gebhart/patrepeval huggingface dataset:
Pathogenic Autoantibodies in Systemic Lupus Erythematosus Are Derived from Both Self-Reactive and Non-Self-Reactive B Cells (2008)

Previous studies have shown that both murine and human anti-double-stranded DNA (anti-dsDNA) antibodies can develop from non-DNA-reactive B cells and suggest a crucial role for somatic mutation in dsDNA binding. However, since only a limited number of human anti-dsDNA antibodies have been analyzed previously, we could not exclude other mechanisms for the generation of anti-dsDNA antibodies in patients with systemic lupus erythematosus (SLE). Therefore, we isolated IgM anti-dsDNA antibodies from peripheral blood B cells of a patient with SLE. Three somatically mutated IgM anti-DNA antibodies with pathogenic potential (glomerular binding) were reverted to their germline configuration. Although all three IgM anti-dsDNA antibodies came from the same lupus patient, they displayed different profiles. Reversion to the germline sequence of autoantibodies A9 and B5 resulted in decreased dsDNA binding. In contrast, the germline form of G3-recognized dsDNA as well as the mutated counterpart. These results suggest that mutated IgM anti-dsDNA antibodies may develop from both DNA- and non-DNA-reactive B cells. The implications are that B cell activation occurs in response to self and non-self antigens, while selection after activation may be mediated by self antigen in SLE. Moreover, ineffective tolerance checkpoints may exist before and after antigen activation in SLE.
Ammonium and arsenic trioxide are potent facilitators of oligonucleotide function when delivered by gymnosis (2018)

Oligonucleotide (ON) concentrations employed for therapeutic applications vary widely, but in general are high enough to raise significant concerns for off target effects and cellular toxicity. However, lowering ON concentrations reduces the chances of a therapeutic response, since typically relatively small amounts of ON are taken up by targeted cells in tissue culture. It is therefore imperative to identify new strategies to improve the concentration dependence of ON function. In this work, we have identified ammonium ion (NH4+) as a non-toxic potent enhancer of ON activity in the nucleus and cytoplasm following delivery by gymnosis. NH4+ is a metabolite that has been extensively employed as diuretic, expectorant, for the treatment of renal calculi and in a variety of other diseases. Enhancement of function can be found in attached and suspension cells, including in difficult-to-transfect Jurkat T and CEM T cells. We have also demonstrated that NH4+ can synergistically interact with arsenic trioxide (arsenite) to further promote ON function without producing any apparent increased cellular toxicity. These small, inexpensive, widely distributed molecules could be useful not only in laboratory experiments but potentially in therapeutic ON-based combinatorial strategy for clinical applications.
Processes to achieve vibrating beams for an angular rate measurement sensor (2002)

Vibrating beam structures may be used as sensing elements in an angular rate measurement sensor. Achieving a square cross-sectional area with smooth vertical side walls and sharp edges is necessary for these beams. In this work, fabrication of beams with reasonably smooth vertical sidewalls and accurate dimensions, using anisotropic etching of silicon in TMAH, has been investigated. Beams with various thicknesses (500-100 microns) are fabricated. It is shown that by carefully aligning the mask at 45/spl deg/ from the <110> wafer flat, and by maintaining the concentration of TMAH at 25%, it is possible to achieve smooth vertical sidewalls with good uniformity along the length of the beam. Adequate control over the beam lateral dimension is achieved by etching in a 2-step procedure with the second step at a lower temperature (lower etch rate). Single-sided and double-sided masking techniques are investigated in order to fabricate the beams. An alternative design is presented to form the beams using a standard CMOS process.
Characterization of crystals of an antibody-recognition fragment of the cancer differentiation antigen mesothelin in complex with the therapeutic antibody MORAb-009 (2012)

