gebhart/patrepeval huggingface dataset:
The Seven S Criteria for Evaluating the Performance of a MALDI Mass Spectrometer for MSI (2020)

Our goal in this work is to evaluate a new combination linear/reflector MALDI-TOF instrument toward satisfying all "7S criteria" for the ideal MSI mass spectrometer. The linear analyzer satisfies all of the 7 criteria except for Specificity. The new instrument described here adds a reflector to provide up to 50,000 mass resolving power with ppm mass accuracy and with no sacrifice in speed, spatial resolution, and sensitivity demonstrated earlier for the linear MALDI-TOF. This instrument employs new laser optics that produces a 5 kHz laser beam with 2.5-25 μm diameter under computer control. The most important advance is the patented combination of laser and ion optics that provides very high efficiency for production and detection of ions generated by laser desorption using small diameter laser beams. This provides spectra with a wide dynamic range summing a relatively small number of laser shots/pixels. Rat and mouse brain tissues have been used for these initial studies. Examples of negative ion images of lipids and positive ion images from tryptic digestion of proteins are presented. These results demonstrate a very high speed for MSI. This speed is derived from a combination of high laser rate (5 kHz), fast motion of sample relative to the laser beam (20 mm/s), very high ionization efficiency (up to 50%), and the ability to acquire, process, and save spectra at a very high rate (1000/s). As a result, the speed that is possible is imposed by other limits, including the mass range, concentration of samples on the surface, and the spatial resolution required.
β-Relaxation of PMMA: Tip Size and Stress Effects in Friction Force Microscopy (2015)

The kinetic signature of the β-relaxation of poly(methyl methacrylate) (PMMA) is investigated by friction force microscopy. The variation in friction force was measured as a function of scan velocity, temperature (300 K-410 K), and applied load using both sharp and blunt probe tips. The friction data show distinct maxima, which can be ascribed to the β-relaxation of PMMA. The contact area was varied over the ranges of approximately 20 to 70 nm(2) and 12,000 to 43,000 nm(2) through the use of probe tips with radii of approximately 15, 18, 1350, and 2650 nm. Kinetic analysis shows that the apparent activation energy of the β-relaxation decreases with the tip radius. Accompanying finite element simulations indicate that for the sharp tips a substantial subvolume of the polymer underneath the tip exceeds the yield stress of PMMA. This suggests that for small contact sizes and high stresses the activation barrier of the β-process decreases through the activation of the α-process by material yielding.
Biological Properties of a Type C Virus Isolated from a Human X Mouse Hybrid Cell Line (1975)

The biological properties of the HMV-1 virus, spontaneously released from a human X C57BL/6 mouse hybrid cell line, were similar to those of RadLV, the prototype B-tropic virus of C57BL/6 mice. Both viruses replicated on B-type mouse cells and in the wild mouse cell line SC-1. The plaque-forming abilities of the two viruses were relatively low, but gradually increased after passage in new host cells. Both viruses were neutralized by AKR antisera but not by FMR antisera. HMV-1 virus could rescue the defective sarcoma genome from S+H- mouse cells. The pseudotype sarcoma virus so produced was deficient in "helper virus" activity. Newborn mice inoculated with HMV-1 virus remained tumor-free over a 1-yr observation period.
Fabrication of silicon-based flexible optical waveguide by edge-cutting transfer technique (2016)

Owing to remarkable advantages in flexible, portable, and large area characteristics, inorganic flexible electronics/ photonics have attracted widespread attentions and got full progresses. The key technique for fabrication of inorganic flexible electrical/optical devices is transferring nano-building blocks from conventional rigid substrates to flexible substrates in a manner of controllable, accurate, and ultrahigh alignment. This paper focused on the well-regulated transfer and deterministic assembly of these nano-building blocks onto flexible substrate during transfer printing process, and proposed edge-cutting transfer technique to fabricate and deterministically assemble silicon nanoribbon arrays on flexible substrate. Based on the beam theory and finite element model, the relationships between stress existing in suspended silicon nanoribbons and thickness and width of nanoribbons during edge-cutting transfer process are studied. Moreover, the edge morphologies of the fabricated nanoribbons are investigated with different directions of the initially defined silicon strips. And the silicon nanoribbons with sharp edges can be obtained by optimizing the defined directions of the silicon strips. Ultimately, silicon-based flexible optical waveguide was demonstrated by using the obtained silicon nanoribbon.
Neural Unloading using Intravenous Vagal Nerve Stimulation for Acute Myocardial Infarction (AMI) Improves Cardiac Function and Prevents Heart Failure in the Long Term (2015)

