gebhart/patrepeval huggingface dataset:
Interspecies Chimeric Conditions Affect the Developmental Rate of Human Pluripotent Stem Cells (2020)

ABSTRACT Human pluripotent stem cells hold significant promise for regenerative medicine. However, long differentiation protocols and immature characteristics of stem cell-derived cell types remain challenges to the development of many therapeutic applications. In contrast to the slow differentiation of human stem cells in vitro that mirrors a nine-month gestation period, mouse stem cells develop according to a much faster three-week gestation timeline. Here, we tested if co-differentiation with mouse pluripotent stem cells could accelerate the differentiation speed of human embryonic stem cells. Following a six-week RNA-sequencing time course of neural differentiation, we identified 929 human genes that were upregulated earlier and 535 genes that exhibited earlier peaked expression profiles in chimeric cell cultures than in human cell cultures alone. Genes with accelerated upregulation were significantly enriched in Gene Ontology terms associated with neurogenesis, neuron differentiation and maturation, and synapse signaling. Moreover, chimeric mixed samples correlated with in utero human embryonic samples earlier than human cells alone, and acceleration was dose-dependent on human-mouse co-culture ratios. Differences in the timing and expression levels of genes corresponding to neuron cell types and brain region identity under chimeric conditions were also observed. The altered developmental rates and lineage outcomes described in this report have implications for accelerating human stem cell differentiation and the use of interspecies chimeric embryos in developing human organs for transplantation. Author Summary Human pluripotent stem cells often require long in vitro protocols to form mature cell types of clinical relevance for potential regenerative therapies, a ramification of a nine-month developmental clock in utero that also runs ex utero . What controls species-specific developmental time and whether the timer is amenable to acceleration is unknown. Further, interspecies chimeric embryos are increasingly being created to study early human development or explore the potential growth of human organs for transplantation. How the conflicting developmental speeds of cells from different species co-differentiating together affect each other is not understood. Here, using genome-wide transcriptional analysis of RNA-sequencing time courses, we show that 1) co-differentiating human embryonic stem cells intermixed with mouse stem cells accelerated elements of human developmental programs, 2) the acceleration was dose-dependent on the proportion of mouse cells, and 3) human cells in chimeric samples correlated to in utero samples earlier than human only samples. Our results provide evidence that some components of species-specific developmental clocks may be susceptible to acceleration.
Tau Phosphorylation by Cyclin-dependent Kinase 5/p39 during Brain Development Reduces Its Affinity for Microtubules (2003)

The microtubule-associated protein tau is a developmentally regulated neuronal phosphoprotein. The phosphorylation of tau reduces its ability to bind and stabilize axonal microtubules during axonal growth. Although tau is phosphorylated by cyclin-dependent kinase 5 (Cdk5) in vitro, its in vivo roles remain unclear. Here, we show that tau is phosphorylated by Cdk5/p39 during brain development, resulting in a reduction of its affinity for microtubules. The activity of Cdk5 is tightly regulated by association with its neuronal activators, p35 or p39. The p35 and p39 expression levels were investigated in the developing mouse brain; the p39 expression level was higher in embryonic hind brain and spinal cord and in postnatal cerebral cortex, whereas that of p35 was most prominent in cerebral cortex at earlier stages of development. The ability of Cdk5 to phosphorylate tau was higher when in association with p39 than in association with p35. Tau phosphorylation at Ser-202 and Thr-205 was decreased in Cdk5/ mouse brain but not in p35/ mouse brain, suggesting that Cdk5/p39 is responsible for the in vivo phosphorylation of tau at these sites. Our data suggest that tau phosphorylation by Cdk5 may provide the neuronal microtubules with dynamic properties in a region-specific and developmentally regulated manner.
Development of a Novel Proteomic Approach for Mitochondrial Proteomics from Cardiac Tissue from Patients with Atrial Fibrillation (2011)