The mesothelin-specific monoclonal antibody MORAb-009 is capable of blocking the binding of mesothelin to CA-125 and displays promising anticancer potential. It is currently undergoing clinical trials. In order to understand the basis of the interaction between MORAb-009 and mesothelin at atomic resolution, both the Fab fragment of MORAb-009 and the complex between the Fab and an N-terminal fragment of mesothelin (residues 7-64) were crystallized. The crystals of the Fab diffracted X-rays to 1.75 Å resolution and had the symmetry of space group P4(1)2(1)2, with unit-cell parameters a = b = 140.6, c = 282.0 Å. The crystals of the mesothelin-Fab complex diffracted to 2.6 Å resolution and belonged to the hexagonal space group P6(4), with unit-cell parameters a = b = 146.2, c = 80.9 Å. Structural analyses of these molecules are in progress.
Thermal Performance of a Miniature Variable Conductance Loop Heat Pipe (2000)

&lt;div class="htmlview paragraph"&gt;Loop Heat Pipes (LHP) of different designs are currently used in aerospace applications worldwide. Historically, LHPs were considered primarily as candidates for high power, high adverse elevation and high heat flux applications such as deployable radiators for large satellites, thermal bus devices, high heat flux payloads, etc.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A new look at the LHP technology was presented in 1998 (Ref. &lt;span class="xref"&gt;1&lt;/span&gt;), and the miniature LHP concept was introduced to the industry. Because miniature LHPs are frequently serving as “thermal shunts” for payloads and instruments, controllability issues played an important role from the very beginning of their development.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;For instance, the electrical power that is available for thermal control of Mars rovers on the Martian surface is limited. Because of this limitation, the thermal control systems for the new generation of Mars rovers were required to be absolutely passive. A prototype of a miniature variable conductance LHP with a three-way valve was developed and built in 1999 for evaluation as the thermal control unit for the Mars ‘03/’05 rover. This LHP has two condensers, one integrated with the internal equipment which needs to be heated and the other serving as an external radiator. A three-way valve is used to activate the external radiator whenever the evaporator temperature exceeds a pre-set value. If the vapor temperature drops below the valve's set-point, the valve opens a by-pass line and the heat is no longer rejected at the external condenser. Warm vapor bypasses the condenser and enters the evaporator from the liquid side and keeps the evaporator warm. If the system's temperature has increased and exceeded the set-point, the valve closes the bypass line and opens the line to the external condenser. The miniature VCLHP was subjected to a test program that verified the reliability of temperature control provided by this type of LHP; it also highlighted the pluses and minuses of this technology. The design of the LHP, the test setup, test plan and test results are discussed in this paper. An interesting behavior was demonstrated during the course of the evaluation program. It was demonstrated that the three-way valve approach to control LHP temperatures is very attractive for the thermal control systems.&lt;/div&gt;
LoopTree: Enabling Exploration of Fused-layer Dataflow Accelerators (2023)

Many accelerators today process deep neural networks layer by layer. As a consequence of this processing style, every intermediate feature map incurs expensive off-chip transfers. Layer fusion eliminates off-chip transfers of intermediate results, leading to better latency and energy efficiency. Prior works have explored only subsets of the fused-layer design space, looking only at a particular choice of tiling, scheduling, and buffering strategy. Their architectural models are also tailored for their proposed datatlow. The lack of a unified, systematic representation of designs and a versatile evaluation method has prevented thorough exploration of the design space. To enable systematic exploration of this design space, we present LoopTree, a framework for describing and evaluating any design in our expanded fused-layer datatlow design space. With a case study, we explore new designs to show that exploring our larger design space uncovers more efficient designs, especially for recent workloads with diverse layer types. Our design achieves 2.5× speedup and 2× lower energy compared to an optimized layer-by-layer design. Compared to a state-of-the-art fused-layer design, we match latency and energy while using 25% less onchip buffer space.
Nano/HEDM Technology: Late Stage Exploratory Effort (2003)

