bluuebunny/crossref_metadata_2025 huggingface dataset:
Topically Applied Cross-Linked Hyaluronan Attenuates the Formation of Spinal Epidural Fibrosis in a Swine Model of Laminectomy
Authors: Lin Cheng-Li , Jou I-Ming , Wu Cheng-Yi , Kuo Yuh-Ruey , Yang Shih-Chieh , Lee Jung-Shun , Tu Yuan-Kun , Chen Sung-Ching , Huang Yi-Hung
Published: October 2019

Epidural fibrosis is an inevitable aspect of the postoperative healing process which is one of the causes of failed back surgery syndrome following spinal surgery. The aim of the present study was to examine the inhibitory effect of 1,4-butanediol diglycidyl ether-crosslinked hyaluronan (cHA) on spinal epidural fibrosis in a swine model. Epidural fibrosis was induced through conduction of hemi-laminotomy (L2 and L3) or laminectomy (L4 and L5), while L1 was assigned as the control group in six pigs. The cHA was applied to L3 and L5 surgical sites. MRI evaluation, histologic examination, expressions of matrix metalloproteinases (MMPs), and cytokines in scar tissue were assessed four months after surgery. cHA treatment significantly decreased the scar formation in both hemi-laminotomy and laminectomy sites. cHA also significantly increased MMP-3 and MMP-9 expression in scar tissue. Further, the epithelial-mesenchymal transition -related factors (transforming growth factor-β and vimentin) were suppressed and the anti-inflammatory cytokines (CD44 and interleukin-6) were increasingly expressed in cHA-treated sites. The current study demonstrated that cHA may attenuate spinal epidural fibrosis formation after laminectomy surgery by enhancing the expression of MMPs and anti-inflammatory pathways.
MiR-499 Responsive Lethal Construct for Removal of Human Embryonic Stem Cells after Cardiac Differentiation
Authors: Elovic Edan , Etzion Sharon , Cohen Smadar
Published: October 2019

Deriving cell populations from human embryonic stem cells (hESCs) for cell-based therapy is considered a promising strategy to achieve functional cells, yet its translation to clinical practice depends on achieving fully defined differentiated cells. In this work, we generated a miRNA-responsive lethal mRNA construct that selectively induces rapid apoptosis in hESCs by expressing a mutant (S184del) Bax variant. Insertion of miR-499 target sites in the construct enabled to enrich hESC-derived cardiomyocytes (CMs) in culture. A deterministic non-linear model was developed and validated with experimental data, to predict the outcome for each treatment cycle and the number of treatment cycle repetitions required to achieve completely purified cTNT-positive cells. The enriched hESC-CMs displayed physiological sarcomere orientation, functional calcium handling and after transplantation into SCID-NOD mice did not form teratomas. The modular miRNA responsive lethal mRNA construct could be employed in additional directed differentiation protocols, by adjusting the miRNA to the specific cells of choice.
Blue and green luminescent carbon nanodots from controllable fuel-rich flame reactors
Authors: Russo Carmela , Apicella Barbara , Ciajolo Anna
Published: October 2019

The continuous synthesis in controlled gas flame reactors is here demonstrated as a very effective approach for the direct and easy production of structurally reproducible carbon nanodots. In this work, the design of a simple deposition system, inserted into the reactor, is introduced. A controlled flame reactor is employed in the present investigation. The system was optimized for the production of carbon nanoparticles including fluorescent nanocarbons. Blue and green fluorescent carbon could be easily separated from the carbon nanoparticles by extraction with organic solvents and characterized by advanced chemical (size exclusion chromatography and mass spectrometry) and spectroscopic analysis. The blue fluorescent carbon comprised a mixture of molecular fluorophores and aromatic domains; the green fluorescent carbon was composed of aromatic domains (10–20 aromatic condensed rings), bonded and/or turbostratically stacked together. The green-fluorescent carbon nanodots produced in the flame reactor were insoluble in water but soluble in N-methylpyrrolidinone and showed excitation-independent luminescence. These results provide insights for a simple and controlled synthesis of carbon nanodots with specific and versatile features, which is a promising pathway for their use in quite different applicative sectors of bioimaging.
An in-vitro assay using human spermatozoa to detect toxicity of biologically active substances
Authors: Vollmer Tino , Ljungberg Börje , Jankowski Vera , Jankowski Joachim , Glorieux Griet , Stegmayr Bernd G.
Published: October 2019

Identifying the key toxic players within an in-vivo toxic syndrome is crucial to develop targeted therapies. Here, we established a novel method that characterizes the effect of single substances by means of an ex-vivo incubation set-up. We found that primary human spermatozoa elicit a distinct motile response on a (uremic) toxic milieu. Specifically, this approach describes the influence of a bulk toxic environment (uremia) as well as single substances (uremic toxins) by real-time analyzing motile cellular behavior. We established the human spermatozoa-based toxicity testing (HSTT) for detecting single substance-induced toxicity to be used as a screening tool to identify in-vivo toxins. Further, we propose an application of the HSTT as a method of clinical use to evaluate toxin-removing interventions (hemodialysis).
Choosing Clinical Variables for Risk Stratification Post-Acute Coronary Syndrome
Authors: Myers Paul D. , Huang Wei , Anderson Fred , Stultz Collin M.
Published: October 2019

