julilili42/papers huggingface dataset:
Association of circulating Progesterone Receptor Membrane Component-1 (PGRMC1) with breast tumor characteristics and comparison with known tumor markers
2019-12-23

Abstract Objectives: Progesterone receptor membrane component-1 (PGRMC1) expressed in breast cancer tissue has been suggested to predict a worse prognosis. The aim of this study was to assess for the first time if blood concentrations of PGRMC1 are also associated with receptor status, tumor diameter, grading, and lymphatic status. The second aim was comparison with known tumor markers. Methods: A total of 372 women, including 278 patients with invasive breast cancer, 65 with benign breast disease, and 29 healthy women (control), were recruited. PGRMC1 blood concentrations were measured by a recently developed enzyme-linked immunosorbant assay, and were correlated to predictive tumor characteristics and compared with serum carcinoembryonic antigen (CEA), CA125, and CA153. Results: PGRMC1 levels in the cancer group were significantly higher than in the control and benign group and increased with higher cancer stages ( P &lt; 0.05). PGRMC1 concentrations in the estrogen receptor (ER)+/progesterone receptor (PR)+ group were higher than in the ER−/PR− group, related to larger tumor diameter and the presence of lymph node metastasis ( P &lt; 0.05). Multivariable linear regression analysis was used to control the confounding factors. Tumor diameter, lymphatic metastasis, and ER (but not PR) were positively associated with PGRMC1 ( P &lt; 0.05). The receiver-operating characteristic curve (ROC) analysis was used to assess area under the curve (AUC). AUC was 87.9% for stages III+IV and 80.8% for stages I+II ( P &lt; 0.01). ROC did not find significant effects on AUC for CA125, only significant for CEA and CA153 for stages III+IV. Conclusion: As PGRMC1 levels are positively associated with breast tumor characteristics known to predict a worse diagnosis, PGRMC1 may be valuable as a new tumor marker, and superior to CEA, C125, and CA153. Because of the positive association with ER-expression, PGRMC1 may interact with this receptor.
When geometric phases turn topological
2019-12-23

Geometric phases, accumulated when a quantum system traces a cycle in quantum\\nstate space, do not depend on the parametrization of the cyclic path, but do\\ndepend on the path itself. In the presence of noise that deforms the path, the\\nphase gets affected, compromising the robustness of possible applications,\\ne.g., in quantum computing. We show that for a special class of spin states,\\ncalled anticoherent, and for paths that correspond to a sequence of rotations\\nin physical space, the phase only depends on topological characteristics of the\\npath, in particular, its homotopy class, and is therefore immune to noise.\\n
OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module specifying phloem identity
2019-12-23

Abstract Spatial specificity of cell fate decisions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How a phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBE3 forms a central module with the phloem- specific SMXL5 protein for establishing phloem identity in Arabidopsis thaliana . By protein interaction studies and phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins form a complex in nuclei of phloem stem cells where they establish a phloem-specific chromatin profile. This profile allows expression of OPS , BRX , BAM3 , and CVP2 genes acting as mediators of phloem differentiation. Our findings demonstrate that OBE3/SMXL5 protein complexes establish nuclear features essential for determining phloem cell fate and highlight how a combination of ubiquitous and local regulators generate specificity of developmental decisions in plants.
Evidence and Bias: The Case of the Evidential Future in Italian
2019-12-23

Evidential markers encode the source of information that an individual (the evidential Origo) has for a proposition. In root declaratives, the Origo is always the speaker (see Korotkova 2016 and references therein). Instead, questions often display interrogative flip: the Origo shifts to the hearer (Garrett 2001; Speas &amp; Tenny 2003, a.o.). While interrogative flip is widely attested across languages, some evidentials have been reported not to flip in questions (see, e.g., San Roque, Floyd &amp; Norcliffe 2017; Bhadra 2017). What determines whether evidentials flip or not? Recent work (Korotkova 2016; Bhadra 2017) has proposed that there is a correlation between lack of flip and bias in questions. This paper contributes to our understanding of the interaction of evidentials and bias by investigating the behaviour of questions with the Italian non-predictive future. We characterize the non-predictive future as an inferential evidential marker (see also Mari 2009; Eckardt &amp; Beltrama forthcoming), and show that lack of flip for the future correlates only with a particular type of bias: a reversal of the default bias associated with negative polar questions (Frana &amp; Rawlins forthcoming). We trace back this pattern to an interaction between the evidential component of the future and the operator that triggers bias reversal.
Do polystyrene microplastics affect juvenile brown trout (Salmo trutta f. fario) and modulate effects of the pesticide methiocarb?
2019-12-23

