gebhart/patrepeval huggingface dataset:
The Scaffold Protein Cybr Is Required for Cytokine-Modulated Trafficking of Leukocytes In Vivo (2006)

Trafficking and cell adhesion are key properties of cells of the immune system. However, the molecular pathways that control these cellular behaviors are still poorly understood. Cybr is a scaffold protein highly expressed in the hematopoietic/immune system whose physiological role is still unknown. In vitro studies have shown it regulates LFA-1, a crucial molecule in lymphocyte attachment and migration. Cybr also binds cytohesin-1, a guanine nucleotide exchange factor for the ARF GTPases, which affects actin cytoskeleton remodeling during cell migration. Here we show that expression of Cybr in vivo is differentially modulated by type 1 cytokines during lymphocyte maturation. In mice, Cybr deficiency negatively affects leukocytes circulating in blood and lymphocytes present in the lymph nodes. Moreover, in a Th1-polarized mouse model, lymphocyte trafficking is impaired by loss of Cybr, and Cybr-deficient mice with aseptic peritonitis have fewer cells than controls present in the peritoneal cavity, as well as fewer leukocytes leaving the bloodstream. Mutant mice injected with Moloney murine sarcoma/leukemia virus develop significantly larger tumors than wild-type mice and have reduced lymph node enlargement, suggesting reduced cytotoxic T-lymphocyte migration. Taken together, these data support a role for Cybr in leukocyte trafficking, especially in response to proinflammatory cytokines in stress conditions.
HydraFusion: Context-Aware Selective Sensor Fusion for Robust and Efficient Autonomous Vehicle Perception (2022)

Although autonomous vehicles (AVs) are expected to revolutionize transportation, robust perception across a wide range of driving contexts remains a significant challenge. Techniques to fuse sensor data from camera, radar, and lidar sensors have been proposed to improve AV perception. However, existing methods are insufficiently robust in difficult driving contexts (e.g., bad weather, low light, sensor obstruction) due to rigidity in their fusion implementations. These methods fall into two broad categories: (i) early fusion, which fails when sensor data is noisy or obscured, and (ii) late fusion, which cannot leverage features from multiple sensors and thus produces worse estimates. To address these limitations, we propose HydraFusion: a selective sensor fusion framework that learns to identify the current driving context and fuses the best combination of sensors to maximize robustness without compromising efficiency. HydraFusion is the first approach to propose dynamically adjusting between early fusion, late fusion, and combinations in-between, thus varying both how and when fusion is applied. We show that, on average, Hydrafusionoutperforms early and late fusion approaches by 13.66% and 14.54%, respectively, without increasing computational complexity or energy consumption on the industry-standard Nvidia Drive PX2 AV hardware platform. We also propose and evaluate both static and deep-learning-based context identification strategies. Our open-source code and model implementation are available at https://github.com/AICPS/hydrafusion.
Merkel Cell Carcinoma: Incidence, Mortality, and Risk of Other Cancers (2010)

These results support the existence of shared risk factors for MCC and other cancers. Heightened awareness of the association between MCC and other cancers, particularly squamous cell carcinoma and chronic lymphocytic leukemia, may facilitate earlier clinical detection and treatment of MCC, thereby improving patient survival.
Teleport messaging for distributed stream programs (2005)

In this paper, we develop a new language construct to address one of the pitfalls of parallel programming: precise handling of events across parallel components. The construct, termed teleport messaging, uses data dependences between components to provide a common notion of time in a parallel system. Our work is done in the context of the Synchronous Dataflow (SDF) model, in which computation is expressed as a graph of independent components (or actors) that communicate in regular patterns over data channels. We leverage the static properties of SDF to compute a stream dependence function, SDEP, that compactly describes the ordering constraints between actor executions.Teleport messaging utilizes SDEP to provide powerful and precise event handling. For example, an actor A can specify that an event should be processed by a downstream actor B as soon as B sees the "effects" of the current execution of A. We argue that teleport messaging improves readability and robustness over existing practices. We have implemented messaging as part of the StreamIt compiler, with a backend for a cluster of workstations. As teleport messaging exposes optimization opportunities to the compiler, it also results in a 49% performance improvement for a software radio benchmark.
Sliding mode control for agents and humans (2008)

A new sliding mode control of attitude and position of an autonomous satellite within a cluster is presented. Asymptotic stability is proven by Lyapunov's method. The result is unique in that it handles discrete time control and includes potential function guidance in the scheme. This theoretical result has been written down in a second contribution of the paper: the introduction of natural language publications that can be read by humans and agents (machines) as well. As a first example of natural language programming, system English (sEnglish for short) is introduced to the reader as a new programming paradigm, not a natural language interface. The most important feature of sEnglish is that it compiles into MATLAB code unambiguously. sEnglish is suitable to program complex programs, personal assistants and autonomous agents but its main purpose is to be used for passing on knowledge to agents. As such it is a publication for humans as well as for machines. This paper is a call for participation in a community effort to use natural language programming and and sEnglish in our work in
academia and companies.
Oxidation of glycerol and propanediols in methanol over heterogeneous gold catalysts (2008)