Most risk stratification methods use expert opinion to identify a fixed number of clinical variables that have prognostic significance. In this study our goal was to develop improved metrics that utilize a variable number of input parameters. We first used Bootstrap Lasso Regression (BLR) – a Machine Learning method for selecting important variables – to identify a prognostic set of features that identify patients at high risk of death 6-months after presenting with an Acute Coronary Syndrome. Using data derived from the Global Registry of Acute Coronary Events (GRACE) we trained a logistic regression model using these features and evaluated its performance on a development set (N = 43,063) containing patients who have values for all features, and a separate dataset (N = 6,363) that contains patients who have missing feature values. The final model, Ridge Logistic Regression with Variable Inputs (RLRVI), uses imputation to estimate values for missing features. BLR identified 19 features, 8 of which appear in the GRACE score. RLRVI had modest, yet statistically significant, improvement over the standard GRACE score on both datasets. Moreover, for patients who are relatively low-risk (GRACE≤87), RLRVI had an AUC and Hazard Ratio of 0.754 and 6.27, respectively, vs. 0.688 and 2.46 for GRACE, (p < 0.007). RLRVI has improved discriminatory performance on patients who have values for the 8 GRACE features plus any subset of the 11 non-GRACE features. Our results demonstrate that BLR and data imputation can be used to obtain improved risk stratification metrics, particularly for patients who are classified as low risk using traditional methods.
Increasing prevalence, time trend and seasonality of gastroschisis in São Paulo state, Brazil, 2005–2016
Authors: Calderon Mauricio Giusti , Santos Edige Felipe de Sousa , Abreu Luiz Carlos de , Raimundo Rodrigo Daminello
Published: October 2019

To estimate the gastroschisis seasonality and trend of prevalence in recent years, stratified by maternal age and geographical clusters of São Paulo state, a population–based study was designed. We used data from the Live Births Information System (SINASC) in São Paulo state, Brazil, from 2005 to 2016. Trends of prevalence were evaluated for the specific subgroups using the Prais–Winsten regression model, and the Durbin–Watson test was used, to estimate the regression coefficient, the annual percent change (APC), and 95% confidence interval (CI). We observed 1576 cases of gastroschisis among 7,317,657 live births (LB), a prevalence of 2.154 (95% CI: 2.047–2.260) per 10,000 LB which included, 50.6% males, 67.4% Caucasians, 53.4% preterm births, and 80.9% caesarean births. The prevalence of gastroschisis significantly increased by 2.6% (95% CI: 0.0–5.2) per year, and this trend was higher in mothers aged 30–34 years (APC: 10.2, 95% CI: 1.4–19.4) than in mothers of other age groups. Between 2011 and 2016, we identified the existence of seasonality based on the date of conception in the middle months of the year (p = 0.002). This is the first and largest population–based study summarizing current epidemiology and identifying trend of prevalence of gastroschisis in São Paulo state.
Clinical-like cryotherapy improves footprint patterns and reduces synovial inflammation in a rat model of post-traumatic knee osteoarthritis
Authors: Barbosa Germanna Medeiros , Cunha Jonathan Emanuel , Cunha Thiago Mattar , Martinho Lizandra Botaro , Castro Paula Aiello Tomé Souza , Oliveira Francisco Fábio Bezerra , Cunha Fernando Queiróz , Ramalho Fernando Silva , Salvini Tania Fátima
Published: October 2019

Cryotherapy is a non-pharmacological treatment commonly used to control inflammation and improve function after acute traumas. However, there are no definitive findings about its effects on chronic joint diseases such as knee osteoarthritis (KOA). The aim of this study was to investigate the effects of clinical-like cryotherapy on functional impairment and synovial inflammation in a rat model of KOA generated by anterior cruciate ligament transection (ACLT). Thirty-two male Wistar rats were randomly divided into four groups (n = 8/group): Control, KOA, KOA + Cryotherapy and KOA + Placebo. The last two groups were submitted to the relevant interventions twice a day for five days (61 to 65), with each session lasting 20 min. Gait test, skin temperature, thermal response threshold and joint swelling were assessed in all groups before ACLT surgery, and pre (60th day) and post (66th day) intervention protocols. On day 66, the animals were euthanized and exsanguinated to remove the synovial membrane for histopathological examination and synovial fluid to determine the leukocyte count and cytokine concentration. After the intervention period (66th day), footprint area only increased in the KOA + Cryotherapy group (P = 0.004; 14%) when compared to KOA and KOA + Placebo, but did not differ from controls. Cryotherapy lowered the synovial fluid leukocyte count (P < 0.0001; ≥95.0%) and cytokine concentration (P < 0.0001; ≥55%) when compared to the KOA and Placebo groups. Synovial score and synovial fibrosis did not differ in the KOA groups. In conclusion, footprint patterns improved in rats with ACLT-induced KOA as a result of clinical-like cryotherapy, which also lowered the synovial fluid leukocyte count and inflammatory cytokine concentration in these rats.
Distribution and quantification of bioluminescence as an ecological trait in the deep sea benthos
Authors: Martini Séverine , Kuhnz Linda , Mallefet Jérôme , Haddock Steven H. D.
Published: October 2019