Abstract Background During the last decade, there has been rising interest of the scientific community and the public in the environmental risk related to the abundance of microplastics in aquatic environments. Besides potential effects of the particles themselves, also their interaction with organic micropollutants is of particular concern. Up to now, however, scientific knowledge in this context is scarce and insufficient for a reliable risk assessment. This is especially true for data on microplastics in freshwater ecosystems.Results Against the background of this shortage, we investigated possible adverse effects of polystyrene particles (10 4 particles/L) and the pesticide methiocarb (1 mg/L) both alone as well as in combination in juvenile brown trout ( Salmo trutta f. fario ) after a 96 h laboratory exposure. PS beads (density 1.05 g/mL) were cryogenically milled and fractionated resulting in irregular shaped particles (&lt;50 μm). Besides body weight of the animals, biomarkers for proteotoxicity (stress protein family Hsp70), oxidative stress (superoxide dismutase, lipid peroxidation) and neurotoxicity (acetylcholinesterase, carboxylesterases) were analysed. As an indicator of overall health histopathological effects were studied in liver and gills of exposed fish. Polystyrene particles alone did not influence any of the investigated biomarkers. In contrast, the exposure to methiocarb led to a significant reduction of the activity of acetylcholinesterase and the two carboxylesterases. Moreover, the tissue integrity of liver and gills was impaired by the pesticide. Body weight, the oxidative stress and the stress protein levels were not influenced by methiocarb. Effects caused by the mixture of polystyrene microplastics and methiocarb were the same as those caused by methiocarb alone.Conclusions Overall, methiocarb led to strong effects in juvenile brown trout. In contrast, polystyrene microplastics in the tested concentration did not negatively affect the health of juvenile brown trout and did not modulate the toxicity of methiocarb in this fish species.
Classical stochastic discrete time crystals
2019-12-24

We describe a general and simple paradigm for discrete time crystals (DTCs), systems with a stable subharmonic response to an external driving field, in a classical thermal setting. We consider, specifically, an Ising model in two dimensions, as a prototypical system with a phase transition into stable phases distinguished by a local order parameter, driven by thermal dynamics and periodically kicked with a noisy protocol. By means of extensive numerical simulations for large sizes-allowed by the classical nature of our model-we show that the system features a true disorder-DTC order phase transition as a function of the noise strength, with a robust DTC phase extending over a wide parameter range. We demonstrate that, when the dynamics is observed stroboscopically, the phase transition to the DTC state appears to be in the equilibrium two-dimensional Ising universality class. However, we explicitly show that the DTC is a genuine nonequilibrium state. More generally, we speculate that systems with thermal phase transitions to multiple competing phases can give rise to DTCs when appropriately driven.
A novel waterjet technology for transurethral cystoscopic injection of viable cells in the urethral sphincter complex
2019-12-24