Atrial fibrillation (AF) is the most common cardiac arrhythmia affecting approximately 2.2 million Americans. Because several studies have suggested that changes in mitochondrial function and morphology may contribute to AF, we developed a novel proteomic workflow focused on the identification of differentially expressed mitochondrial proteins in AF patients. Right human atrial tissue was collected from 20 patients, 10 with and 10 without AF, and the tissue was subjected to hydrostatic pressure cycling-based lysis followed by label-free mass spectrometric (MS) analysis of mitochondrial enriched isolates. Approximately 5% of the 700 proteins identified by MS analysis were differentially expressed between the AF and non-AF samples. We chose four differentially abundant proteins for further verification using reverse phase protein microarray analysis based on their known importance in energy production and regulatory association with atrial ion channels: four and a half LIM, destrin, heat shock protein 2, and chaperonin-containing TCP1. These initial study results provide evidence that a workflow to identify AF-related proteins that combines a powerful upfront tissue cell lysis with high resolution MS for discovery and protein array technology for verification may be an effective strategy for discovering candidate markers in highly fibrous tissue samples.
Direct linkage of EGF to its receptor: Characterization and biological relevance (1980)

A small portion of the 125I-EGF that binds specifically to intact cells or isolated membrane from a variety of sources becomes directly and irreversibly linked to EGF receptors. This provides a simple technique for affinity labeling the EGF receptor. Membranes isolated from the human epidermoid carcinoma cell line A431, which possesses extraordinarily high numbers of EGF receptors, gave rise to three major direct linkage complexes of MW = 160,000, 145,000, and 115,000. The time course for information of each is similar, showing that 125I-EGF can form direct linkage complexes with several preexisting forms of the EGF receptor. The direct linkage of EGF to receptor is slow in comparison to 125I-EGF binding, but both processes have similar susceptibilities to competition by unlabeled EGF. EGF was modified chemically with the amino site-specific reagent, N-hydroxysuccinimidyl biotin. The biotinyl-EGF had a reduced capacity to engage in direct linkage complex formation with no concomitant reduction in its ability to bind to EGF receptors. Since native and biotinyl EGF have identical abilities to stimulate the uptake of 3H-thymidine into DNA when incubated with cultured murine 3T3 cells, the direct linkage of EGF to its receptor does not appear to play an important role in EGF-stimulated mitogenesis.
The Row and Column Spaces of S (2006)

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Studies on the ability of hemodialysis membranes to induce, bind, and clear human interleukin-1. (1988)

Interleukin-1 (IL-1) is a polypeptide cytokine predominantly produced by monocytes in response to injury or infection. Effects of IL-1 such as fever, acute phase protein synthesis, hypotension, and loss of body mass are complications of hemodialysis. Endotoxin-contaminated dialysate fluid, sodium acetate as a dialysate buffer, and activated complement can induce IL-1 during hemodialysis. In the present study, we investigated the intrinsic property of hemodialysis membranes to stimulate human blood mononuclear cells (MNC) to produce IL-1. Incubation of MNC on sheets of two commonly used hemodialysis membranes, regenerated cellulose (RC) and polyacrylonitrile (PAN) resulted in significant induction of IL-1 in the absence of endotoxin or complement. Production of intracellular and extracellular IL-1 was greater in MNC exposed to PAN compared with RC (p less than 0.01). Similar results were obtained when MNC were exposed to strips of hemodialysis membranes in rotating tubes. However, compared with RC, PAN binds significant amounts of human IL-1. In a model of in vitro hemodialysis, radiolabeled recombinant human IL-1 was added to the blood compartment of a PAN and a RC dialyzer. Forty percent of radiolabeled IL-1 bound to the PAN dialyzer membrane compared with 10% to the membrane of a RC dialyzer. In addition, 22% of radiolabeled IL-1 was found in the dialysate compartment of a PAN dialyzer after 1 hour whereas 1% was found in the dialysate side of a RC dialyzer; these results were confirmed by measuring bioactivity of IL-1. These studies demonstrate the intrinsic property of hemodialysis membranes to stimulate human IL-1 production; in addition they establish that dialysis membranes differ in their ability to bind and clear IL-1.
Composite fuselage crown panel manufacturing technology (1992)

