological lesions included necrosis and lymphohistiocytic inflammation within spleen, Bursa fabricii, liver, heart, brain, lung and intestine. Immunohistochemistry revealed USUV antigen positive cells in heart, spleen, pancreas, lung, brain, proventriculus/gizzard, Bursa fabricii, kidney, intestine, skeletal muscle, and liver. Analysis of viral genome allocated the virus to Europe 3 or Africa 2 lineage. This study investigated whether immunohistochemical detection of double-stranded ribonucleic acid (dsRNA) serves as an alternative tool to detect viral intermediates. Tissue samples of six animals with confirmed USUV infection by qRT-PCR but lacking viral antigen in liver and spleen, were further examined immunohistochemically. Two animals exhibited a positive signal for dsRNA. This could indicate either an early state of infection without sufficient formation of virus translation products, occurrence of another concurrent virus infection or endogenous dsRNA not related to infectious pathogens and should be investigated in more detail in future studies.
Removal of Ag remanence and improvement in structural attributes of silicon nanowires array via sintering
Authors: Kale Paresh , Sahoo Mihir Kumar 
Published: December 2021

AbstractMetal-assisted chemical etching (MACE) is popular due to the large-area fabrication of silicon nanowires (SiNWs) exhibiting a high aspect ratio at a low cost. The remanence of metal, i.e., silver nanoparticles (AgNPs) used in the MACE, deteriorates the device (especially solar cell) performance by acting as a defect center. The superhydrophobic behavior of nanowires (NWs) array prohibits any liquid-based solution (i.e., thorough cleaning with HNO3 solution) from removing the AgNPs. Thermal treatment of NWs is an alternative approach to reduce the Ag remanence. Sintering temperature variation is chosen between the melting temperature of bulk-Ag (962 °C) and bulk-Si (1412 °C) to reduce the Ag particles and improve the crystallinity of the NWs. The melting point of NWs decreases due to surface melting that restricts the sintering temperature to 1200 °C. The minimum sintering temperature is set to 1000 °C to eradicate the Ag remanence. The SEM–EDS analysis is carried out to quantify the reduction in Ag remanence in the sintered NWs array. The XRD analysis is performed to study the oxides (SiO and Ag2O) formed in the NWs array due to the trace oxygen level in the furnace. The TG-DSC characterization is carried out to know the critical sintering temperature at which remanence of AgNPs removes without forming any oxides. The Raman analysis is studied to determine the crystallinity, strain, and size of Si nanocrystals (SiNCs) formed on the NWs surface due to sidewalls etching. An optimized polynomial equation is derived to find the SiNCs size for various sintering temperatures.
Placental acute inflammation infiltrates and pregnancy outcomes: a retrospective cohort study
Authors: Orsaria Maria , Liviero Stefania , Rossetti Emma , Pittini Carla , Driul Lorenza , Londero Ambrogio P. , Mariuzzi Laura 
Published: December 2021

AbstractChorioamnionitis can be either an infection or a sterile inflammation. This study aims to analyze the prevalence of acute inflammatory lesions of the placenta, the association with a positive result of the microbiological examination, and the fetal-maternal outcomes. This retrospective study considered all single, consecutive pregnancies and their placental pathological examination during 2014–2017. The evidence of funisitis, chorionic vasculitis, and chorioamnionitis was assessed by a pathologist, including stage and grade. Moreover, maternal fever, placental microbiological examination, and neonatal outcomes were also recorded. Among the 5910 pregnancies in the considered period, 1770 had a placental pathological examination, and 358 (6.06%) had acute placental inflammation. Microbiological examination was performed in 125 cases, revealing 64 cases with a positive microbiological outcome. In the presence of acute placental inflammation, there was a higher rate of neonatal cardiopulmonary resuscitation, admission to neonatal intensive care unit, and postnatal death of the newborn. Multivariate analysis inferred that acute inflammation of membranes was a risk factor for neonatal cardiopulmonary resuscitation (OR 2.12; CI.95 1.36–3.31; p < 0.05), acute funisitis was a risk factor for admission to intensive neonatal care unit (OR 3.2; CI.95 1.67–6.12; p < 0.05), and chorionic vasculitis was a risk factor for postnatal death of the newborn (OR 5.38; CI.95 1.37–21.06; p < 0.05). The prevalence of chorioamnionitis was 6.06%, and about half of the cases were sterile inflammation. Chorioamnionitis was associated with higher rates of adverse fetal and neonatal outcomes; in particular, chorionic vasculitis was a risk factor for postnatal death.
Optimization of use-wear detection and characterization on stone tool surfaces
Authors: Borel Antony , Deltombe Raphaël , Moreau Philippe , Ingicco Thomas , Bigerelle Maxence , Marteau Julie 
Published: December 2021