Background Vagal nerve stimulation (VNS) in AMI is known to have a powerful anti-ischemic effect, but the technical difficulties associated with VNS limit its application under emergency settings. Furthermore, how the acute phase VNS translates into the long term benefit remains unknown. In this study, we developed a novel technique to stimulate the vagal nerves intravenously (iVNS), and evaluated how the iVNS impacts on the infarction size and cardiac function in the long term. Methods/results: In mongrel dogs, we ligated the left anterior descending coronary artery for 3 hours then reperfused (I/R). We delivered iVNS by an electrode catheter placed in the superior vena cava from 1.5 hours after the onset of ischemia to 1 hour after the reperfusion. During I/R iVNS significantly lowered HR (122±25 vs. 167±15 bpm, p<0.05), while did not change blood pressure. At 1 month after I/R, iVNS strikingly decreased the infarct size more than 60% (4.3±4.8 vs. 11.6±3.5%, p<0.05), lowered LVEDP (4.4±3.0 vs. 15.8±7.6 mmHg, p<0.05), and increased Ees (10.8±0.9 vs. 7.4±3.4 mmHg/ml, p<0.05), suggesting the preserved LV systolic function. Conclusion iVNS is capable of reducing the infarct size in AMI and improving cardiac function in the long term. This is a novel neural unloading strategy to prevent chronic heart failure.
Adenophostin A and ribophostin, but not inositol 1,4,5-trisphosphate or manno-adenophostin, activate the Ca2+ release-activated Ca2+ current, ICRAC, in weak intracellular Ca2+ buffer (2002)

Under physiological conditions of weak intracellular Ca(2+) buffering (0.1 mM EGTA), the second messenger Ins(1,4,5)P(3) often fails to activate any detectable store-operated Ca(2+) current. However, it has been reported that the fungal metabolite adenophostin A [which has a severalfold higher affinity than Ins(1,4,5)P(3) for Ins(1,4,5)P(3) receptors] consistently activates the current under similar conditions. Here, whole-cell patch clamp experiments have been performed to examine how adenophostin A can activate the store-operated Ca(2+) current (I(CRAC)) in RBL-1 (rat basophilic leukaemia) cells. In a strong intracellular Ca(2+) buffer, saturating concentrations of adenophostin A activated I(CRAC) maximally and the current amplitude and kinetics were indistinguishable from those obtained with high concentrations of Ins(1,4,5)P(3). In a weak Ca(2+) buffer, adenophostin A consistently activated I(CRAC), but the current was submaximal. High concentrations of Ins(1,4,5)P(3) or the non-metabolizable analogue Ins(2,4,5)P(3) were largely ineffective under these conditions. The size of I(CRAC) to adenophostin A in weak Ca(2+) buffer could be significantly increased by either inhibiting sarcoplasmic/endoplasmic-reticulum Ca(2+)-ATPase ('SERCA') pumps with thapsi-gargin or enhancing mitochondrial Ca(2+) uptake, although blocking the mitochondrial Ca(2+) uniporter with Ruthenium Red did not suppress the activation of the current. Changing the levels of free ATP in the recording pipette did not enhance the size of I(CRAC) evoked by adenophostin A. We also examined two structurally distinct analogues of adenophostin A (manno-adenophostin and ribophostin), for which the affinities for the Ins(1,4,5)P(3) receptor are similar to that of Ins(1,4,5)P(3) in equilibrium binding experiments. Although these analogues were able to activate I(CRAC) to its maximal extent in strong buffer, ribophostin, but not manno-adenophostin, consistently activated the current in weak buffer. We conclude that adenophostin A and ribophostin are able to activate I(CRAC) in weak buffer through a mechanism that is quite distinct from that employed by Ins(1,4,5)P(3) and manno-adenophostin and is not related to equilibrium affinities.
Aspects cliniques de la neoplasie endocrinienne multiple de type 2 (NEM-2). (1993)

peer reviewed
SAG: a Schwann cell membrane glycoprotein (1992)