Commercial fuselage structures contain significant challenges in attempting to save manufacturing costs with advanced composite technology. Assembly issues, material costs, and fabrication of elements with complex geometry are each expected to drive the cost of composite fuselage structures. Boeing's efforts under the NASA ACT program have pursued key technologies for low-cost, large crown panel fabrication. An intricate bond panel design and manufacturing concepts were selected based on the efforts of the Design Build Team (DBT). The manufacturing processes selected for the intricate bond design include multiple large panel fabrication with the Advanced Tow Placement (ATP) process, innovative cure tooling concepts, resin transfer molding of long fuselage frames, and utilization of low-cost material forms. The process optimization for final design/manufacturing configuration included factory simulations and hardware demonstrations. These efforts and other optimization tasks were instrumental in reducing cost by 18 percent and weight by 45 percent relative to an aluminum baseline. The qualitative and quantitative results of the manufacturing demonstrations were used to assess manufacturing risks and technology readiness.
Nanoparticles for Imaging and Tumor Gene Delivery (2008)

Molecular imaging of receptors expressed on the surface of tumor cells is becoming a major field of investigation in clinical oncology, especially for the detection of cancer at its earliest stages. Nowadays, MRI, microcomputed tomography (microCT), ultrasound, positron emission tomography (PET), optical coherence tomography (OCT), and other major imaging systems are available to scientists and clinicians. Each technique has advantages and limitations, thus making them complementary. We report herein our investigations on the synthesis and use of new probes for small animal imaging as well as on the preparation and use of targeting complexes to deliver specific gene in tumors cells.
Digital filter design for a PAL TV modulator (2003)

This paper develops a multirate digital filter design for the vestigial sideband (VSB) modulator required in the analog TV transmission systems, like PAL. The design is based on a complex baseband VSB filter running at 13.5 MHz sampling rate, digital multirate techniques for increasing the sampling rate by the factor of 9, and a combination of multirate techniques and digital mixing to translate the signal to the 38.9 MHz IF picture carrier frequency.
Study about FZ/MCZ Si Wafer (Mother) Material Carbon and Oxygen density for RC-IGBT with Electron Beam Irradiation Based on Electrical and Physical Analysis (2021)

In this paper, the electric characteristics and DLTS profiles of 600V RC-IGBT (Reverse Conducting Insulated Gate Bipolar Transistor) with electron beam (EB) irradiation are compared in order to investigate the influence of wafer materials. Floating Zone (FZ) and Magnetic Czochralski (MCZ) wafers with various kinds of carbon (C) and oxygen (O) concentration are evaluated. O concentration does not have a clear impact on V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CEsat</sub> . In contrast, C concentration has a clear tendency. DLTS analysis shows that C concentration affects the degree of Si defects induced by EB irradiation which results in the differences of the electric characteristics.
IBM Research Division cloud computing initiative (2009)

Cloud computing represents the latest phase in the evolution of Internet-based computing. In this paper, we describe the fundamental building blocks of cloud computing and the initiative undertaken by the IBM Research Division in this area, which includes work on Internet-scale data centers, virtualization, scalable storage, and cloud computing services. The focus of this project has been the Research Compute Cloud, an environment for cloud computing research that is also used as a computing resource by various groups in the IBM Research Division.
Virtualized Traffic at Metropolitan Scales (2015)

Few phenomena are more ubiquitous than traffic, and few are more significant economically, socially, or environmentally. Any virtual reality system, including virtual globes and immersive multi-player worlds that are set in a modern or futuristic setting feature traffic systems. Virtual reality models can also aid in addressing the challenges of real-world traffic systems, the ever-present gridlock and congestion in cities worldwide: traffic engineers and planners can diagnose system instabilities and explore control strategies in virtual worlds reconstructed from available sensor data. To create these systems, road network models need to be created and represented. Traffic needs to be realistically and efficiently simulated. To analyze real-world scenarios, the traffic conditions need to be estimated and reconstructed. To create virtual scenarios, such as simulated cities, traffic needs to be intelligently and efficiently routed.
Pre-Columbian Mesoamerican and Caribbean Ballgames: An Example of Cultural Diffusion (2012)