Bioluminescence is a prominent functional trait used for visual communication. A recent quantification showed that in pelagic ecosystems more than 75% of individual macro-planktonic organisms are categorized as able to emit light. In benthic ecosystems, only a few censuses have been done, and were based on a limited number of observations. In this study, our dataset is based on observations from remotely operated vehicle (ROV) dives conducted from 1991–2016, spanning 0–3,972 m depth. Data were collected in the greater Monterey Bay area in central California, USA and include 369,326 pelagic and 154,275 epibenthic observations at Davidson Seamount, Guide Seamount, Sur Ridge and Monterey Bay. Because direct observation of in situ bioluminescence remains a technical challenge, taxa from ROV observations were categorized based on knowledge gained from the literature to assess bioluminescence status. We found that between 30–41% of the individual observed benthic organisms were categorized as capable of emitting light, with a strong difference between benthic and pelagic ecosystems. We conclude that overall variability in the distribution of bioluminescent organisms is related to the major differences between benthic and pelagic habitats in the deep ocean. This study may serve as the basis of future investigations linking the optical properties of various habitats and the variability of bioluminescent organism distributions.
Macrophage polarization impacts tunneling nanotube formation and intercellular organelle trafficking
Authors: Goodman Spencer , Naphade Swati , Khan Meisha , Sharma Jay , Cherqui Stephanie
Published: October 2019

Tunneling nanotubes (TNTs) are cellular extensions enabling cytosol-to-cytosol intercellular interaction between numerous cell types including macrophages. Previous studies of hematopoietic stem and progenitor cell (HSPC) transplantation for the lysosomal storage disorder cystinosis have shown that HSPC-derived macrophages form TNTs to deliver cystinosin-bearing lysosomes to cystinotic cells, leading to tissue preservation. Here, we explored if macrophage polarization to either proinflammatory M1-like M(LPS/IFNγ) or anti-inflammatory M2-like M(IL-4/IL-10) affected TNT-like protrusion formation, intercellular transport and, ultimately, the efficacy of cystinosis prevention. We designed new automated image processing algorithms used to demonstrate that LPS/IFNγ polarization decreased bone marrow-derived macrophages (BMDMs) formation of protrusions, some of which displayed characteristics of TNTs, including cytoskeletal structure, 3D morphology and size. In contrast, co-culture of macrophages with cystinotic fibroblasts yielded more frequent and larger protrusions, as well as increased lysosomal and mitochondrial intercellular trafficking to the diseased fibroblasts. Unexpectedly, we observed normal protrusion formation and therapeutic efficacy following disruption of anti-inflammatory IL-4/IL-10 polarization in vivo by transplantation of HSPCs isolated from the Rac2−/− mouse model. Altogether, we developed unbiased image quantification systems that probe mechanistic aspects of TNT formation and function in vitro, while HSPC transplantation into cystinotic mice provides a complex in vivo disease model. While the differences between polarization cell culture and mouse models exemplify the oversimplicity of in vitro cytokine treatment, they simultaneously demonstrate the utility of our co-culture model which recapitulates the in vivo phenomenon of diseased cystinotic cells stimulating thicker TNT formation and intercellular trafficking from macrophages. Ultimately, we can use both approaches to expand the utility of TNT-like protrusions as a delivery system for regenerative medicine.
Double Interferometer Design for Independent Wavefront Manipulation in Spectral Domain Optical Coherence Tomography
Authors: Kanngiesser Jonas , Rahlves Maik , Roth Bernhard
Published: October 2019

Spectral domain optical coherence tomography (SD-OCT) is a highly versatile method which allows for three dimensional optical imaging in scattering media. A number of recent publications demonstrated the technique to benefit from structured illumination and beam shaping approaches, e.g. to enhance the signal-to-noise ratio or the penetration depth with samples such as biological tissue. We present a compact and easy to implement design for independent wavefront manipulation and beam shaping at the reference and sample arm of the interferometric OCT device. The design requires a single spatial light modulator and can be integrated to existing free space SD-OCT systems by modifying the source arm only. We provide analytical and numerical discussion of the presented design as well as experimental data confirming the theoretical analysis. The system is highly versatile and lends itself for applications where independent phase or wavefront control is required. We demonstrate the system to be used for wavefront sensorless adaptive optics as well as for iterative optical wavefront shaping for OCT signal enhancement in strongly scattering media.
Electrophysiological responses of relatedness to consecutive word stimuli in relation to an actively recollected target word
Authors: Dijkstra Karen , Farquhar Jason , Desain Peter
Published: October 2019

In this paper, we investigate the robustness of electrophysiological responses of relatedness to multiple consecutive word stimuli (probes), in relation to an actively recollected target word. Such relatedness information could be used by a Brain Computer Interface to infer the active semantic concept on a user’s mind, by integrating the knowledge of the relationship between the multiple probe words and the ‘unknown’ target. Such a BCI can take advantage of the N400: an event related potential that is sensitive to semantic content of a stimulus in relation to an established semantic context. However, it is unknown whether the N400 is suited for the multiple probing paradigm we propose, as other intervening words might distract from the established context (i.e., the target word). We perform an experiment in which we present up to ten words after an initial target word, and find no attenuation of the strength of the N400 in grand average ERPs and no decrease in classification accuracy for probes occurring later in the sequences. These results are groundwork for developing a BCI that infers the concept on a user’s mind through repeated probing, however, low single trial decoding accuracy, and high subject variability may limit practical applicability.
Upper-tropospheric bridging of wintertime surface climate variability in the Euro-Atlantic region and northern Asia
Authors: Schlichtholz Pawel
Published: October 2019