AbstractDebates and doubt around the interpretation of use-wear on stone tools called for the development of quantitative analysis of surfaces to complement the qualitative description of traces. Recently, a growing number of studies showed that prehistoric activities can be discriminated thanks to quantitative characterization of stone tools surface alteration due to use. However, stone tool surfaces are microscopically very heterogeneous and the calculated parameters may highly vary depending on the areas selected for measurement. Indeed, it may be impacted by the effects from the raw material topography and not from the altered zones only, if non-altered part of the surface is included in the measurement. We propose here to discuss this issue and present a workflow involving the use of masks to separate worn and unworn parts of the surface. Our results show that this step of extraction, together with suitable filtering, could have a high impact on the optimization of the detection and thus characterization of use traces. This represents the basis for future automatic routines allowing the detection, extraction and characterization of wear on stone tools.
Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution
Authors: Pang Yu , Chen Mengru , Lu Wei , Chen Ming , Yan Yongliang , Lin Min , Zhang Wei , Zhou Zhengfu 
Published: December 2021

AbstractEchinicola, carotenoid-pigmented bacteria, are isolated from various hypersaline environments. Carotenoid accumulation in response to salt stress can stabilize the cell membrane in order to survive. A pink-colored strain SCS 3–6 was isolated from the deep-sea sediment of the South China Sea. Growth was found to occur at 10–45 °C. The strain could tolerate 10% (w/v) NaCl concentration and grow at pH 5–9. The complete genome of SCS 3–6 comprises 5053 putative genes with a total 5,693,670 bp and an average G + C content of 40.11 mol%. The 16S rRNA gene sequence analysis indicated that strain SCS 3–6 was affiliated with the genus Echinicola, with the closely strains were Echinicola arenosa CAU 1574T (98.29%)and Echinicola shivajiensis AK12T (97.98%). For Echinicola species with available genome sequences, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANIb values from 70.77 to 74.71%, ANIm values from 82.72 to 88.88%, and DDH values from 18.00 to 23.40%. To identify their genomic features, we compared their genomes with those of other Echinicola species. Phylogenetic analysis showed that strain SCS 3–6 formed a monophyletic clade. Genomic analysis revealed that strain SCS 3–6 possessed a complete synthetic pathway of carotenoid and speculated that the production was astaxanthin. Based on phenotypic and genotypic analyses in this study, strain SCS 3–6 is considered to represent a novel species of the genus Echinicola for which the name Echinicola marina sp. nov. is proposed. The type strain is SCS 3-6T (= GDMCC 1.2220T = JCM 34403T).
No neutralizing effect of pre-existing tick-borne encephalitis virus antibodies against severe acute respiratory syndrome coronavirus-2: a prospective healthcare worker study
Authors: Kohler Philipp , Jonsdottir Hulda R. , Risch Lorenz , Vernazza Pietro , Ackermann-Gäumann Rahel , Kahlert Christian R. 
Published: December 2021

AbstractCertain immunizations including vaccination against tick-borne encephalitis virus (TBEV) have been suggested to confer cross-protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Within a prospective healthcare worker (HCW) cohort, we assessed the potentially protective role of anti-TBEV antibodies against SARS-CoV-2 infection. Among 3352 HCW, those with ≥ 1 previous TBEV vaccination (n = 2018, 60%) showed a reduced risk of SARS-CoV-2 seroconversion (adjusted odds ratio: 0.8, 95% CI: 0.7–1.0, P = 0.02). However, laboratory testing of a subgroup of 26 baseline and follow-up samples did not demonstrate any neutralizing effect of anti-TBEV antibodies against SARS-CoV-2 in live-virus neutralization assay. However, we observed significantly higher anti-TBEV antibody titers in follow-up samples of participants with previous TBEV vaccination compared to baseline, both TBEV neutralizing (p = 0.001) and total IgG (P < 0.0001), irrespective of SARS-CoV-2 serostatus. Based on these data, we conclude that the observed association of previous TBEV vaccination and reduced risk of SARS-CoV-2 infection is likely due to residual confounding factors. The increase in TBEV follow-up antibody titers can be explained by natural TBEV exposure or potential non-specific immune activation upon exposure to various pathogens, including SARS-CoV-2. We believe that these findings, although negative, contribute to the current knowledge on potential cross-immunity against SARS-CoV-2 from previous immunizations.
Exquisite air sac histological traces in a hyperpneumatized nanoid sauropod dinosaur from South America
Authors: Aureliano Tito , Ghilardi Aline M. , Navarro Bruno A. , Fernandes Marcelo A. , Ricardi-Branco Fresia , Wedel Mathew J. 
Published: December 2021