We report on characterization of a 170,000 Da glycoprotein found exclusively in the PNS. We refer to this protein as the Schwann cell membrane glycoprotein (SAG). SAG contains the HNK-1 carbohydrate, which is considered by some to be a marker of adhesion molecules. Its N-terminal sequence is not similar to previously known polypeptide sequences. SAG is found exclusively in the PNS, is present in rat sciatic nerve prior to myelination, and is in both myelinating and nonmyelinating Schwann cells. Tumors of Schwann cell lineage express SAG where axons are present (neurofibromas) but do not in the absence of axons (schwannomas). Schwannoma cells in culture do not express SAG even when exposed to forskolin, an activator of adenylate cyclase. However, schwannoma cells grown in the presence of a neuronal cell line (PC12) express SAG.
Multiprocessing extensions in Spur Lisp (1989)

The authors describe their multiprocessing extensions to Common Lisp. They have added a few simple, expressive features on which one can build high-level constructs. These consist of a multithreading mechanism, primitives for communication and synchronization (mailboxes and signals), and a feature called futures. A few examples clarify how the primitives work and demonstrate their expressiveness. When Spur Lisp is ported to and optimized on the Spur workstation (a shared memory multiprocessor), programmers can use it to make symbolic programs parallel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
GaSb quantum-well-based “buffer-free” vertical light emitting diode monolithically embedded within a GaAs cavity incorporating interfacial misfit arrays (2006)

The authors demonstrate a monolithic, electrically injected, vertically emitting GaSb∕AlGaSb light emitting diode (LED) emitting at 1.6μm comprised of a hybrid GaAs∕GaSb-based structure. The LED is comprised of a GaSb∕AlGaSb quantum well/barrier active region embedded within high index contrast GaAs∕AlGaAs distributed Bragg reflectors (DBRs) using two interfacial misfit (IMF) arrays to relieve the strain induced from the high 8% lattice mismatch between the material systems. The first IMF is formed under compressive strain conditions to enable strain-free, defect-free deposition of GaSb active region directly on the lower GaAs∕AlAs DBRs without need for thick buffer. The second IMF is formed under tensile conditions to enable the upper GaAs∕AlAs DBRs on the GaSb active region. The device demonstrates a maximum output power of 3.5μW. Initial diode optical and electrical characteristics along with IMF band structure are discussed.
High speed parallel multi-chip interconnection with free space optics (2003)

In many MCM applications, data distribution from and to the memory chips that may reside on an MCM or on a adjacent board can become one of the key bottlenecks in high performance system implementation. This type of performance-limited data paths can be replaced by using an free-space optical interconnect (FSOI) module with crossbar connectivity between point to point interconnects. This system can be made into a standard data communication module for various applications (interconnect processors, DSP chips, memory and telecom interface circuits).
A 0.9 V embedded ferroelectric memory for microcontrollers (2002)

This work demonstrates application of ferroelectric technology in the embedded "system-on-chip" area. The focus of this paper is twofold: (1) Optimization of the material properties and cell design to achieve 0.9 V operation with fully-saturated hysteresis loops, and high speed (<100ns); and, (2) Demonstration of the overall "system-on-chip" device architecture and operation using the ferroelectric memory in an embedded environment.
Interplay of Solvent Additive Concentration and Active Layer Thickness on the Performance of Small Molecule Solar Cells (2014)

A relationship between solvent additive concentration and active layer thickness in small-molecule solar cells is investigated. Specifically, the additive concentration must scale with the amount of semiconductor material and not as absolute concentration in solution. Devices with a wide range of active layers with thickness up to 200 nm can readily achieve efficiencies close to 6% when the right concentration of additive is used.
A Batch Detection Algorithm Installed on a Test Bench (2012)

