bluuebunny/crossref_metadata_2025_split huggingface dataset:
The expression of the long NEAT1_2 isoform is associated with human epidermal growth factor receptor 2-positive breast cancers
Authors: Knutsen Erik , Lellahi Seyed Mohammad , Aure Miriam Ragle , Nord Silje , Fismen Silje , Larsen Kenneth Bowitz , Gabriel Marta Tellez , Hedberg Annica , Bjørklund Sunniva Stordal ,   Oslo Breast Cancer Research Consortium (OSBREAC), Geisler Jürgen , Hofvind Solveig , Bathen Tone F. , Borgen Elin , Børresen-Dale Anne-Lise , Engebråten Olav , Garred Øystein , Geitvik Gry Aarum , Langerød Anita , Naume Bjørn , Russnes Hege G. , Schlichting Ellen , Lingjærde Ole Christian , Kristensen Vessela N. , Skjerven Helle Kristine , Papathomas Thomas , Hartman-Johnsen Olaf-Johan , Sahlberg Kristine Kleivi , Bofin Anna Mary , Mælandsmo Gunhild Mari , Sørlie Therese , Mortensen Elin Synnøve , Perander Maria 
Published: January 2020

AbstractThe long non-coding RNA NEAT1 locus is transcribed into two overlapping isoforms, NEAT1_1 and NEAT1_2, of which the latter is essential for the assembly of nuclear paraspeckles. NEAT1 is abnormally expressed in a wide variety of human cancers. Emerging evidence suggests that the two isoforms have distinct functions in gene expression regulation, and recently it was shown that NEAT1_2, but not NEAT1_1, expression predicts poor clinical outcome in cancer. Here, we report that NEAT1_2 expression correlates with HER2-positive breast cancers and high-grade disease. We provide evidence that NEAT1_1 and NEAT1_2 have distinct expression pattern among different intrinsic breast cancer subtypes. Finally, we show that NEAT1_2 expression and paraspeckle formation increase upon lactation in humans, confirming what has previously been demonstrated in mice.
Advances in Kriging-Based Autonomous X-Ray Scattering Experiments
Authors: Noack Marcus M. , Doerk Gregory S. , Li Ruipeng , Fukuto Masafumi , Yager Kevin G. 
Published: January 2020

AbstractAutonomous experimentation is an emerging paradigm for scientific discovery, wherein measurement instruments are augmented with decision-making algorithms, allowing them to autonomously explore parameter spaces of interest. We have recently demonstrated a generalized approach to autonomous experimental control, based on generating a surrogate model to interpolate experimental data, and a corresponding uncertainty model, which are computed using a Gaussian process regression known as ordinary Kriging (OK). We demonstrated the successful application of this method to exploring materials science problems using x-ray scattering measurements at a synchrotron beamline. Here, we report several improvements to this methodology that overcome limitations of traditional Kriging methods. The variogram underlying OK is global and thus insensitive to local data variation. We augment the Kriging variance with model-based measures, for instance providing local sensitivity by including the gradient of the surrogate model. As with most statistical regression methods, OK minimizes the number of measurements required to achieve a particular model quality. However, in practice this may not be the most stringent experimental constraint; e.g. the goal may instead be to minimize experiment duration or material usage. We define an adaptive cost function, allowing the autonomous method to balance information gain against measured experimental cost. We provide synthetic and experimental demonstrations, validating that this improved algorithm yields more efficient autonomous data collection.
Predicting clustered weather patterns: A test case for applications of convolutional neural networks to spatio-temporal climate data
Authors: Chattopadhyay Ashesh , Hassanzadeh Pedram , Pasha Saba 
Published: January 2020

