gebhart/patrepeval huggingface dataset:
The frequency of IGH‐BCL6 translocations in PCNSL is less than that seen in systemic DLBCL, suggesting a distinct pathogenesis (2007)

PCNSL molecular pathogenesis in immunocompetent patients is largely unknown. Small studies suggest a role for immunoglobulin heavy chain (IGH) gene translocations. We studied the incidence of IGH, BCL6, and MYC gene rearrangements in 44 PCNSL affecting immunocompetent patients, diagnosed and treated at Mayo Clinic (1992–2006). All cases were DLBL according to the WHO classification, confined to the CNS. Interphase fluorescence in‐situ hybridization (FISH) was performed using a two‐color IGH‐BCL6 dual‐fusion probe and a two‐color MYC breakapart (BAP) probe on paraffin‐embedded tumor samples. Two‐color BCL6 or IGH BAP FISH probes were also used in cases showing extra FISH signals other than IGH‐BCL6 fusion. Sufficient tumor cells for FISH analysis using the IGH‐BCL6 and MYC probes were available in 43 and 39 cases, respectively. IGH‐BCL6 fusion was present in 6 (14%) cases, one also with a separated MYC signal. Three (7%) cases showed 3 intact BCL6 signals using both the IGH‐BCL6 and BCL6 BAP probes, indicating trisomy 3. One (2%) showed 3 intact IGH signals using both the IGH‐BCL6 and IGH BAP probes, indicating trisomy 14. Remaining 33 (77%) cases lacked abnormalities involving IGH, BCL6 or MYC. IGH‐BCL6 fusion was present in 14% of cases, 1 of which also had a translocation involving MYC and an unknown partner gene. All other cases lacked translocations involving IGH, BCL6, and MYC. The frequency of IGH‐BCL6 translocations in PCNSL is less than that seen in systemic DLBCL. Other translocations involving IGH that are not uncommon in systemic DLBCL, such as IGH‐BCL2 and IGH‐MYC, are rare to absent in PCNSL, suggesting a distinct pathogenesis for PCNSL compared to systemic DLBCL.
Experimental investigation of bare silicon wafer warp (2004)

IC packaging trends demand smaller packaging, which translates to thinner silicon; in some cases as thin as 50um. Thinning below 305um induces significant warp in product/metal wafers, which continues to increases as wafers are thinned further. Increased wafer warp results in handling/processing issues. Studies have been performed on product/metal wafers to characterize warp. These studies have shown a linear relationship between wafer warp and 1/thickness^2. Several factors, in combination, have been shown to contribute to warp in product/metal wafers such as: metal layers, polyimide layers, BCB layers, metal density, thermal stress, tilt direction, front side tension, backside tension, and gravity. The wafer warp phenomenon observed in product/metal wafers is also observed in bare silicon wafers. The difference between bare silicon test wafers and product wafers is the layering of the circuitry side on product/metal wafers, which has shown to be a large contributor to wafer warp. Damage to the wafer backside during conventional grinding can induce a large amount of warp in both product/metal and bare silicon wafers.
Nanosecond, high‐intensity pulsed laser ablation of myocardium tissue at the ultraviolet, visible, and near‐infrared wavelengths: In‐vitro study (2001)

At the laser intensity of approximately 2 GW/cm(2), ablation characteristics were drastically changed for the different laser wavelengths. The results indicated that for 266, 355, and 532 nm, the tissue removal was achieved mainly through a photothermal process, but for 266 nm the intense laser-induced plasma formation would result in a reduced laser energy coupling to the tissue. For 1064 nm, a photodisruption was most probable as a dominant tissue removal process. Because of the high ablation rate and limited thermal denaturation, the 355- and 1064-nm lasers could be potential laser sources for TMLR, although further investigation is needed to discuss the clinical issues.
Central and peripheral pulse wave velocity and subclinical myocardial stress and damage in older adults (2019)

Central stiffness measures showed stronger associations with cardiac biomarkers (particularly NT-proBNP) than peripheral measures among older adults without cardiac disease. Our findings are consistent with the concept of ventricular-vascular coupling and suggest that central rather than peripheral arterial hemodynamics are more closely related to myocardial stress rather than damage.
Determination of patient-specific material properties of cardiovascular tissue through noninvasive measurements (2012)