This work is focused on a continued, escalating effort to develop new energetic functional groups which offer enhanced energy, oxygen balance, and density in that order of priority. A continuation of the study of addition of nitrene precursors to N,N-dialkyl nitrosamines is described; the nitrene derived from 1-amino-3,5-dinitro-1 ,2,4-triazole has been approached by oxidation of the parent amine. Initial results were not successful; aminodinitrotriazole in the presence of lead tetra-acetate does not produce detectable yields of dinitrotriazolyl azoxy dimethyl amine when aminodinitrotriazole and lead tetra-acetate are reacted in the presence of N,N-dimethylnitrosamine. The synthesis of the 5-nitrotetrazole-2-N-oxide anion has been realized and optimized; it is carried out in water/potassium acetate buffer, and proceeds in 90% yield; due to the small enthalpy of this oxidation, scale up and heat dissipation do not present a problem. The density of hydroxyl ammonium 5-nitrotetrazole-2-oxide is 1.82 g/cc; its enthalpy of formation is +40 kcal/mole. Finally, a practical pathway to 1-alkoxy-5-amino tetrazoles has been developed; it is hoped that this will enable the synthesis of 5-nitrotetrazole-1 ,3-bis-N-oxides, a family of unprecedented materials with excellent heats of formation and oxygen balance that rivals ammonium perchlorate and ammonium dinitramide.
Automated Indentation Demonstrates Structural Stiffness of Femoral Articular Cartilage and Temporomandibular Joint Mandibular Condylar Cartilage Is Altered in FgF2KO Mice (2020)

Automated indentation spatially resolved differences in structural stiffness between WT and Fgf2KO tissue, demonstrating FGF2 expression affects femoral AC and TMJ MCC. This quantitative method will provide a valuable approach for functional characterization of cartilage tissues in murine models relevant to knee joint and TMJ health and disease.
Combination chemotherapy with doxorubicin and mitomycin C in non small cell bronchogenic carcinoma (1984)

Forty-five patients with advanced, measurable, or evaluable non-small bronchogenic carcinoma (NSCBC) were treated with doxorubicin and mitomycin C combination chemotherapy. The first 27 patients received doxorubicin 50 mg/m2 I.V. every 3 weeks and mitomycin C 10 mg/m2 I.V. every 3 weeks. Because of severe cardiopulmonary toxicity in seven patients, with four otherwise unexplained deaths, the next 18 patients were treated with the mitomycin C dose reduced to 10 mg/m2 every 6 weeks. Overall, 11 patients (25%) responded, with one complete and 10 partial remissions. Eight responses (30%) were observed in the patients who received mitomycin C every 3 weeks and three responses (17%) were found in those given mitomycin C every 6 weeks (p less than 0.5), with no cardiopulmonary toxicity in the latter group. The median survival was 21 weeks for the entire group of patients, with the group receiving mitomycin C every 3 weeks living a median of 15.5 weeks and those given mitomycin C every 6 weeks surviving 35.5 weeks (p less than 0.025). We conclude that there is a higher tumor response rate but more cardiopulmonary toxicity and shorter survival among the group receiving mitomycin C every 3 weeks compared to those receiving mitomycin C every 6 weeks. Future studies should consider this toxicity of mitomycin C administered on an every-3-week schedule.
Influence of motion on image quality with a 64 -channel CT scanner (2008)

Physiological motions can affect Computed Tomography (CT) exam. While the impact of some motions on CT imaging can be reduced, other physiological motions are unavoidable. To attempt correcting the resulting images, it is necessary to understand how the artifacts are formed and their influence on the image quality. Using a cardiac phantom and a dynamic platform, we have studied the influence of a translation in the z-axis associated with a rotation in the z-axis (at different speeds) on the quality of axial images using a <i>64</i>-channel scanner. The results show that, the deformation, the detectability and the contrast of the calcifications are of course dependent on the density and size of the calcification but also on the movement they undergo. The noise in CT imaging is also affected by motion. The influence of motion on the image quality depends on the examined object and unfortunately cannot be predicted. The corruption of the data results in the loss of information about the form, the contrast and/or the size of the scanned object. This corruption can lead to diagnosis errors by mimicking diseases or by masking physiologic details.
Cooperative Robotic Fabrication of Timber Dowel Assemblies (2019)