A remarkable feature of interannual climate variability is a robust link of wintertime anomalies of surface air temperature (SAT) in northern Asia to pan-Atlantic SAT variations associated with the North Atlantic Oscillation (NAO). Here statistical analyses of data from the era of satellite observations (1979–2017) are used to show that about 80% of the variance of the winter (December-March) mean area-averaged SAT anomalies in northern Asia can be explained by the anomalous surface circulation associated with an NAO-like mode of sea level pressure variability over extratropical Eurasia. These SAT anomalies are related equally strongly to the “Lake Baikal” vortex representing variations of the upper-tropospheric circulation over northern Asia. Support is given for the scenario that this vortex drives SAT anomalies in northern Asia via surface-reaching displacements of isentropic surfaces and that it is coupled to climate variability in the Euro-Atlantic sector via interactions between the North Atlantic storm track, quasi-stationary planetary waves, and zonal-mean zonal winds. The results underpin the importance of a lesser-known zonal wavenumber-3 structure of disturbances trapped over Eurasia by the polar front jet rather than the better-known zonal wavenumber-5 structure of disturbances trapped by the subtropical jet for NAO teleconnections.
All-optical majority gate based on an injection-locked laser
Authors: von Lerber Tuomo , Lassas Matti , Lyubopytov Vladimir S. , Ylinen Lauri , Chipouline Arkadi , Hofmann Klaus , Küppers Franko
Published: October 2019

An all-optical computer has remained an elusive concept. To construct a practical computing primitive equivalent to an electronic Boolean logic, one should utilize nonlinearity that overcomes weaknesses that plague many optical processing schemes. An advantageous nonlinearity provides a complete set of logic operations and allows cascaded operations without changes in wavelength or in signal encoding format. Here we demonstrate an all-optical majority gate based on a vertical-cavity surface-emitting laser (VCSEL). Using emulated signal coupling, the arrangement provides Bit Error Ratio (BER) of 10−6 at the rate of 1 GHz without changes in the wavelength or in the signal encoding format. Cascaded operation of the injection-locked laser majority gate is simulated on a full adder and a 3-bit ripple-carry adder circuits. Finally, utilizing the spin-flip model semiconductor laser rate equations, we prove that injection-locked lasers may perform normalization operations in the steady-state with an arbitrary linear state of polarization.
Stable reference genes for RT-qPCR analysis of gene expression in the Musa acuminata-Pseudocercospora musae interaction
Authors: Rego Erica Cristina Silva , Pinheiro Tatiana David Miranda , Antonino Jose Dijair , Alves Gabriel Sergio Costa , Cotta Michelle Guitton , Fonseca Fernando Campos De Assis , Miller Robert Neil Gerard
Published: October 2019

Leaf pathogens are limiting factors in banana (Musaspp.) production, withPseudocercosporaspp. responsible for the important Sigatoka disease complex. In order to investigate cellular processes and genes involved in host defence responses, quantitative real-time PCR (RT-qPCR) is an analytical technique for gene expression quantification. Reliable RT-qPCR data, however, requires that reference genes for normalization of mRNA levels in samples are validated under the conditions employed for expression analysis of target genes. We evaluated the stability of potential reference genesACT1,α-TUB,UBQ1,UBQ2,GAPDH,EF1α,APTandRAN. Total RNA was extracted from leaf tissues ofMusa acuminatagenotypes Calcutta 4 (resistant) and Cavendish Grande Naine (susceptible), both subjected toP.musaeinfection. Expression stability was determined with NormFinder, BestKeeper, geNorm and RefFinder algorithms.UBQ2andRANwere the most stable across allM.acuminatasamples, whereas when considering inoculated and non-inoculated leaf samples,APTandUBQ2were appropriate for normalization in Calcutta 4, withRANandα-TUBmost stable in Cavendish Grande Naine. This first study of reference genes for relative quantification of target gene expression in theM.acuminata-P.musaeinteraction will enable reliable analysis of gene expression in this pathosystem, benefiting elucidation of disease resistance mechanisms.
Maternal energy insufficiency affects testicular development of the offspring in a swine model
Authors: Lin Yan , Xu Xue-Yu , Wu De , Lin Hao , Fang Zheng-Feng , Feng Bin , Xu Sheng-Yu , Che Lian-Qiang , Li Jian , Zhuo Yong , Wu Cai-Mei , Zhang Jun-Jie , Dong Hong-Jun
Published: October 2019

We determined the effects of insufficient maternal energy on testicular development in offspring in a swine model. Thirty-six sows were divided into control (CON) and low-energy diet (LE) groups during gestation. We observed that the number of Sertoli, germ, and Leydig cells in the offspring of the CON group were significantly higher than those in the LE group at 28 and 120 d after birth. Furthermore, the percentage of apoptotic testis cells was significantly higher in the offspring of the LE group than in the CON group. Transcriptome analysis of differentially expressed mRNAs and long noncoding RNAs in offspring testes indicated that these RNAs were mainly involved in lipid metabolism, apoptosis, cell proliferation, and some pivotal regulatory pathways. Results revealed that AMPK–PI3K–mTOR, MAPK, and oxidative phosphorylation signaling pathways play an important role in mediating the programming effect of insufficient maternal energy on testicular development, and that this effect occurs mainly at an early stage in life. mRNA and protein expression analyses confirmed the importance of certain signaling pathways in the regulation of testicular development. This study provides insights into the influence and possible mechanism underlying the effect of inadequate maternal energy intake on testicular development in the offspring.
Associations between Neonatal Serum Bilirubin and Childhood Obesity in Term Infants
Authors: Zou Lile , Yu Huan , He Yuan , Luo Lijuan , Dong Wenbin , Zhang Jun , Lei Xiaoping , Wieg Christian
Published: October 2019