Upon examining the archaeological record and the historical accounts of&#13;\npre-Columbian cultures in Mesoamerica and in the islands of the Caribbean Sea, one&#13;\nsees evidence of similar ballgames played in both regions. The question then arises,&#13;\nwhen the geographical and chronological proximity of these cultures is considered,&#13;\nwhether these games developed separately, or whether their existence was a product&#13;\nof cultural diffusion. Drawing on insights from archaeology and geography, I argue&#13;\nthat there is a connection between Mesoamerican ballgames and those played in&#13;\nthe Caribbean. I prove this connection between the two cultures by establishing&#13;\nwhere and when the ballgame originated, showing when the ballgame arrived in&#13;\nthe Caribbean, examining the similarities between the ballgames played in the two&#13;\nregions, and considering whether there is incontrovertible evidence of contact between&#13;\nthem. I conclude by addressing what such an intercultural exchange signifies for our&#13;\nunderstanding of pre-Columbian cultures.
Autonomous biomimetic solid dispensing using a dual-arm robotic manipulator (2023)

An automated solid dispenser was developed using a dual-arm robot and fuzzy logic controller, mimicking the operations of human researchers.
High and Low Molecular Weight Fluorescein Isothiocyanate (FITC)–Dextrans to Assess Blood-Brain Barrier Disruption: Technical Considerations (2010)

This note is to report how histological preparation techniques influence the extravasation pattern of the different molecular sizes of fluorescein isothiocyanate (FITC)-dextrans, typically used as markers for blood-brain barrier leakage. By using appropriate preparation methods, false negative results can be minimized. Wistar rats underwent a 2-h middle cerebral artery occlusion and magnetic resonance imaging. After the last imaging scan, Evans blue and FITC-dextrans of 4, 40, and 70 kDa molecular weight were injected. Different histological preparation methods were used. Sites of blood-brain barrier leakage were analyzed by fluorescence microscopy. Extravasation of Evans blue and high molecular FITC-dextrans (40 and 70 kDa) in the infarcted region could be detected with all preparation methods used. If exposed directly to saline, the signal intensity of these FITC-dextrans decreased. Extravasation of the 4-kDa low molecular weight FITC-dextran could only be detected using freshly frozen tissue sections. Preparations involving paraformaldehyde and sucrose resulted in the 4-kDa FITC-dextran dissolving in these reactants and being washed out, giving the false negative result of no extravasation. FITC-dextrans represent a valuable tool to characterize altered blood-brain barrier permeability in animal models. Diffusion and washout of low molecular weight FITC-dextran can be avoided by direct immobilization through immediate freezing of the tissue. This pitfall needs to be known to avoid the false impression that there was no extravasation of low molecular weight FITC-dextrans.
Colon Cancer Associated Transcript-1 (CCAT1) Expression in Adenocarcinoma of the Stomach (2014)

CCAT1 is up-regulated in gastric cancer, and may serve as a potential bio-marker for early detection and surveillance.
A Rate Splitting Strategy for Mitigating Intra-Cell Pilot Contamination in Massive MIMO (2020)

The spectral efficiency (SE) of Massive MIMO (MaMIMO) systems is affected by low quality channel estimates. Rate-Splitting (RS) has recently gained some interest in multiuser multiple antenna systems as an effective means to mitigate the multi-user interference due to imperfect channel state information. This paper investigates the benefits of RS in the downlink of a single-cell MaMIMO system when all the users use the same pilot sequence for channel estimation. Novel expressions for the SE achieved in the downlink by a single-layer RS strategy (that relies on a single successive interference cancellation at each user side) are derived and used to design precoding schemes and power allocation strategies for common and private messages. Numerical results are used to show that the proposed RS solution achieves higher spectral efficiency that conventional MaMIMO with maximum ratio precoding.
A pilot study of the Earable device to measure facial muscle and eye movement tasks among healthy volunteers (2022)