AbstractDeep learning techniques such as convolutional neural networks (CNNs) can potentially provide powerful tools for classifying, identifying, and predicting patterns in climate and environmental data. However, because of the inherent complexities of such data, which are often spatio-temporal, chaotic, and non-stationary, the CNN algorithms must be designed/evaluated for each specific dataset and application. Yet CNN, being a supervised technique, requires a large labeled dataset to start. Labeling demands (human) expert time which, combined with the limited number of relevant examples in this area, can discourage using CNNs for new problems. To address these challenges, here we (1) Propose an effective auto-labeling strategy based on using an unsupervised clustering algorithm and evaluating the performance of CNNs in re-identifying and predicting these clusters up to 5 days ahead of time; (2) Use this approach to label thousands of daily large-scale weather patterns over North America in the outputs of a fully-coupled climate model and show the capabilities of CNNs in re-identifying and predicting the 4 clustered regimes up to 5 days ahead of time. The deep CNN trained with 1000 samples or more per cluster has an accuracy of 90% or better for both identification and prediction while prediction accuracy scales weakly with the number of lead days. Accuracy scales monotonically but nonlinearly with the size of the training set, e.g. reaching 94% with 3000 training samples per cluster for identification and 93–76% for prediction at lead day 1–5, outperforming logistic regression, a simpler machine learning algorithm, by ~ 25%. Effects of architecture and hyperparameters on the performance of CNNs are examined and discussed.
Position and Direction Tracking of a Magnetic Object Based on an Mx-Atomic Magnetometer
Authors: Soheilian Asieh , Ranjbaran Maliheh , Tehranchi Mohammad Mehdi 
Published: January 2020

AbstractRemote and non-invasive tracking of a moving magnetic object based on an atomic magnetometer has been developed recently. The sensitivity of atomic magnetometers is limited by mechanisms that relax the spin precession of alkali atoms. Meanwhile, some of these mechanisms such as magnetic field gradient are applicable in magnetic object tracking. Correspondingly, we have illustrated a way of operating an Mx atomic magnetometer to measure the magnetic field and its gradient simultaneously for a moving magnetic microwire, which resulted in recording a spike-like signal. We described the dependency of the signal on the position, velocity, and direction of the microwire. According to the results, the measurement of the inhomogeneous local magnetic field gradient opens new ways for obtaining the direction of the velocity of magnetic objects accessible in cells with large sizes. Furthermore, the accuracy of the velocimetry was found as 40 µm/s which could be an important means for assessing the microvascular blood flow.
CA19-9 for detecting recurrence of pancreatic cancer
Authors: Azizian Azadeh , Rühlmann Felix , Krause Tanja , Bernhardt Markus , Jo Peter , König Alexander , Kleiß Mathias , Leha Andreas , Ghadimi Michael , Gaedcke Jochen 
Published: January 2020

AbstractCA19-9 values are regularly measured in patients with pancreatic cancer. Certainly, its potential as a biomarker has been compromised by false negative results in CA19-9 negative patients and false positive results in benign pancreatico-biliary diseases. For detection of PDAC recurrence, however, CA19-9 might play an important role. The aim of this study is to analyze the accuracy of CA19-9 for detecting recurrence of pancreatic cancer. All included patients were treated either at the University Medical Center Goettingen, or at the Department of Interdisciplinary Oncology and Pneumonology, DRK-Kliniken Nordhessen, Kassel. We analyzed data of 93 patients with pancreatic cancer in the training set and 41 in the validation set, both retrospectively. Pre- and postoperative CA19-9 values and results of imaging techniques were compared. We performed ROC-analysis. The association between longitudinally measured CA19-9 values and relapse was studied with a joint model between a random effects model for the longitudinal CA19-9 measurements and a Cox proportional hazards models for the survival data. In the test set (n = 93 patients) the median follow-up time was 644 days (22 months). Overall, 71 patients (76.3%) developed recurrence during follow-up. Patients with CA19-9 values of <10kU/l were considered as CA19-9 negative patients (n = 11) and excluded from further analysis. Among the rest, approximately 60% of the patients showed significantly elevated CA19-9 prior to detection of recurrence by imaging techniques. Recurrence was shown by 2.45 times elevated CA19-9 values with 90% positive predictive value. In the validation set, 2.45 times elevated CA19-9 values showed recurrence with 90% sensitivity and 83,33% specificity, with an area under the curve of 95%. Based on measured CA19-9 values during follow-up care, the joint model estimates in recurrence-free patients the probability of recurrence-free survival. CA19-9 elevation is an early and reliable sign for PDAC recurrence. On the strength of a very high accuracy in CA19-9 positive patients, it should be considered to use CA19-9 for therapy decision even without a correlate of imaging technics. Using the joint model, follow-up care of PDAC patients after curative therapy can be stratified.
Cucurbitacin B and I inhibits colon cancer growth by targeting the Notch signaling pathway
Authors: Dandawate Prasad , Subramaniam Dharmalingam , Panovich Peyton , Standing David , Krishnamachary Balaji , Kaushik Gaurav , Thomas Sufi Mary , Dhar Animesh , Weir Scott J. , Jensen Roy A. , Anant Shrikant 
Published: January 2020