Inverse correlations between serum bilirubin level and obesity had been reported in adults. We aimed to investigate the associations between neonatal hyperbilirubinemia and childhood obesity. Data was obtained from the U.S. Collaborative Perinatal Project (CPP), a multicenter study from 1959 to 1976. Data of serum bilirubin in term newborns were used to observe the association with obesity at age of 7 years. Logistic regression models were performed to calculate adjusted odds ratios (aORs) for obesity. For children from the same mother sharing similar factors, Generalized Estimating Equation (GEE) model was used to correct for intracluster correlation. Relative to newborns with total serum bilirubin (TSB) < 3 mg/dl, there are lower risks for obesity in those with 3 mg/dl ≤ TSB < 6 mg/dl (aOR 0.91; 95%CI 0.81, 1.02), 6 mg/dl ≤ TSB < 9 mg/dl (aOR 0.88; 95%CI 0.78, 0.99), 9 mg/dl ≤ TSB<13 mg/dl (aOR 0.83; 95%CI 0.71, 0.98). By stratifying for subtypes of bilirubin, the inverse correlations only existed in exposure to unconjugated bilirubin. By using the GEE model correcting for intracluster correlations, the results are consistent. In summary, exposure to bilirubin up to 13 mg/dl is inversely associated with obesity at the age of 7 years in term infants.
Phase Space Reconstruction Based CVD Classifier Using Localized Features
Authors: Vemishetty Naresh , Gunukula Ramya Lakshmi , Acharyya Amit , Puddu Paolo Emilio , Das Saptarshi , Maharatna Koushik
Published: October 2019

This paper proposes a generalized Phase Space Reconstruction (PSR) based Cardiovascular Diseases (CVD) classification methodology by exploiting the localized features of the ECG. The proposed methodology first extracts the ECG localized features including PR interval, QRS complex, and QT interval from the continuous ECG waveform using features extraction logic, then the PSR technique is applied to get the phase portraits of all the localized features. Based on the cleanliness and contour of the phase portraits CVD classification will be done. This is first of its kind approach where the localized features of ECG are being taken into considerations unlike the state-of-art approaches, where the entire ECG beats have been considered. The proposed methodology is generic and can be extended to most of the CVD cases. It is verified on the PTBDB and IAFDB databases by taking the CVD including Atrial Fibrillation, Myocardial Infarction, Bundle Branch Block, Cardiomyopathy, Dysrhythmia, and Hypertrophy. The methodology has been tested on 65 patients’ data for the classification of abnormalities in PR interval, QRS complex, and QT interval. Based on the obtained statistical results, to detect the abnormality in PR interval, QRS complex and QT interval the Coefficient Variation (CV) should be greater than or equal to 0.1012, 0.083, 0.082 respectively with individual accuracy levels of 95.3%, 96.9%, and 98.5% respectively. To justify the clinical significance of the proposed methodology, the Confidence Interval (CI), the p-value using ANOVA have been computed. The p-value obtained is less than 0.05, and greater F-statistic values reveal the robust classification of CVD using localized features.
Low-grade glioma harbors few CD8 T cells, which is accompanied by decreased expression of chemo-attractants, not immunogenic antigens
Authors: Weenink Bas , Draaisma Kaspar , Ooi Han Z. , Kros Johan M. , Sillevis Smitt Peter A. E. , Debets Reno , French Pim J.
Published: October 2019

In multiple tumor types, prediction of response to immune therapies relates to the presence, distribution and activation state of tumor infiltrating lymphocytes (TILs). Although such therapies are, to date, unsuccessful in gliomas, little is known on the immune contexture of TILs in these tumors. We assessed whether low and high-grade glioma (LGG and HGG, grade II and IV respectively) differ with respect to number, location and tumor reactivity of TILs; as well as expression of molecules involved in the trafficking and activation of T cells. Intra-tumoral CD8 T cells were quantified by flow cytometry (LGG: n = 12; HGG: n = 8) and immunofluorescence (LGG: n = 28; HGG: n = 28). Neoantigen load and expression of Cancer Germline Antigens (CGAs) were assessed using whole exome sequencing and RNA-seq. TIL-derived DNA was sequenced and the variable domain of the TCRβ chain was classified according to IMGT nomenclature. QPCR was used to determine expression of T cell-related genes. CD8 T cell numbers were significantly lower in LGG and, in contrast to HGG, mainly remained in close vicinity to blood vessels. This was accompanied by lower expression of chemo-attractants CXCL9, CXCL10 and adhesion molecule ICAM1. We did not observe a difference in the number of expressed neoantigens or CGAs, nor in diversity of TCR-Vβ gene usage. In summary, LGG have lower numbers of intra-tumoral CD8 T cells compared to HGG, potentially linked to decreased T cell trafficking. We have found no evidence for distinct tumor reactivity of T cells in either tumor type. The near absence of TILs in LGG suggest that, at present, checkpoint inhibitors are unlikely to have clinical efficacy in this tumor type.
DNA-PKcs and ATM epistatically suppress DNA end resection and hyperactivation of ATR-dependent G2-checkpoint in S-phase irradiated cells
Authors: Mladenov Emil , Fan Xiaoxiang , Paul-Konietzko Katja , Soni Aashish , Iliakis George
Published: October 2019