Test benches are used to evaluate the performance of new turbofan engine parts during development phases. This can be especially risky for the bench itself because no one can predict in advance whether the component will behave properly. Moreover, a broken bench is often much more expensive than the deterioration of the component under test. Therefore, monitoring this environment is appropriate, but as the system is new, the algorithms must automatically adapt to the component and to the driver's behavior who wants to experience the system at the edge of its normal domain. In this paper we present a novelty detection algorithm used in batch mode at the end of each cycle. During a test cycle, the pilot increases the shaft speed by successive steps then finally ends the cycle by an equivalent slow descent. The algorithm takes a summary of the cycle and works at a cycle frequency producing only one result at the end of each cycle. Its goal is to provide an indication to the pilot on the reliability of the bench's use for a next cycle.
Oxygen Sensitivity of Reporter Genes: Implications for Preclinical Imaging of Tumor Hypoxia (2007)

Reporter gene techniques have been applied toward studying the physiologic phenomena associated with tumor hypoxia, a negative prognostic indicator. The purpose of this study was to assess the potential adverse effects of hypoxic conditions on the effectiveness of four commonly used reporter genes: Renilla luciferase, monomeric red fluorescent protein, thymidine kinase, and lacZ. Tumor-forming A375 cells expressing a trifusion reporter consisting of Renilla luciferase, monomeric red fluorescent protein, and thymidine kinase were subjected to decreasing oxygen tensions and assayed for reporter expression and activity. A375 cells expressing beta-galactosidase were similarly exposed to hypoxia, with activity of the reporter monitored by cleavage of the fluorescent substrate 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one)-beta-galactoside (DDAOG). Generation of signal in in vivo tumor models expressing bioluminescent or beta-galactosidase reporters were also examined over the course of hypoxic stresses, either by tumor clamping or the antivascular agent 5,6-dimethylxanthenone-4-acetic acid (DMXAA). Our findings indicate that bioluminescent and fluorescent reporter activity are decreased under hypoxia despite minimal variations in protein production, whereas beta-galactosidase reporter activity per unit protein was unchanged. These results demonstrate that combining beta-galactosidase with the DDAOG optical probe may be a robust reporter system for the in vivo study of tumor hypoxia.
Physiological and genetic analysis ofArabidopsis thalianaanthocyanin biosynthesis mutants under chronic adverse environmental conditions (2012)

Anthocyanin production is a characteristic response of flowering plants to unfavourable environmental conditions. The potential roles of flavonoids and anthocyanins in plant growth were investigated by growing Arabidopsis thaliana anthocyanin production mutants (transparent testa) under limiting nitrogen and high light conditions. Inability to produce kaempferol or subsequent intermediate compounds by some transparent testa lines was correlated with less biomass accumulation in mature plants compared with wild-type control plants under all growth conditions tested. However, under both limiting nitrogen and high light chronic stress conditions, mutant lines defective in later steps of the anthocyanin production pathway produced the same or more biomass than wild-type plants. No difference in senescence between transparent testa and wild-type plants was found using chlorophyll catabolism and SAG12 expression measurements, and no mutants were impaired in the ability to remobilize nutrients from the vegetative to reproductive tissues. Moreover, the absence of anthocyanin and/or upstream flavonoids does not affect the ability of plants to respond to limiting nitrogen by reducing photosynthetic capacity. These results support a role for kaempferol and quercetin accumulation in normal plant growth and development. Further, the absence of anthocyanins has no effect on plant growth under the chronic stress conditions tested.
Scaling laws for cache-aided device-to-device networks for wireless video (2021)

Chapter Contents: 9.1 Introduction 9.1.1 Motivation for D2D-based video distribution 9.1.2 D2D scaling laws without caching 9.2 System model 9.2.1 Popularity model 9.2.2 Network model 9.2.3 Target functions for scaling 9.3 Single-hop networks 9.3.1 Scaling law results 9.3.2 Numerical studies under realistic setups 9.4 Multihop networks 9.5 D2D-coded caching 9.5.1 Single-hop-coded D2D caching 9.5.2 An improved coded D2D caching schemes 9.5.3 Extension to multihop coded D2D caching networks 9.6 Practical implementation considerations for D2D caching networks 9.6.1 D2D caching under realistic channel model 9.6.2 D2D caching in mobile networks 9.6.3 Complexity of D2D-coded caching 9.7 Conclusions and further readings References
Knockout of both miR-15/16 loci induces acute myeloid leukemia (2018)