AbstractCancer stem cells (CSCs) have the ability to self-renew and induce drug resistance and recurrence in colorectal cancer (CRC). As current chemotherapy doesn’t eliminate CSCs completely, there is a need to identify novel agents to target them. We investigated the effects of cucurbitacin B (C-B) or I (C-I), a natural compound that exists in edible plants (bitter melons, cucumbers, pumpkins and zucchini), against CRC. C-B or C-I inhibited proliferation, clonogenicity, induced G2/M cell-cycle arrest and caspase-mediated-apoptosis of CRC cells. C-B or C-I suppressed colonosphere formation and inhibited expression of CD44, DCLK1 and LGR5. These compounds inhibited notch signaling by reducing the expression of Notch 1–4 receptors, their ligands (Jagged 1-2, DLL1,3,4), γ-secretase complex proteins (Presenilin 1, Nicastrin), and downstream target Hes-1. Molecular docking showed that C-B or C-I binds to the ankyrin domain of Notch receptor, which was confirmed using the cellular thermal shift assay. Finally, C-B or C-I inhibited tumor xenograft growth in nude mice and decreased the expression of CSC-markers and notch signaling proteins in tumor tissues. Together, our study suggests that C-B and C-I inhibit colon cancer growth by inhibiting Notch signaling pathway.
Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253
Authors: Ara Kazi Zubaida Gulshan , Månberger Anna , Gabriško Marek , Linares-Pastén Javier A. , Jasilionis Andrius , Friðjónsson Ólafur H. , Hreggviðsson Guðmundur Ó. , Janeček Štefan , Nordberg Karlsson Eva 
Published: January 2020

AbstractThe genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252TRmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.
Temperature Dependency of Proton Pumping Activity for Marine Microbial Rhodopsin from Antartic Ocean
Authors: Kim Se-Hwan , Jung ByungHoon , Hong Soon Gyu , Jung Kwang-Hwan 
Published: January 2020

AbstractProteorhodopsin (PR) is discovered from marine bacteria and it has proton pumping activity from inside to outside of the cell using light energy. In general, PR classified into two groups by the maximum absorption spectra. In this study, we isolated the two of a full sequence of opsin homologues by PCR from the seawater sample near King George Island, Antarctica. One was the same sequence as the first reported GPR (Green-light absorbing PR) from Monterey Bay. Another named HSG119 was a newly discovered sequence which shows high sequence similarity with BPR (Blue-light absorbing PR). HSG119 has an absorption maximum at 493 nm with broader spectrum at pH7.0 and it can pump protons out of the cell membrane. Interestingly, it showed a similar temperature dependence to GPR(Y200N) that isolated near the North pole.
Structure, optical and magnetic properties of a novel homometallic coordination polymers: Experimental and Computational studies
Authors: Ammari Y. , Baaalla N. , Hlil E. K. , Abid S. 
Published: January 2020