Aerobic oxidation of glycerol over metal oxide supported gold nanoparticles in methanol results in the formation of dimethyl mesoxalate in selectivities up to 89% at full conversion. The oxidative esterification takes place in methanol, acting both as solvent and reactant, and in the presence of base. Thus, it constitutes a direct transformation of the glycerol by-product phase from biodiesel production or from glycerol obtained e.g. by fermentation. Au/TiO2 and Au/Fe2O3 was found to have similar catalytic activity, whereas Au/C was inactive. 1,2-Propanediol was oxidized to methyl lactate with a selectivity of 72% at full conversion, while 1,3-propanediol yielded methyl 3-hydroxypropionate with 90% selectivity at 94% conversion. Methyl 3-hydroxy propionate can be easily converted into methyl acrylate, which is then a green polymer building block.
Disparity and texture gradients are combined in a slant estimate and a homogeneity estimate (2005)

Different combinations of depth cues are relevant for different perceptual judgments. For judgments of slant, disparity and texture gradients should be combined in a weighted sum. For judgments of texture homogeneity, the slants specified by disparity and texture should be compared; this can be accomplished by subtracting one from the other. An analogous transformation occurs in color vision where L- and M-cone signals are added in luminance channels and subtracted in color-opponent channels. We asked whether the same occurs with disparity and texture signals. Specifically, are disparity and texture actually combined in a weighted sum for slant estimation and in a subtraction for judging texture homogeneity? And is access to the disparity and texture signals themselves lost in the process? To answer these questions, we presented planes whose slants were defined by disparity and texture gradients. There were three types of trials (conducted in different sessions). 1) 3-interval “oddity”, in which three stimuli were presented, one (or two) at a base slant with no conflict between disparity and texture, and two (or one) with a conflict between disparity and texture (but the same values). Observers indicated the interval containing the “odd” stimulus. 2) 2-interval “slant”, in which two stimuli were presented, one with conflict and one without. Observers indicated the interval containing the greater slant. 3) 2-interval “homogeneity”, in which two stimuli were again presented, one with conflict and one without. Observers indicated the interval containing the texture that was more compressed on one side. The slant and homogeneity thresholds predicted the oddity thresholds. This is consistent with the hypothesis that disparity and texture cues are indeed added to estimate slant and subtracted to estimate texture homogeneity, and that access to the disparity and texture signals themselves is lost in the process
Laparoscopic Replacement of Urinary Tract Segments Using Biodegradable Materials in a Large-Animal Model (1999)

We were able to develop a reliable laparoscopic technique for both segmental ureteral and partial bladder replacement in a porcine model. With AMX and SIS replacement, regeneration of urothelium occurred in both ureter and bladder. However, functional replacement was successful only in the bladder.
Method and apparatus for endoscopic blood flow detection by the use of ultrasonic energy (1989)

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Thermo-Optical Spectrophotometries in Analytical Chemistry (1987)

I. INTRODUCTION A. Background The incorporation of lasers as light sources in analytical spectroscopic instrumentation has resulted in spectacular detection limits. These detection limits arise from several unique properties of laser radiation. As an example, the spectral purity and high power of the laser facilitates detection of individual gas phase atoms with isotopic resolution by both fluorescence and ionization techniques.1−3 The temporal coherence of the laser has been used to discriminate signals generated by very fast scatter processes from relatively slower luminescence relaxation.4, 5 In addition, the spatial coherence of the laser allows measurement by thermo-optical techniques of very small absorbance, the subject of this review. A recent review in this journal considered the related technique of photoacoustic spectroscopy, another high-sensitivity absorbance method.6
The Aurora kinase Ipl1 is necessary for spindle pole body cohesion during budding yeast meiosis (2011)

In budding yeast, the microtubule-organizing center is called the spindle pole body (SPB) and shares structural components with the centriole, the central core of the animal centrosome. During meiotic interphase I, the SPB is duplicated when DNA replication takes place. Duplicated SPBs are linked and then separate to form a bipolar spindle required for homolog separation in meiosis I. During interphase II, SPBs are duplicated again, in the absence of DNA replication, to form four SPBs that establish two spindles for sister-chromatid separation in meiosis II. Here, we report that the Aurora kinase Ipl1, which is necessary for sister-chromatid cohesion, is also required for maintenance of a tight association between duplicated SPBs during meiosis, which we term SPB cohesion. Premature loss of cohesion leads to SPB overduplication and the formation of multipolar spindles. By contrast, the Polo-like kinase Cdc5 is necessary for SPB duplication and interacts antagonistically with Ipl1 at the meiotic SPB to ensure proper SPB separation. Our data suggest that Ipl1 coordinates SPB dynamics with the two chromosome segregation cycles during yeast meiosis.
Targeting Transforming Growth Factor β to Enhance Cancer Immunotherapy (2006)