We previously reported that cells exposed to low doses of ionizing radiation (IR) in the G2-phase of the cell cycle activate a checkpoint that is epistatically regulated by ATM and ATR operating as an integrated module. In this module, ATR interphases exclusively with the cell cycle to implement the checkpoint, mainly using CHK1. The ATM/ATR module similarly regulates DNA end-resection at low IR-doses. Strikingly, at high IR-doses, the ATM/ATR coupling relaxes and each kinase exerts independent contributions to resection and the G2-checkpoint. DNA-PKcs links to the ATM/ATR module and defects cause hyper-resection and hyperactivation of G2-checkpoint at all doses examined. Surprisingly, our present report reveals that cells irradiated in S-phase utilize a different form of wiring between DNA-PKcs/ATM/ATR: The checkpoint activated in G2-phase is regulated exclusively by ATR/CHK1; similarly at high and low IR-doses. DNA end-resection supports ATR-activation, but inhibition of ATR leaves resection unchanged. DNA-PKcs and ATM link now epistatically to resection and their inhibition causes hyper-resection and ATR-dependent G2-checkpoint hyperactivation at all IR-doses. We propose that DNA-PKcs, ATM and ATR form a modular unit to regulate DSB processing with their crosstalk distinctly organized in S- and G2- phase, with strong dependence on DSB load only in G2-phase.
Immobilisation of living coral embryos and larvae
Authors: Randall Carly J. , Giuliano Christine , Mead David , Heyward Andrew J. , Negri Andrew P.
Published: October 2019

Embedding and immobilisation of living cells and microorganisms is used in a variety of research and commercial applications. Here we report the successful extended immobilisation of coral larvae in a low-gelling temperature agarose. Embryos and larvae of five broadcast-spawning Scleractinian species were immobilised in agarose gel and tested in a series of exploratory survival and settlement assays. The optimal developmental stage for immobilisation was after ciliation at approximately 24 hours post-fertilisation, after which, survival of immobilised larvae of all species was nearly 100%. In long-term assays, 50% of Montipora digitata larvae survived immobilised for 89 days. Furthermore, immobilised larvae of multiple species, that were released from the agarose, generally remained capable of settlement. These results demonstrate that the immobilisation of the early life-history stages of corals is possible for a variety of applications in basic and applied science.
Association of oral health status with the CD4+ cell count in children living with HIV in Phnom Penh, Cambodia
Authors: Kikuchi Kimiyo , Furukawa Yusuke , Tuot Sovannary , Pal Khuondyla , Huot Chantheany , Yi Siyan
Published: October 2019

The association between oral and overall health, and particularly between dental and immune health, in children living with HIV remains unclear. This study examined the association between the decayed, missing and filled teeth (DMFT) score and CD4+ cell counts in 142 children living with HIV aged 8–15 years (male, 51%) from Phnom Penh, Cambodia. Other indicators of oral health (e.g., debris index, salivary flow, salivary pH and oral health-related quality of life) and overall health (e.g., nutritional status and quality of life) were also evaluated. DMFT scores were negatively associated with the CD4+ cell count in male children (β: −0.13, 95% confidence interval [CI]: −0.25, −0.02). In all children, positive associations were observed between salivary pH and CD4+ count (β: −0.645, 95% CI: 0.02, 1.25) and between salivary flow and height-for-age Z-score (β: 1.22, 95% CI: 0.50, 1.95). The debris index was negatively associated with the height-for-age Z-score (β: −2.04, 95% CI: −3.38, −0.71). In summary, oral health was associated with immune and nutritional status. Oral health policies for children living with HIV should be emphasised, and further studies should evaluate the mechanism underlying the relationship between oral and overall health.
A one-step tRNA-CRISPR system for genome-wide genetic
interaction mapping in mammalian cells
Authors: Zhao Yulei , Tyrishkin Kathrin , Sjaarda Calvin , Khanal Prem , Stafford Jeff , Rauh Michael , Liu Xudong , Babak Tomas , Yang Xiaolong
Published: October 2019

Mapping genetic interactions in mammalian cells is limited due to
technical obstacles. Here we describe a method called TCGI (tRNA-CRISPR for genetic
interactions) to generate a high-efficient, barcode-free and scalable pairwise
CRISPR libraries in mammalian cells for identifying genetic interactions. We have
generated a genome- wide library to identify genes genetically interacting with TAZ
in cell viability regulation. Validation of candidate synergistic genes reveals the
screening accuracy of 85% and TAZ-MCL1 is characterized as combinational drug
targets for non-small cell lung cancer treatments. TCGI has dramatically improved
the current methods for mapping genetic interactions and screening drug targets for
combinational therapies.
Noninvasive intravital high-resolution imaging of pancreatic neuroendocrine tumours
Authors: Balan Mirela , Trusohamn Marta , Ning Frank Chenfei , Jacob Stefan , Pietras Kristian , Eriksson Ulf , Berggren Per-Olof , Nyqvist Daniel
Published: October 2019