Abstract Aims In a recent preclinical study, we noticed that injection of cells in the urethral sphincter by needle through a cystoscope under visual control frequently yielded in misplacement or loss of cells. We, therefore, investigated if a needle‐free waterjet device delivers viable cells under defined settings, including injection volume and pressure, fluid velocity and transportation media, precisely through the urothelium and connective tissue close to the sphincter muscle without full penetration of the sphincter apparatus. Methods Mesenchymal stromal cells (MSCs) were prepared for needle‐free waterjet injections. Upon injections into liquids cell viability and yield were investigated by trypan blue dye exclusion. Upon injection into cadaveric urethral tissue samples, cells were isolated from the urethrae and expanded to prove that this novel method delivered viable cells into the tissue. MSC injections by William's needle served as controls. Results Waterjet injections of MSCs into isotonic cell culture medium resulted in equal or better yields of viable cells when compared with needle injections. Upon injection in urethral tissue samples, the waterjet technology facilitated fast and precise injections of viable cells through urothelial, mucosal and submucosal layers to reach the sphincter muscle. By controlling the injection pressure, loss of cells due to insufficient thrust or unintended full penetration was avoided. Conclusions Needle‐free waterjet injections deliver cells in the urethra faster and more precisely when compared with needle injections without compromising their viability. This is the first proof‐of‐concept study providing evidence that a waterjet transports viable cells precisely into the targeted tissue.
Favorable 90-Day Mortality in Obese Caucasian Patients with Septic Shock According to the Sepsis-3 Definition
2019-12-24

Septic shock is a frequent life-threatening condition and a leading cause of mortality in intensive care units (ICUs). Previous investigations have reported a potentially protective effect of obesity in septic shock patients. However, prior results have been inconsistent, focused on short-term in-hospital mortality and inadequately adjusted for confounders, and they have rarely applied the currently valid Sepsis-3 definition criteria for septic shock. This investigation examined the effect of obesity on 90-day mortality in patients with septic shock selected from a prospectively enrolled cohort of septic patients. A total of 352 patients who met the Sepsis-3 criteria for septic shock were enrolled in this study. Body-mass index (BMI) was used to divide the cohort into 24% obese (BMI ≥ 30 kg/m2) and 76% non-obese (BMI &lt; 30 kg/m2) patients. Kaplan-Meier survival analysis revealed a significantly lower 90-day mortality (31% vs. 43%; p = 0.0436) in obese patients compared to non-obese patients. Additional analyses of baseline characteristics, disease severity, and microbiological findings outlined further statistically significant differences among the groups. Multivariate Cox regression analysis estimated a significant protective effect of obesity on 90-day mortality after adjustment for confounders. An understanding of the underlying physiologic mechanisms may improve therapeutic strategies and patient prognosis.
X-ray spectral and flux variability of the microquasar GRS 1758−258 on timescales from weeks to years
2019-12-24

We present the spectral and timing evolution of the persistent black hole X-ray binary GRS 1758−258 based on almost 12 years of observations using the Rossi X-ray Timing Explorer Proportional Counter Array. While the source was predominantly found in the hard state during this time, it entered the thermally dominated soft state seven times. In the soft state GRS 1758−258 shows a strong decline in flux above 3 keV rather than the pivoting flux around 10 keV more commonly shown by black hole transients. In its 3–20 keV hardness intensity diagram, GRS 1758−258 shows a hysteresis of hard and soft state fluxes typical for transient sources in outburst. The RXTE-PCA and RXTE-ASM long-term light curves do not show any orbital modulations in the range of 2–30 d. However, in the dynamic power spectra significant peaks drift between 18.47 and 18.04 d for the PCA data, while less significant signatures between 19 d and 20 d are seen for the ASM data as well as for the Swift /BAT data. We discuss different models for the hysteresis behavior during state transitions as well as possibilities for the origin of the long term variation in the context of a warped accretion disk.
Redox cycling of Fe(II) and Fe(III) in magnetite accelerates aceticlastic methanogenesis by Methanosarcina mazei
2019-12-25