AbstractSingle crystal of 1D homometallic coordination polymer involving cobalt metal ion and P2Mo5 Strandberg type polyoxometallate cluster (C6H10N2)2[Co(H2O)4P2Mo5O23].6H2O, is prepared in aqueous solution and characterized by X-ray diffraction (XRD), UV-vis diffuse reflectance, fluorescence and magnetism. Single crystal X-ray diffraction analysis reveals that this compound crystallizes in the triclinic system with space group P $$\,\bar{1}$$1¯. The 3-(ammoniomethyl)pyridine C6H8N2 organic fragment is used merely as stabilizer for the promotion of topological structure. DRS data indicate that the synthesized material can be identified as a ferromagnetic semiconductor with optical bands gaps energy of 1.81 and 2.74 eV, respectively. The large value of refractive index observed in the visible region make the simple a promising candidate for visible optical communication devices and fluorescent emisson result provides that the complex belongs to a blue luminescent compounds. Moreover, magnetic measurements and electronic structure calculations show that P2Mo5 Strandberg polyoxoanion can be reported as a new class of ligand that is candidate to construct metal-inorganic framworks with long distance ferromagnetic superechange between Co(II) centers. The evidence from this study suggests that the syntesized polymer can become a great multifunctional material openning the door for the developpement of new coordination polymers based on Strandberg type polyxoxmetalate with potential applications.
Rapid detection of terbinafine resistance in Trichophyton species by Amplified refractory mutation system-polymerase chain reaction
Authors: Shankarnarayan Shamanth A. , Shaw Dipika , Sharma Arunima , Chakrabarti Arunaloke , Dogra Sunil , Kumaran Muthu Sendhil , Kaur Harsimran , Ghosh Anup , Rudramurthy Shivaprakash M. 
Published: January 2020

AbstractDermatophytosis has gained interest in India due to rise in terbinafine resistance and difficulty in management of recalcitrant disease. The terbinafine resistance in dermatophytes is attributed to single nucleotide polymorphisms (SNPs) in squalene epoxidase (SE) gene. We evaluated the utility of amplified refractory mutation system polymerase chain reaction (ARMS PCR) for detection of previously reported point mutations, including a mutation C1191A in theSEgene inTrichophytonspecies. ARMS PCR was standardized using nine non-wild type isolates and two wild type isolates ofTrichophytonspecies. Study included 214 patients with dermatophyte infection from March through December 2017. Antifungal susceptibility testing of isolated dermatophytes was performed according to CLSI-M38A2 guidelines. Among dermatophytes isolated in 68.2% (146/214) patients,Trichophytonspecies were predominant (66.4%). High (>2 mg/L, cut off) minimum inhibitory concentrations to terbinafine were noted in 15 (15.4%)Trichophyton mentagrophytescomplex isolates. A complete agreement was noted between ARMS PCR assay and DNA sequencing. C to A transversion was responsible for amino acid substitution in 397thposition ofSEgene in terbinafine resistant isolates. Thus, the ARMS PCR assay is a simple and reliable method to detect terbinafine-resistantTrichophytonisolates.
Multi-level anomalous Hall resistance in a single Hall cross for the applications of neuromorphic device
Authors: Kim Y.-U. , Kwon J. , Hwang H.-K. , Purnama I. , You C.-Y. 
Published: January 2020

AbstractWe demonstrate the process of obtaining memristive multi-states Hall resistance (RH) change in a single Hall cross (SHC) structure. Otherwise, the working mechanism successfully mimics the behavior of biological neural systems. The motion of domain wall (DW) in the SHC was used to control the ascend (or descend) of the RH amplitude. The primary synaptic functions such as long-term potentiation (LTP), long-term depression (LTD), and spike-time-dependent plasticity (STDP) could then be emulated by regulating RH. Applied programmable magnetic field pulses are in varying conditions such as intensity and duration to adjust RH. These results show that analog readings of DW movement can be closely resembled with the change of synaptic weight and have great potentials for bioinspired neuromorphic computing.
Near-Infrared Fluorescent pH Responsive Probe for Targeted Photodynamic Cancer Therapy
Authors: Siriwibool Siriwalee , Kaekratoke Nantawat , Chansaenpak Kantapat , Siwawannapong Kittipan , Panajapo Pannipa , Sagarik Kritsana , Noisa Parinya , Lai Rung-Yi , Kamkaew Anyanee 
Published: January 2020