This research is developed within the Master of Advanced Studies in Architecture and Digital Fabrication program at ETH Zurich. This paper presents a novel constructive system made solely of wood, enabled by a cooperative robotic fabrication process. The constructive system builds on recent developments in dowel-laminated timber (DLT) as well as advances made in the field of digital fabrication. The paper demonstrates through three experiments how the design space of the dowel-laminated timber constructive system can be expanded, through the implementation of cooperative robotic arms, from purely planar geometries to more complex and curved ones. To connect the individual slats, two types of dowel connectors were tested: the fluted dowel and the dry dowel. The fabrication process employs a large robotic setup allowing for the prefabrication of full-scale building elements and enables a method of in place fabrication that counteracts the inaccuracy buildup that occurs during assembly. Two custom robot end-effectors for gripping and drilling timber slats are also introduced. Finally, a conclusion and outlook as to what the next steps in this research could be are presented.
Influences of group-III source preflow on the polarity, optical, and structural properties of GaN grown on nitridated sapphire substrates by metal-organic chemical vapor deposition (2015)

We report the influences of group-III source preflow, which were introduced prior to the growth of the low temperature GaN on the polarity, photoluminescence (PL), and crystallographic properties of GaN epilayers grown on nitridated c-plane sapphire substrates by metal-organic chemical vapor deposition. By studying the surface morphology evolutions under chemical etching in KOH, we found that with increasing the trimethyl-gallium (TMGa) preflow duration (t), the polarity of the GaN film can be changed from a complete N-polarity to a mixture of N- and Ga-polarity and further to a complete Ga-polarity. PL and high-resolution X-ray diffraction studies revealed that the impurity incorporation and the edge- and screw-type threading dislocations are strongly polarity dependent. A further study at the optimized t (i.e., 30 s for TMGa) shows that the polarity inversion of GaN can be realized not only by TMGa preflow but also by trimethyl-aluminium preflow and by trimethyl-indium preflow. A two-monolayer model was employed to explain the polarity inversion mechanism.
Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data (2019)

Widefield calcium imaging enables recording of large-scale neural activity across the mouse dorsal cortex. In order to examine the relationship of these neural signals to the resulting behavior, it is critical to demix the recordings into meaningful spatial and temporal components that can be mapped onto well-defined brain regions. However, no current tools satisfactorily extract the activity of the different brain regions in individual mice in a data-driven manner, while taking into account mouse-specific and preparation-specific differences. Here, we introduce Localized semi-Nonnegative Matrix Factorization (LocaNMF), a method that efficiently decomposes widefield video data and allows us to directly compare activity across multiple mice by outputting mouse-specific localized functional regions that are significantly more interpretable than more traditional decomposition techniques. Moreover, it provides a natural subspace to directly compare correlation maps and neural dynamics across different behaviors, mice, and experimental conditions, and enables identification of task- and movement-related brain regions.
Table S7 from Clinical Importance of the lncRNA <i>NEAT1</i> in Cancer Patients Treated with Immune Checkpoint Inhibitors (2023)

&lt;p&gt;Genes enriched in NEAT1-high glioblastoma tumor cells&lt;/p&gt;
Single‐cell recordings in the human medial temporal lobe (2014)