AbstractThis study reports the occurrence of pneumosteum (osteohistological structure related to an avian-like air sac system) in a nanoid (5.7-m-long) saltasaurid titanosaur from Upper Cretaceous Brazil. We corroborate the hypothesis of the presence of an air sac system in titanosaurians based upon vertebral features identified through external observation and computed tomography. This is the fifth non-avian dinosaur taxon in which histological traces of air sacs have been found. We provided a detailed description of pneumatic structures from external osteology and CT scan data as a parameter for comparison with other taxa. The camellate pattern found in the vertebral centrum (ce) of this taxon and other titanosaurs shows distinct architectures. This might indicate whether cervical or lung diverticula pneumatized different elements. A cotylar internal plate of bone tissue sustains radial camellae (rad) in a condition similar to Alamosaurus and Saltasaurus. Moreover, circumferential chambers (cc) near the cotyle might be an example of convergence between diplodocoids and titanosaurs. Finally, we also register for the first time pneumatic foramina (fo) and fossae connecting camellate structures inside the neural canal in Titanosauria and the second published case in non-avian dinosaurs. The extreme pneumaticity observed in this nanoid titanosaur contrasts with previous assumptions that this feature correlates with the evolution of gigantic sizes in sauropodomorphs. This study reinforces that even small-bodied sauropod clades could present a hyperpneumatized postcranial skeleton, a character inherited from their large-bodied ancestors.
Clonal dynamics of BRAF-driven drug resistance in EGFR-mutant lung cancer
Authors: Schaufler Diana , Ast David F. , Tumbrink Hannah L. , Abedpour Nima , Maas Lukas , Schwäbe Ayla E. , Spille Inga , Lennartz Stefanie , Fassunke Jana , Aldea Mihaela , Besse Benjamin , Planchard David , Nogova Lucia , Michels Sebastian , Kobe Carsten , Persigehl Thorsten , Westphal Theresa , Koleczko Sophia , Fischer Rieke , Weber Jan-Phillip , Altmüller Janine , Thomas Roman K. , Merkelbach-Bruse Sabine , Gautschi Oliver , Mezquita Laura , Büttner Reinhard , Wolf Jürgen , Peifer Martin , Brägelmann Johannes , Scheffler Matthias , Sos Martin L. 
Published: December 2021

AbstractActivation of MAPK signaling viaBRAFmutations may limit the activity of EGFR inhibitors inEGFR-mutant lung cancer patients. However, the impact ofBRAFmutations on the selection and fitness of emerging resistant clones during anti-EGFR therapy remains elusive. We tracked the evolution of subclonal mutations by whole-exome sequencing and performed clonal analyses of individual metastases during therapy. Complementary functional analyses of polyclonalEGFR-mutant cell pools showed a dose-dependent enrichment ofBRAFV600Eand a loss of EGFR inhibitor susceptibility. The clones remain stable and become vulnerable to combined EGFR, RAF, and MEK inhibition. Moreover, only osimertinib/trametinib combination treatment, but not monotherapy with either of these drugs, leads to robust tumor shrinkage inEGFR-driven xenograft models harboringBRAFV600Emutations. These data provide insights into the dynamics of clonal evolution ofEGFR-mutant tumors and the therapeutic implications ofBRAFco-mutations that may facilitate the development of treatment strategies to improve the prognosis of these patients.
High TGF-β signature predicts immunotherapy resistance in gynecologic cancer patients treated with immune checkpoint inhibition
Authors: Ni Ying , Soliman Ahmed , Joehlin-Price Amy , Rose Peter G. , Vlad Anda , Edwards Robert P. , Mahdi Haider 
Published: December 2021