Preclinical trials of cancer drugs in animal models are important for drug development. The Rip1Tag2 (RT2) transgenic mouse, a model of pancreatic neuroendocrine tumours (PNET), has provided immense knowledge about PNET biology, although tumour progression occurs in a location inaccessible for real-time monitoring. To overcome this hurdle we have developed a novel platform for intravital 3D imaging of RT2 tumours to facilitate real-time studies of cancer progression. Pre-oncogenic islets retrieved from RT2 mice were implanted into the anterior chamber of the eye (ACE) of host mice, where they engrafted on the iris, recruited blood vessels and showed continuous growth. Noninvasive confocal and two-photon laser-scanning microscopy through the transparent cornea facilitated high-resolution imaging of tumour growth and angiogenesis. RT2 tumours in the ACE expanded up to 8-fold in size and shared hallmarks with tumours developing in situ in the pancreas. Genetically encoded fluorescent reporters enabled high-resolution imaging of stromal cells and tumour cell migration. Sunitinib treatment impaired RT2 tumour angiogenesis and growth, while overexpression of the vascular endothelial growth factor (VEGF)-B increased tumour angiogenesis though tumour growth was impaired. In conclusion, we present a novel platform for intravital high-resolution and 3D imaging of PNET biology and cancer drug assessment.
Microbial metabolite deoxycholic acid controls Clostridium perfringens-induced chicken necrotic enteritis through attenuating inflammatory cyclooxygenase signaling
Authors: Wang Hong , Latorre Juan D. , Bansal Mohit , Abraha Mussie , Al-Rubaye Bilal , Tellez-Isaias Guillermo , Hargis Billy , Sun Xiaolun
Published: October 2019

Necrotic enteritis (NE) caused by Clostridium perfringens infection has reemerged as a prevalent poultry disease worldwide due to reduced usage of prophylactic antibiotics under consumer preferences and regulatory pressures. The lack of alternative antimicrobial strategies to control this disease is mainly due to limited insight into the relationship between NE pathogenesis, microbiome, and host responses. Here we showed that the microbial metabolic byproduct of secondary bile acid deoxycholic acid (DCA), at as low as 50 µM, inhibited 82.8% of C. perfringens growth in Tryptic Soy Broth (P < 0.05). Sequential Eimeria maxima and C. perfringens challenges significantly induced NE, severe intestinal inflammation, and body weight (BW) loss in broiler chickens. These negative effects were diminished (P < 0.05) by 1.5 g/kg DCA diet. At the cellular level, DCA alleviated NE-associated ileal epithelial death and significantly reduced lamina propria cell apoptosis. Interestingly, DCA reduced C. perfringens invasion into ileum (P < 0.05) without altering the bacterial ileal luminal colonization. Molecular analysis showed that DCA significantly reduced inflammatory mediators of Infγ, Litaf, Il1β, and Mmp9 mRNA accumulation in ileal tissue. Mechanism studies revealed that C. perfringens induced (P < 0.05) elevated expression of inflammatory mediators of Infγ, Litaf, and Ptgs2 (Cyclooxygenases-2 (COX-2) gene) in chicken splenocytes. Inhibiting the COX signaling by aspirin significantly attenuated INFγ-induced inflammatory response in the splenocytes. Consistent with the in vitro assay, chickens fed 0.12 g/kg aspirin diet protected the birds against NE-induced BW loss, ileal inflammation, and intestinal cell apoptosis. In conclusion, microbial metabolic product DCA prevents NE-induced BW loss and ileal inflammation through attenuating inflammatory response. These novel findings of microbiome protecting birds against NE provide new options on developing next generation antimicrobial alternatives against NE.
A Guanidine-Based Superbase as Efficient Chemiluminescence Booster
Authors: Geiselhart Christina M. , Schmitt Christian W. , Jöckle Philipp , Mutlu Hatice , Barner-Kowollik Christopher
Published: October 2019

We introduce the guanidine-based superbase 1,5,7-triaza-bicyclo-[4.4.0]dec-5-ene (TBD) as efficient enabler for chemiluminescence (CL) based on luminol in a simple, ready-to-use two component system. The strong CL is generated by the superbase’s properties as peroxidase mimetic and bifunctional coreactant. The herein established concept allows for CL enabling molecules (superbases) to be readily implemented in larger molecular structures, including in polymers.
Lowered anti-beta1 adrenergic receptor antibody concentrations may have prognostic significance in acute coronary syndrome
Authors: Ernst Diana , Westerbergh Johan , Sogkas Georgios , Jablonka Alexandra , Ahrenstorf Gerrit , Schmidt Reinhold Ernst , Heidecke Harald , Wallentin Lars , Riemekasten Gabriela , Witte Torsten
Published: October 2019

Although several risk factors exist for acute coronary syndrome (ACS) no biomarkers for survival or risk of re-infarction have been validated. Previously, reduced serum concentrations of anti-ß1AR Ab have been implicated in poorer ACS outcomes. This study further evaluates the prognostic implications of anti-ß1AR-Ab levels at the time of ACS onset. Serum anti-ß1AR Ab concentrations were measured in randomly selected patients from within the PLATO cohort. Stratification was performed according to ACS event: ST-elevation myocardial infarct (STEMI) vs. non-ST elevation myocardial infarct (NSTEMI). Antibody concentrations at ACS presentation were compared to 12-month all-cause and cardiovascular mortality, as well as 12-month re-infarction. Sub-analysis, stratifying for age and the correlation between antibody concentration and conventional cardiac risk-factors was subsequently performed. Serum anti-ß1AR Ab concentrations were measured in 400/799 (50%) STEMI patients and 399 NSTEMI patients. Increasing anti-ß1AR Ab concentrations were associated with STEMI (p = 0.001). Across all ACS patients, no associations between anti-ß1AR Ab concentration and either all-cause cardiovascular death or myocardial re-infarction (p = 0.14) were evident. However among STEMI patients ≤60 years with anti-ß1AR Ab concentration  median (14/198 (7.1%) vs. 2/190 (1.1%)); p = 0.01). Similarly, the same sub-group demonstrated greater risk of cardiovascular death in year 1, including re-infarction and stroke (22/198 (11.1%) vs. 10/190 (5.3%); p = 0.017). ACS Patients ≤60 years, exhibiting lower concentrations of ß1AR Ab carry a greater risk for early re-infarction and cardiovascular death. Large, prospective studies quantitatively assessing the prognostic relevance of Anti-ß1AR Ab levels should be considered.
Disruption of hmgA by DNA Duplication is Responsible for Hyperpigmentation in a Vibrio anguillarum Strain
Authors: Batallones Veronica , Fernandez Jennifer , Farthing Brett , Shoemaker Jordan , Qian Keizen Li , Phan Kimberly , Fung Eric , Rivera Ashley , Van Kevin , de la Cruz Francesca , Ferreri Alexandra J. , Burinski Krystle , Zhang Jackie , Lizarraga Vicente , Doan Kevin , Rocha Kenneth , Traglia German , Ramirez Maria S. , Tolmasky Marcelo E.
Published: October 2019