Recordings from individual neurons in patients who are implanted with depth electrodes for clinical reasons have opened the possibility to narrow down the gap between neurophysiological studies in animals and non-invasive (e.g. functional magnetic resonance imaging, electroencephalogram, magnetoencephalography) investigations in humans. Here we provide a description of the main procedures for electrode implantation and recordings, the experimental paradigms used and the main steps for processing the data. We also present key characteristics of the so-called 'concept cells', neurons in the human medial temporal lobe with selective and invariant responses that represent the meaning of the stimulus, and discuss their proposed role in declarative memory. Finally, we present novel results dealing with the stability of the representation given by these neurons, by studying the effect of stimulus repetition in the strength of the responses. In particular, we show that, after an initial decay, the response strength reaches an asymptotic value after approximately 15 presentations that remains above baseline for the whole duration of the experiment.
Anti-spike T-cell and Antibody Responses to SARS-CoV-2 mRNA Vaccines in Patients with Hematologic Malignancies (2022)

This study represents the first investigation of SARS-CoV-2-specific immune responses to vaccination in a patient registry using an NGS-based method for T-cell receptor repertoire-based analysis combined with anti-spike antibody assessments. Vaccinated patients with B cell-derived hematologic malignancies are likely at higher risk of infection or severe COVID-19. This article is highlighted in the In This Issue feature, p. 476.
Metal-Free Catalyzed Ring-Opening Polymerization of β-Lactones: Synthesis of Amphiphilic Triblock Copolymers Based on Poly(dimethylmalic acid) (2006)

A polylactide-block-(dimethyl β-malic acid-co-β-butyrolactone)-block-polylactide (PLA-b-P(dMMLA-co-BL)-b-PLA) triblock copolymer has been synthesized according to a totally original three-step strategy. In a first step, the ring-opening polymerization (ROP) of dimethyl benzyl β-malolactonate (dMMLABz) and β-butyrolactone (BL) has been carried out in a toluene/t-BuOH solvent mixture at 80 °C by using ethylene glycol as initiator and the commercially available 1,3,4-triphenyl-4,5-dihydro-1H-1,2,4-triazol-5-ylidene carbene 1 as catalyst. The ROP mechanism selectively involves O-acyl cleavage of both dMMLABz and BL cyclic comonomers with a preferential incorporation of dMMLABz units in the growing polyester chains as attested by 1H NMR spectroscopy. In a second step, the so-produced α,ω-dihydroxy P(dMMLABz-co-BL) copolyester have been further considered as difunctional macroinitiatior in l,l-lactide (LA) monomer ROP at 90 °C. In the third and last step, the benzylic ester functions pending along the recovered PLA-b-P(dMMLABz-co-BL)-b-PLA triblock copolymer have been reduced/deprotected by catalytic hydrogenation leading to the expected PLA-b-P(dMMLA-co-BL)-b-PLA symmetric triblock copolyester. The amphiphilic character of this novel type of A−B−A triblock copolymers has been evidenced by some preliminary dynamic light scattering experiments in aqueous solution. While “flower” type micelles are formed at low temperature (e.g., 4 °C), microgelation occurs at higher temperature (at ca. 25 °C). By a further increase in the temperature and consistent with a temperature-dependent reversible gel−sol transition, the microgel dissolves at ca. 40 °C to the benefit of primary micelles. These observations have allowed for drawing a preliminary sol−gel phase diagram in water characterized by lower and upper concentration-dependent critical gelation temperatures.
Local Histograms of Character N-grams for Authorship Attribution (2011)

This paper proposes the use of local histograms (LH) over character n-grams for authorship attribution (AA). LHs are enriched histogram representations that preserve sequential information in documents; they have been successfully used for text categorization and document visualization using word histograms. In this work we explore the suitability of LHs over n-grams at the character-level for AA. We show that LHs are particularly helpful for AA, because they provide useful information for uncovering, to some extent, the writing style of authors. We report experimental results in AA data sets that confirm that LHs over character n-grams are more helpful for AA than the usual global histograms, yielding results far superior to state of the art approaches. We found that LHs are even more advantageous in challenging conditions, such as having imbalanced and small training sets. Our results motivate further research on the use of LHs for modeling the writing style of authors for related tasks, such as authorship verification and plagiarism detection. 1