AbstractVarious immune signatures predictive of resistance to immune checkpoint inhibitors (ICI) have been described in multiple solid cancers, but still under-investigated in gynecological (GYN) cancer. For 49 GYN cancer patients included in our study, without transcriptome signature, immune-related toxicity was the only clinical predictor of ICI treatment response (p = 0.008). The objective clinical response was the only predictor of progression-free survival (ICI-PFS, p = 0.0008) and overall survival (ICI-OS, p = 0.01). Commonly used ICI marker PD-L1 expression negatively correlated with progression-free survival (ICI-PFS) (p = 0.0019). We performed transcriptome and signaling pathway enrichment analyses based on ICI treatment responses and the survival outcome, and further estimated immune cell abundance using 547 gene markers. Our data revealed that TGF-β regulated signaling pathway was noted to play an important role in immunotherapy failure. Using our 6-genes TGF-β score, we observed longer ICI-PFS associated with lower TGF-β score (8.1 vs. 2.8 months, p = 0.046), which was especially more prominent in ovarian cancer (ICI-PFS 16.6 vs. 2.65 months, p = 0.0012). Further, abundant immunosuppressive cells like T-regulatory cells, eosinophils, and M2 macrophages were associated with shorter ICI-OS and correlated positively with CD274 and CTLA4 expressions. This study provides insight on the potential role of TGF-β in mediating immunotherapy resistance and cross-talking to immunosuppressive environment in GYN cancer. The TGF-β score, if validated in a larger cohort, can identify patients who likely to fail ICI and benefit from targeting this pathway to enhance the response to ICI.
Lewis acid-mediated Suzuki–Miyaura cross-coupling reaction
Authors: Niwa Takashi , Uetake Yuta , Isoda Motoyuki , Takimoto Tadashi , Nakaoka Miki , Hashizume Daisuke , Sakurai Hidehiro , Hosoya Takamitsu 
Published: December 2021

AbstractThe palladium-catalysed Suzuki–Miyaura cross-coupling reaction of organohalides and organoborons is a reliable method for carbon–carbon bond formation. This reaction involves a base-mediated transmetalation process, but the presence of a base also promotes competitive protodeborylation. Herein, we established a Suzuki–Miyaura cross-coupling reaction via Lewis acid-mediated transmetalation of an organopalladium(II) intermediate with organoborons. Experimental and theoretical investigations indicate that the controlled release of the transmetalation-active intermediate enables base-independent transmetalation under heating conditions and enhances the applicable scope of this process. This system enables us to avoid the addition of a traditional base and, thus, renders substrates with base-sensitive moieties available. Results from this research further expand the overall utility of cross-coupling chemistry.
Co-option of an extracellular protease for transcriptional control of nutrient degradation in the fungus Aspergillus nidulans
Authors: Li Ang , Parsania Chirag , Tan Kaeling , Todd Richard B. , Wong Koon Ho 
Published: December 2021

AbstractNutrient acquisition is essential for all organisms. Fungi regulate their metabolism according to environmental nutrient availability through elaborate transcription regulatory programs. In filamentous fungi, a highly conserved GATA transcription factor AreA and its co-repressor NmrA govern expression of genes involved in extracellular breakdown, uptake, and metabolism of nitrogen nutrients. Here, we show that the Aspergillus nidulans PnmB protease is a moonlighting protein with extracellular and intracellular functions for nitrogen acquisition and metabolism. PnmB serves not only as a secreted protease to degrade extracellular nutrients, but also as an intracellular protease to control the turnover of the co-repressor NmrA, accelerating AreA transcriptional activation upon nitrogen starvation. PnmB expression is controlled by AreA, which activates a positive feedback regulatory loop. Hence, we uncover a regulatory mechanism in the well-established controls determining the response to nitrogen starvation, revealing functional evolution of a protease gene for transcriptional regulation and extracellular nutrient breakdown.
Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids
Authors: Larison Brenda , Pinho Gabriela M. , Haghani Amin , Zoller Joseph A. , Li Caesar Z. , Finno Carrie J. , Farrell Colin , Kaelin Christopher B. , Barsh Gregory S. , Wooding Bernard , Robeck Todd R. , Maddox Dewey , Pellegrini Matteo , Horvath Steve 
Published: December 2021

AbstractEffective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC’s ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms
Authors: Matsuzaki Hitomi , Miyajima Yu , Fukamizu Akiyoshi , Tanimoto Keiji 
Published: December 2021

AbstractThe mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.