AbstractWe developed a pH dependent amino heptamethine cyanine based theranostic probe (I2-IR783-Mpip) that can be activated by near infrared light. I2-IR783-Mpip, in acidic condition, exhibited an intense, broad NIR absorption band (820–950 nm) with high singlet oxygen generation upon exposure to NIR light (~850 nm). Theoretical calculations showed that the protonation of the probe in an acidic environment decreased the molecular orbital energy gaps and increased the intramolecular charge transfer efficiency. I2-IR783-Mpip exhibited good photodynamic efficiency towards liver hepatocellular carcinoma cells under physiological and slightly acidic conditions while normal human embryonic kidney cells remained alive under the same conditions. Detection of intracellular reactive oxygen species (ROS) in cells treated with I2-IR783-Mpip after NIR light exposure confirmed PDT efficiency of the probe in acidic environment. Moreover, I2-IR783-Mpip also demonstrated efficient phototoxicity under deep-seated tumour cell system. We believed this is the first PDT agent that possesses intrinsic tumour binding and selectively eradicate tumour in acidic environment under 850 nm NIR lamp.
Effect of Cutaneous Feedback on the Perception of Virtual Object Weight during Manipulation
Authors: Park Jaeyoung , Son Bukun , Han Ilhwan , Lee Woochan 
Published: January 2020

AbstractHaptic interface technologies for virtual reality applications have been developed to increase the reality and manipulability of a virtual object by creating a diverse tactile sensation. Most evaluation of the haptic technologies, however, have been limited to the haptic perception of the tactile stimuli via static virtual objects. Noting this, we investigated the effect of lateral cutaneous feedback, along with kinesthetic feedback on the perception of virtual object weight during manipulation. We modeled the physical interaction between a participant’s finger avatars and virtual objects. The haptic stimuli were rendered with custom-built haptic feedback systems that can provide kinesthetic and lateral cutaneous feedback to the participant. We conducted two virtual object manipulation experiments, 1. a virtual object manipulation with one finger, and 2. the pull-out and lift-up of a virtual object grasped with a precision grip. The results of Experiment 1 indicate that the participants felt the virtual object rendered with lateral cutaneous feedback significantly heavier than with only kinesthetic feedback (p < 0.05 formref = 100 and 200 g). Similarly, the participants of Experiment 2 felt the virtual objects significantly heavier when lateral cutaneous feedback was available (p < 0.05 formref = 100, 200, and 300 g). Therefore, the additional lateral cutaneous feedback to the force feedback led the participants to feel the virtual object heavier than without the cutaneous feedback. The results also indicate that the contact force applied to a virtual object during manipulation can be a function of the perceived object weight (p = 0.005 for Experiment 1 andp = 0.02 for Experiment 2).
Stacking Fault Energy Analyses of Additively Manufactured Stainless Steel 316L and CrCoNi Medium Entropy Alloy Using In Situ Neutron Diffraction
Authors: Woo W. , Jeong J. S. , Kim D.-K. , Lee C. M. , Choi S.-H. , Suh J.-Y. , Lee S. Y. , Harjo S. , Kawasaki T. 
Published: January 2020

AbstractStacking fault energies (SFE) were determined in additively manufactured (AM) stainless steel (SS 316 L) and equiatomic CrCoNi medium-entropy alloys. AM specimens were fabricated via directed energy deposition and tensile loaded at room temperature.In situneutron diffraction was performed to obtain a number of faulting-embedded diffraction peaks simultaneously from a set of (hkl) grains during deformation. The peak profiles diffracted from imperfect crystal structures were analyzed to correlate stacking fault probabilities and mean-square lattice strains to the SFE. The result shows that averaged SFEs are 32.8 mJ/m2for the AM SS 316 L and 15.1 mJ/m2for the AM CrCoNi alloys. Meanwhile, during deformation, the SFE varies from 46 to 21 mJ/m2(AM SS 316 L) and 24 to 11 mJ/m2(AM CrCoNi) from initial to stabilized stages, respectively. The transient SFEs are attributed to the deformation activity changes from dislocation slip to twinning as straining. The twinning deformation substructure and atomic stacking faults were confirmed by electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM). The significant variance of the SFE suggests the critical twinning stress as 830 ± 25 MPa for the AM SS 316 L and 790 ± 40 MPa for AM CrCoNi, respectively.