Many neuromuscular disorders impair function of cranial nerve enervated muscles. Clinical assessment of cranial muscle function has several limitations. Clinician rating of symptoms suffers from inter-rater variation, qualitative or semi-quantitative scoring, and limited ability to capture infrequent or fluctuating symptoms. Patient-reported outcomes are limited by recall bias and poor precision. Current tools to measure orofacial and oculomotor function are cumbersome, difficult to implement, and non-portable. Here, we show how Earable, a wearable device, can discriminate certain cranial muscle activities such as chewing, talking, and swallowing. We demonstrate using data from a pilot study of 10 healthy participants how Earable can be used to measure features from EMG, EEG, and EOG waveforms from subjects performing mock Performance Outcome Assessments (mock-PerfOs), utilized widely in clinical research. Our analysis pipeline provides a framework for how to computationally process and statistically rank features from the Earable device. Finally, we demonstrate that Earable data may be used to classify these activities. Our results, conducted in a pilot study of healthy participants, enable a more comprehensive strategy for the design, development, and analysis of wearable sensor data for investigating clinical populations. Additionally, the results from this study support further evaluation of Earable or similar devices as tools to objectively measure cranial muscle activity in the context of a clinical research setting. Future work will be conducted in clinical disease populations, with a focus on detecting disease signatures, as well as monitoring intra-subject treatment responses. Readily available quantitative metrics from wearable sensor devices like Earable support strategies for the development of novel digital endpoints, a hallmark goal of clinical research.
Temperature dependent characteristics of 0.98-μm strained-quantum-well lasers (1994)

Semiconductor lasers emitting in the 0.98-μm wavelength regime are promising for pumping optical fiber amplifiers and solid-state lasers. Although the short wavelength lasers are typically observed to have a high characteristic temperature T o , their differential efficiencies often decrease rapidly with temperature increase, which can cause serious problems in many applications. In this work, we investigate the physical causes of this temperature dependence experimentally as well as theoretically with buried heterostructure InGa As / InGaAsP / InGaP strained quantum well lasers. Laser bars of various cavity lengths were measured at temperatures between 10°C to 160°C. Testing unbonded laser bars allows us to perform measurements of many lasers with similar conditions. Thus, effects due to unintentional variations from fabrication or cleaving can be eliminated.
Social and Regional Innovation Activities Based on the Joint Research Laboratories Embedded in the University (2022)

In order to solve complex societal issues that exist in community and to revitalize the community, it is effective to have universities and companies work closely together, and to involve local governments and citizens. We have established joint research centers within universities and are working with the university and local community to understand the issues, develop the necessary technologies, create solutions, and demonstrate the solutions in local fields. In this paper, we will introduce our work in Takaharu Town, Miyazaki Prefecture, with Kyoto University and in Iwamizawa City, Hokkaido, with Hokkaido University, regarding the use of decentralized local energy.
Spatial Characterization of Holographic MIMO Channels. (2019)

Imagine an array with a massive (possibly uncountably infinite) number of antennas in a compact space. We refer to a system of this sort as Holographic MIMO. Given the impressive properties of Massive MIMO, one might expect a holographic array to realize extreme spatial resolution, incredible energy efficiency, and unprecedented spectral efficiency. At present, however, its fundamental limits have not been conclusively established. A major challenge for the analysis and understanding of such a paradigm shift is the lack of mathematically tractable and numerically reproducible channel models that retain some semblance to the physical reality. Detailed physical models are, in general, too complex for tractable analysis. This paper aims to take a closer look at this interdisciplinary challenge. Particularly, we consider the small-scale fading in the far-field, and we model it as a zero-mean, spatially-stationary, and correlated Gaussian scalar random field. Physically-meaningful correlation is obtained by requiring that the random field be consistent with the scalar Helmholtz equation. This formulation leads directly to a rather simple and exact description of the three-dimensional small-scale fading as a Fourier plane-wave spectral representation. Suitably discretized, this leads to a discrete representation for the field as a Fourier plane-wave series expansion, from which a computationally efficient way to generate samples of the small-scale fading over spatially-constrained compact spaces is developed. The connections with the conventional tools of linear systems theory and Fourier transform are thoroughly discussed.