Human tumours have evolved intricate mechanisms to evade the immune system, either by avoiding recognition or by inhibiting and eliminating immune cells. [...]
Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields (2015)

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.
The Clinical and Endoscopic Spectrum of the Watermelon Stomach (1992)

The watermelon stomach is an uncommon but treatable cause of chronic gastrointestinal bleeding. We report our experience with the clinical and endoscopic features of 45 consecutive patients treated by endoscopic Nd:YAG laser coagulation. The prototypic patient was a woman (71%) with an average age of 73 years (range of 53-89 years) who presented with occult (89%) transfusion-dependent (62%) gastrointestinal bleeding over a median period of 2 years (range of 1 month to > 20 years). Autoimmune connective tissue disorders were present in 28 patients (62%), especially Raynaud's phenomena (31%) and sclerodactyly (20%). Atrophic gastritis occurred in 19 of 19 (100%) patients, with hypergastrinemia in 25 (76%) of 33 patients tested. Antral endoscopic appearances included raised or flat stripes of ectatic vascular tissue (89%) or diffusely scattered lesions (11%). Proximal gastric involvement was present in 12 patients (27%), typically in the presence of a diaphragmatic hernia. Endoscopic laser therapy after a median of one treatment (range of 1-4) resulted in complete resolution of visible disease in four patients (13%) and resolution of > 90% in 24 patients (80%). Hemoglobin levels normalized in 87% of patients over a median follow-up period of 2 years (range of 1 month to 6 years) with no major complications. Blood transfusions were not necessary after laser therapy in 86% of 28 initially transfusion-dependent patients. The characteristic clinical, laboratory, and endoscopic features allow for a confident diagnosis that can lead to successful endoscopic treatment.
Zinc Containing Small‐Pore Zeolites for Capture of Low Concentration Carbon Dioxide (2021)

The capture of low concentration CO<sub>2</sub> presents numerous challenges. Here, we report that zinc containing chabazite (CHA) zeolites can realize high capacity, fast adsorption kinetics, and low desorption energy when capturing ca. 400 ppm CO<sub>2</sub> . Control of the state and location of the zinc ions in the CHA cage is critical to the performance. Zn<sup>2+</sup> loaded onto paired anionic sites in the six-membered rings (6MRs) in the CHA cage are the primary sites to adsorb ca. 0.51 mmol CO<sub>2</sub> /g-zeolite with Si/Al=ca. 7, a 17-fold increase compared to the parent H-form. The capacity is increased further to ca. 0.67 mmol CO<sub>2</sub> /g-zeolite with Si/Al=ca. 2 due to more paired sites for zinc exchange. Zeolites with double six-membered rings (D6MRs) that orient 6MRs into the cages give enhanced uptakes for CO<sub>2</sub> adsorption with zinc exchange. The results reveal that zinc exchanged CHA and several other small pore, cage containing zeolites merit further investigation for the capture of low concentration CO<sub>2</sub> .
cAb-Rep: A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence (2019)

Abstract The diversity of B cell receptors provides a basis for recognizing numerous pathogens. Antibody repertoire sequencing has revealed relationships between B cell receptor sequences, their diversity, and their function in infection, vaccination, and disease. However, many repertoire datasets have been deposited without annotation or quality control, limiting their utility. To accelerate investigations of B cell immunoglobulin sequence repertoires and to facilitate development of algorithms for their analysis, we constructed a comprehensive public database of curated human B cell immunoglobulin sequence repertoires, cAb-Rep ( https://cab-rep.c2b2.columbia.edu ), which currently includes 306 immunoglobulin repertoires from 121 human donors, who were healthy, vaccinated, or had autoimmune disease. The database contains a total of 267.9 million V(D)J heavy chain and 72.9 million VJ light chain transcripts. These transcripts are full-length or near full-length, have been annotated with gene origin, antibody isotype, somatic hypermutations, and other biological characteristics, and are stored in FASTA format to facilitate their direct use by most current repertoire-analysis programs. We describe a website to search cAb-Rep for similar antibodies along with methods for analysis of the prevalence of antibodies with specific genetic signatures, for estimation of reproducibility of somatic hypermutation patterns of interest, and for delineating frequencies of somatically introduced N -glycosylation. cAb-Rep should be useful for investigating attributes of B cell sequence repertoires, for understanding characteristics of affinity maturation, and for identifying potential barriers to the elicitation of effective neutralizing antibodies in infection or by vaccination.
Automatic body localization and brain ventricle segmentation in 3D high frequency ultrasound images of mouse embryos (2018)