Summary It has been recently shown that magnetite nanoparticles (nanoFe 3 O 4 ) can facilitate methanogenic syntrophy but the effect of magnetite on methanogenesis alone remains elusive. Here we show that aceticlastic methanogenesis by Methanosarcina mazei is accelerated by magnetite and is correlated with the redox cycling of structural Fe(II) and Fe(III) in the mineral. An enrichment and its closest pure culture relative, Ms . mazei zm‐15, both obtained from a natural wetland of the Tibetan plateau were tested in this experiment. The Fe(II) to Fe(III) ratios in magnetite, as measured by multiple approaches, show an initial increase in both the methanogenic cultures and the blank preparations containing no microbes. The Fe(II)/Fe(III) ratio then displays a distinct decline followed by an increase towards the end of incubation only in the enrichment and pure culture cultivations. This redox cycling of magnetite is in accordance with the stimulation of aceticlastic methanogenesis. Microscopic observation reveals the precipitation of nanoFe 3 O 4 on methanogen cell surface. The genomic analysis predicts that in addition to electron transfer components essential for aceticlastic methanogenesis, Ms . mazei zm‐15 contains an outer‐surface multiheme c ‐type cytochrome (MHC) and a few function‐unknown surface proteins that harbour monoheme motif. We hypothesize that the redox cycling of nanoFe 3 O 4 delivers a positive influence via the MHC to the membrane electron transfer chain and hence promote the aceticlastic methanogenesis.
Application of Piezo-Based Measuring System for Evaluation of Nucleic Acid-Based Drugs Influencing the Coagulation
2019-12-25

During open-heart surgery, the status of hemostasis has to be constantly monitored to quickly and reliably detect bleeding or coagulation disorders. In this study, a novel optimized piezo-based measuring system (PIEZ) for rheological monitoring of hemostasis was established. The applicability of the PIEZ for the evaluation of nucleic acid-based drugs influencing coagulation was analyzed. Thrombin aptamers such as NU172 might be used during extracorporeal circulation (ECC) in combination with a reduced heparin concentration or for patients with heparin-induced thrombocytopenia (HIT). Therefore, the effect of the coagulation inhibiting thrombin aptamer NU172 and the abrogation by its complementary antidote sequence (AD) were investigated by this rheological PIEZ system. After the addition of different NU172 concentrations, the coagulation of fresh human blood was analyzed under static conditions and using an in vitro rotation model under dynamic conditions (simulating ECC). The clotting times (CTs) detected by PIEZ were compared to those obtained with a medical reference device, a ball coagulometer. Additionally, after the circulation of blood samples for 30 min at 37 °C, blood cell numbers, thrombin markers (thrombin-antithrombin III (TAT) and fibrinopeptide A (FPA)) and a platelet activation marker (β-thromboglobulin (β-TG)) were analyzed by enzyme-linked immunosorbent assays (ELISAs). The increase of NU172 concentration resulted in prolonged CTs, which were comparable between the reference ball coagulometer and the PIEZ, demonstrating the reliability of the new measuring system. Moreover, by looking at the slope of the linear regression of the viscous and elastic components, PIEZ also could provide information on the kinetics of the coagulation reaction. The shear viscosity at the end of the measurements (after 300 s) was indicative of clot firmness. Furthermore, the PIEZ was able to detect the abrogation of coagulation inhibition after the equimolar addition of NU172 aptamer ́s AD. The obtained results showed that the established PIEZ is capable to dynamically measure the hemostasis status in whole blood and can be applied to analyze nucleic acid-based drugs influencing the coagulation.
Non-invasive prospection techniques and direct push sensing as high-resolution validation tools in wetland geoarchaeology – Artificial water supply at a Carolingian canal in South Germany?
2019-12-26