MicroRNAs (miRNAs) have been extensively reported to be associated with hematological malignancies. The loss of miR-15a/16-1 at chromosome 13q14 is a hallmark of most of human chronic lymphocytic leukemia (CLL). Deletion of murine miR-15a/16-1 and miR-15b/16-2 has been demonstrated to promote B cell malignancies. Here, we evaluate the biological role of miR-15/16 clusters, crossbreeding miR-15a/16-1 and miR-15b/16-2 knockout mice. Unexpectedly, the complete deletion of both clusters promoted myeloproliferative disorders in the majority of the mice by the age of 5 months with a penetrance of 70%. These mice showed a significant enlargement of spleen and abnormal swelling of lymph nodes. Flow cytometry characterization demonstrated an expanded CD11b/Gr-1 double-positive myeloid population both in spleen and in bone marrow. The transplantation of splenocytes harvested from double-KO mice into wild-type recipient mice resulted in the development of myeloproliferative disorders, as observed in the donors. In vivo, miR-15/16 cluster deletion up-regulated the expression of Cyclin D1, Cyclin D2, and Bcl-2. Taken together, our findings identify a driver oncogenic role for miR-15/16 cluster deletion in different leukocytic cell lineages.
Orientation Change of Diblock Copolymer Thin Films by the Addition of Amphiphilic Surfactants: Effect of Film Thickness and Surfactant Concentration (2011)

We systematically investigated the effect of surfactant addition on the orientational change in polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) block copolymer films as a function of film thickness and surfactant (oleic acids (OAs)) concentration using microscopic analysis, neutron reflectivity, and theoretical calculations. The orientation of PS-b-PMMA films containing OAs as surfactants was found to be determined by the competitions among the surfactant-assisted neutral field and preferential fields at both top surface and bottom interface. In the case of a BCP film containing a small amount of OAs, the integer film thickness of domain spacing L0 (long spacing of lamellae-forming BCP) prefers to form the perpendicular orientation of microdomains while the parallel orientation is observed when the film thickness is close to the half-integers of L0. We also found that the periodic orientation of block domains gradually dies out to the perpendicular orientation as the film thickness as well as the surfactant concentration is increased. Neutron reflectivity analysis of deuterated polystyrene-block-poly(methyl methacrylate) (dPS-b-PMMA) block copolymer thin films containing OA surfactants was also performed to gain insights into the orientation of BCP films across film thickness due to the addition of OAs. With the free energy calculations on BCPs mixed with OA surfactants at different film thicknesses, the periodic orientation of block domains is qualitatively confirmed.
Optical designs for compressive single shot spectral imaging (2007)

Static mask coded aperture spectral imaging enables compact, programmable coding for single shot measurements. We review recent demonstrations of spectral imaging systems in the DISP lab and describes trade-offs in dispersion and coding system design.
More Synergy, Less Redundancy: Exploiting Joint Mutual Information for Self-Supervised Learning (2023)

Self-supervised learning (SSL) is now a serious competitor for supervised learning, even though it does not require data annotation. Several baselines have attempted to make SSL models exploit information about data distribution, and less dependent on the augmentation effect. However, there is no clear consensus on whether maximizing or minimizing the mutual information between representations of augmentation views practically contribute to improvement or degradation in performance of SSL models. This paper is a fundamental work where, we investigate role of mutual information in SSL, and reformulate the problem of SSL in the context of a new perspective on mutual information. To this end, we consider joint mutual information from the perspective of partial information decomposition (PID) as a key step in \textbf{reliable multivariate information measurement}. PID enables us to decompose joint mutual information into three important components, namely, unique information, redundant information and synergistic information. Our framework aims for minimizing the redundant information between views and the desired target representation while maximizing the synergistic information at the same time. Our experiments lead to a re-calibration of two redundancy reduction baselines, and a proposal for a new SSL training protocol. Extensive experimental results on multiple datasets and two downstream tasks show the effectiveness of this framework.
Analysis on Fraud Detection for Internet Service (2013)

In this paper, we proposed the model which can support fraud detection in ICT application service. Fraud detection service monitors and analyzes user activity and behavior at the application level (rather than at the system, database or network level) and watches what transpires inside and across accounts, using any channel available to a user. It also analyzes behavior among related users, accounts or other entities, looking for organized criminal activity, corruption or misuse. This model can be used in e-banking, e-payment, e-government and enterprise remote access, etc.