This paper presents a fully automatic segmentation system for whole-body high-frequency ultrasound (HFU) images of mouse embryos that can simultaneously segment the body contour and the brain ventricles (BVs). Our system first locates a region of interest (ROI), which covers the interior of the uterus, by sub-surface analysis. Then, it segments the ROI into BVs, the body, the amniotic fluid, and the uterine wall, using nested graph cut. Simultaneously multilevel thresholding is applied to the whole-body image to propose candidate BV components. These candidates are further truncated by the embryo mask (body+BVs) to refine the BV candidates. Finally, subsets of all candidate BVs are compared with pre-trained spring models describing valid BV structures, to identify true BV components. The system can segment the body accurately in most cases based on visual inspection, and achieves average Dice similarity coefficient of 0.8924 ± 0.043 for the BVs on 36 HFU image volumes.
Optimization of diodes using the SPEED concept and CIBH (2011)

The surge current ruggedness of free-wheeling diodes can be improved by implementing the SPEED concept (Self-adjusting P Emitter Efficiency Diode). Experiments show that the switching ruggedness of such a diode is worse than that of a conventional diode. Simulations indicate that during diode turn-off filaments are pinned at the cathode side. These filaments can be avoided by implementing CIBH (Controlled Injection of Backside Holes). It turns out that a necessary additional measure is to fully embed the p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -areas of the SPEED anode in the low-doped p-type area to avoid high electrical field strengths and current crowding at the anode side. Combining these measures, the appearance of current filaments with an extremely high current density and their pinning to a certain area in the device during the turn-off period can be avoided.
CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers (2023)

Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within the noncoding regions. We propose a novel, cancer-specific killing approach using CRISPR-Cas9 which exploits the requirement of a protospacer adjacent motif (PAM) for Cas9 activity. Through whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002), we identified an average of 417 somatic PAMs per tumor produced from single base substitutions. We analyzed 591 paired T-N samples from The International Cancer Genome Consortium and discovered medians of ~455 somatic PAMs per tumor in pancreatic, ~2800 in lung, and ~3200 in esophageal cancer cohorts. Finally, we demonstrated >80% selective cell death of two targeted pancreatic cancer cell lines in co-cultures using 4-9 sgRNAs, targeting noncoding regions, designed from the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs through WGS.
Spin Splitting and Even-Odd Effects in Carbon Nanotubes (1998)

The level spectrum of a single-walled carbon nanotube rope, studied by transport spectroscopy, shows Zeeman splitting in a magnetic field parallel to the tube axis. The pattern of splittings implies that the spin of the ground state alternates by $\frac{1}{2}$ as consecutive electrons are added. Other aspects of the Coulomb blockade characteristics, including the current-voltage traces and peak heights, also show corresponding even-odd effects.
Trapping and mixing of particles in water using a microbubble attached to an NSOM fiber probe (2004)

Low power cw laser radiation at lambda=1.32microm was coupled into a chemically etched,metalized Near-Field Scanning Optical Microscopy (NSOM) fiber probe to generate a stable microbubble in water as well as in other fluids.The microbubble,which was attached to the end face of the fiber probe,was used to trap, manipulate and mix micron sized glass,latex and fluorescent particles as well as biological material.
Structural elements that underlie Doc2β function during asynchronous synaptic transmission (2015)

Double C2-like domain-containing proteins alpha and beta (Doc2α and Doc2β) are tandem C2-domain proteins proposed to function as Ca(2+) sensors for asynchronous neurotransmitter release. Here, we systematically analyze each of the negatively charged residues that mediate binding of Ca(2+) to the β isoform. The Ca(2+) ligands in the C2A domain were dispensable for Ca(2+)-dependent translocation to the plasma membrane, with one exception: neutralization of D220 resulted in constitutive translocation. In contrast, three of the five Ca(2+) ligands in the C2B domain are required for translocation. Importantly, translocation was correlated with the ability of the mutants to enhance asynchronous release when overexpressed in neurons. Finally, replacement of specific Ca(2+)/lipid-binding loops of synaptotagmin 1, a Ca(2+) sensor for synchronous release, with corresponding loops from Doc2β, resulted in chimeras that yielded slower kinetics in vitro and slower excitatory postsynaptic current decays in neurons. Together, these data reveal the key determinants of Doc2β that underlie its function during the slow phase of synaptic transmission.