The prospection of (geo-)archaeological sites yield important knowledge about the concept and the utilisation of pre-historical and historical infrastructure. The satisfactory conduction of classical prospection methods like archaeological excavations or geoarchaeological vibra-coring might be challenging in the case of large sites or difficult underground conditions. This is particularly problematic in wetlands featuring a high groundwater table and high compaction rates of organic layers. In this study, we provide an alternative and non- to minimal-invasive exploration approach to discover hydro-engineering structures for artificial water supply in the surrounding of a Carolingian summit canal in South Germany. The Early Medieval Fossa Carolina was intended 792/793 CE to bridge the Central European watershed between Rhine-Main and Danube catchments. As the canal was constructed as a summit canal, an artificial water supply at the highest levels seemed very likely or even obligatory. In order to explore these obligatory hydro-engineering features, we use a wide range of on-site and off-site tools in a spatial hierarchical way. Our approach includes the large-scale SQUID magnetic survey and the sighting of historical maps. Furthermore, we integrate high-resolution direct push colour logs, and subsequent vibra-coring for small-scale stratigraphical verification and sedimentological analyses. The SQUID magnetic survey and related depth models discover two pronounced linear anomalies that might represent potential artificial water inlets in the North-Eastern and Northern Sections of the canal. I) In the North-Eastern Section, direct push colour logs, vibra-coring and 14C dating provide no evidence for a Carolingian hydro-engineering feature but reveal a natural lenticular structure of Early Holocene age. II) The linear magnetic anomaly in the Northern Section can be excluded with high probability as a hydro-engineering structure as well. Here, direct push colour logs, vibra-coring, 14C dating and the comparison with a historic map reveal evidence for a historic gravel road. Thus, we have nicely verified the magnetic information but have no prove for an artificial Carolingian water inlet from the Swabian Rezat River that contradicts with assumptions of former studies.
Micromorphological and FTIR analysis of the Upper Paleolithic early pottery site of Yuchanyan cave, Hunan, South China
2019-12-26

Abstract The site of Yuchanyan cave (Hunan Province, China) contains evidence for some of the earliest‐known (ca. 18,000 cal BP) pottery in the world alongside a typical South China Upper Paleolithic cobble tool (chopper) industry. Here we present the results of a micromorphological study of the deposits with particular attention to site formation processes and recognizable human activities. Our study reveals that the majority of the sediments are anthropogenic and produced by repeated combustion episodes involving the complete expenditure of the fuel and then the refuse being raked out and redistributed across the cave. In relation to the pottery production, clay was also used to line fireplaces. Our results, combined with our Fourier‐transform infrared analysis of the clays and bones, and supported by the zooarchaeological data, suggest that fire and pottery were used here to boil bones and render grease. This behavior must be considered in respect to its associated chopper industry, and the presence of early pottery may be related, suggesting differences in behavioral modernity for hunter‐gatherers in Upper Paleolithic South China. This study demonstrates the advantages of analyzing sediments as a record of past human actions and the value of using micromorphology for the study of Late Pleistocene sites in China.
Simultaneous determination of multiclass antibiotics in sewage sludge based on QuEChERS extraction and liquid chromatography-tandem mass spectrometry
2019-12-27

A QuEChERS based method with dispersive solid-phase extraction (d-SPE) clean-up followed by LC-MS-MS analysis was developed for simultaneous determination of seventeen multiclass antibiotics in sewage sludge and applied to samples from Nigeria.
Burst-induced coronal cooling in GS 1826–24
2019-12-27

Type I X-ray bursts in GS 1826–24, and in several other systems, may induce cooling of the hot inner accretion flow that surrounds the bursting neutron star. Given that GS 1826–24 remained persistently in the hard state over the period 2003–2008 and presented regular bursting properties, we stacked the spectra of the X-ray bursts detected by INTEGRAL (JEM-X and ISGRI) and XMM-Newton (RGS) during that period to study the effect of the burst photons on the properties of the Comptonizing medium. The extended energy range provided by these instruments allows the simultaneous observation of the burst and persistent emission spectra. We detect an overall change in the shape of the persistent emission spectrum in response to the burst photon shower. For the first time, we observe simultaneously a drop in the hard X-ray emission, together with a soft X-ray excess with respect to the burst blackbody emission. The hard X-ray drop can be explained by burst-induced coronal cooling, while the bulk of the soft X-ray excess can be described by fitting the burst emission with an atmosphere model, instead of a simple blackbody model. Traditionally, the persistent emission was assumed to be invariant during X-ray bursts, and more recently to change only in normalization but not in spectral shape; the observed change in the persistent emission level during X-ray bursts may thus trigger the revision of existing neutron star mass-radius constraints, as the derived values rely on the assumption that the persistent emission does not change during X-ray bursts. The traditional burst fitting technique leads to up to a 10% overestimation of the bolometric burst flux in GS 1826–24, which significantly hampers the comparisons of the KEPLER and MESA model against this “textbook burster”.