Vibrio anguillarum 531A, isolated from a diseased fish in the Atlantic Ocean, is a mixture composed of about 95 and 5% of highly pigmented cells (strain 531Ad) and cells with normal levels of pigmentation (strain 531Ac), respectively. Analysis of the V. anguillarum 531Ad DNA region encompassing genes involved in the tyrosine metabolism showed a 410-bp duplication within the hmgA gene that results in a frameshift and early termination of translation of the homogentisate 1,2-dioxygenase. We hypothesized that this mutation results in accumulation of homogentisate that is oxidized and polymerized to produce pyomelanin. Introduction in E. coli of recombinant clones carrying the V. anguillarum hppD (4-hydroxyphenylpyruvate-dioxygenase), and a mutated hmgA produced brown colored colonies. Complementation with a recombinant clone harboring hmgA restored the original color to the colonies confirming that in the absence of homogentisate 1,2-dioxygenase the intermediary in tyrosine catabolism homogentisate accumulates and undergoes nonenzymatic oxidation and polymerization resulting in high amounts of the brown pigment. Whole-genome sequence analysis showed that V. anguillarum 531 Ac and 531Ad differ in the hmgA gene mutation and 23 mutations, most of which locate to intergenic regions and insertion sequences.
Glycerol Monolaurate Contributes to the Antimicrobial and Anti-inflammatory Activity of Human Milk
Authors: Schlievert Patrick M. , Kilgore Samuel H. , Seo Keun Seok , Leung Donald Y. M.
Published: October 2019

Human milk has antimicrobial compounds and immunomodulatory activities. We investigated glycerol monolaurate (GML) in human milk versus bovine milk and infant formula for antimicrobial and anti-inflammatory activities. Human milk contained approximately 3000 µg/ml of GML, compared to 150 μg/ml in bovine milk and none in infant formula. For bacteria tested (Staphylococcus aureus, Bacillus subtilis, Clostridium perfringens, Escherichia coli), except Enterococcus faecalis, human milk was more antimicrobial than bovine milk and formula. The Enterococcus faecalis strain, which was not inhibited, produced reutericyclin, which is an analogue of GML and functions as a growth stimulant in bacteria that produce it. Removal of GML and other lipophilic molecules from human milk by ethanol extraction resulted in a loss of antibacterial activity, which was restored by re-addition of GML. GML addition caused bovine milk to become antimicrobial. Human milk but not bovine milk or formula inhibited superantigen and bacterial-induced IL-8 production by model human epithelial cells. GML may contribute beneficially to human milk compared to bovine milk or infant formula.
Thermal engineering of stone increased prehistoric toolmaking skill
Authors: Mraz Veronica , Fisch Mike , Eren Metin I. , Lovejoy C. Owen , Buchanan Briggs
Published: October 2019

Intentional heat treating of toolstone has been documented to have begun at least by 70 K BP; however, the advantages of such treatment have been debated for decades. There are two schools of thought with regard to its purpose. One, is that it merely reduces the force required for flake propagation. A second is that it also alters flake morphological properties. We systematically tested these hypotheses by generating flakes from cores exposed to three different temperatures (ambient, 300 °C, and 350 °C) using automated propagation procedures that bypassed any human agency. While the force propagation magnitude is altered by heat treatment, the flakes were not. We examined these flakes according to nine measures of morphology. None differed significantly or systematically within the three categories. While our results confirm that heat treatment does reduce the force needed for flake propagation, they also demonstrate that such treatment has no significant effect on major morphological aspects of flake form.
Somatic substitution signature as an innovative tool in lung cancer diagnosis
Authors: Busca Stéphane , Salleron Julia , Boidot Romain , Merlin Jean-Louis , Harlé Alexandre
Published: October 2019

Diagnosis of lung cancer can sometimes be challenging and is of major interest since effective molecular-guided therapies are available. Compounds of tobacco smoke may generate a specific substitutional signature in lung, which is the most exposed organ. To predict whether a tumor is of lung origin or not, we developed and validated the EASILUNG (Exome And SIgnature LUNG) test based on the relative frequencies of somatic substitutions on coding non-transcribed DNA strands from whole-exome sequenced tumors. Data from 7,796 frozen tumor samples (prior to any treatment) from 32 TCGA solid cancer groups were used for its development. External validation was carried out on a local dataset of 196 consecutive routine exome results. Eight out of the 12 classes of substitutions were required to compute the EASILUNG signature that demonstrated good calibration and good discriminative power with a sensitivity of 83% and a specificity of 72% after recalibration on the external validation dataset. This innovative test may be helpful in medical decision-making in patients with unknown primary tumors potentially of lung origin and in the diagnosis of lung cancer in smokers.