The mechanical properties of human biological tissue vary greatly. Hence, patient-specific material properties are a must for realistic intra-operative simulations. The determination of arterial material properties should be based on experimental data (i.e. diameter, length, intramural pressure, axial force and stress-free geometry). Currently, clinical data provide only non-invasively measured pressure-diameter data for superficial arteries (e.g. common carotid and femoral artery). To overcome this lack of information, an approach has been proposed taking into account certain assumptions regarding the in situ configuration and stress states of arterial walls [2]. This paper presents a method towards validation of this and other approaches. A finite element model of a simplified artery was used as a mock experimental situation. This method enables exact knowledge of the actual material properties, thereby allowing a qualitative evaluation of the different approaches. The results of the validation show that the material parameters estimated with the noninvasive approaches can deviate quite a lot from the real material properties. Future work is directed towards improving the existing noninvasive parameter estimation approaches.
Condition monitoring of urban rail transit by local energy harvesting (2018)

The goal of this study is to develop a vibration-based electromagnetic energy harvesting prototype that provides power to rail-side monitoring equipment and sensors by collecting wheel-rail vibration energy when the train travels. This technology helps power rail–side equipment in off-grid and remote areas. This article introduces the principle, modeling, and experimental test of the system, including (1) an electromagnetic energy harvesting prototype with DC-DC boost converter and lithium battery charge management function, (2) wireless sensor nodes integrated with accelerometer and temperature/humidity sensor, and (3) a vehicle-track interaction model that considers wheel out-of-roundness. Field test results, power consumption, Littlewood–Paley wavelet transform method, and feasibility analysis are reported. An application case of the technology is introduced: the sensor nodes of the wireless sensor network are powered by the electromagnetic energy harvester and lithium battery with DC-DC boost converter, thereby continuously monitoring the railway track state; based on the Littlewood–Paley wavelet analysis of measured railway track acceleration data, the abnormal signal caused by the wheel out-of-roundness can be detected.
Age-Related Behavioral Phenotype of an Astrocytic Monoamine Oxidase-B Transgenic Mouse Model of Parkinson’s Disease (2013)

We have previously shown that increases in astrocytic monoamine oxidase-B (MAO-B) expression, mimicking that which occurs with aging and in neurodegenerative disease, in a doxycycline (dox)-inducible transgenic mouse model evokes neuropathological similarities to what is observed in the human parkinsonian brain. Additional behavioral and neuropathological studies could provide further validation for its usage as a model for Parkinson's disease (PD). In the present study, we utilized a battery of behavioral tests to evaluate age-related phenotype in this model. In the open field test, we found that dox-induction impaired motor ability with decreases in movement and ambulatory function as well as diminished stereotypical, repetitive movement episodes in both young and old mice. Older mice also showed decreased motor performance in the pole test when compared to younger mice. Furthermore, dox-induced older mice displayed severe hindlimb clasping and the most significant loss of dopamine (DA) in the striatum when compared to young and non-induced animals. Additionally, increased MAO-B activity significantly correlated with decreased expression of striatal DA. The results of our study further confirms that the dox-inducible astrocytic MAO-B transgenic mouse displays similar age-related behavioral and neuropathological features to other models of PD, and could serve as a useful tool to study PD pathophysiology and for the evaluation of therapeutic interventions.
Entropic and Enthalpic Surface Segregation from Blends of Branched and Linear Polymers (1995)

The surface segregation from blends of branched and linear polymers is investigated using Monte Carlo simulation. It is found that in the athermal system an entropic segregation is possible which favors the linear polymers at the surfaces. When an attraction between the polymer beads is introduced the branched polymers are found preferentially at the surface. The simulations provide a simple explanation of recent experimental observations on polyolefin materials in terms of enthalpic effects, but this suggests that the segregation behavior observed in experiments is not universal but should depend on details of fluid-fluid and fluid-surface interactions.
Acoustic-phonetic characteristics of speech produced with communicative intent to counter adverse listening conditions (2011)

This study investigated whether speech produced in spontaneous interactions when addressing a talker experiencing actual challenging conditions differs in acoustic-phonetic characteristics from speech produced (a) with communicative intent under more ideal conditions and (b) without communicative intent under imaginary challenging conditions (read, clear speech). It also investigated whether acoustic-phonetic modifications made to counteract the effects of a challenging listening condition are tailored to the condition under which communication occurs. Forty talkers were recorded in pairs while engaged in "spot the difference" picture tasks in good and challenging conditions. In the challenging conditions, one talker heard the other (1) via a three-channel noise vocoder (VOC); (2) with simultaneous babble noise (BABBLE). Read, clear speech showed more extreme changes in median F0, F0 range, and speaking rate than speech produced to counter the effects of a challenging listening condition. In the VOC condition, where F0 and intensity enhancements are unlikely to aid intelligibility, talkers did not change their F0 median and range; mean energy and vowel F1 increased less than in the BABBLE condition. This suggests that speech production is listener-focused, and that talkers modulate their speech according to their interlocutors' needs, even when not directly experiencing the challenging listening condition.
Double-tilting specimen holder cooled by liquid helium for JEM-4000EX (1992)

For the study of phase transformation and structure change of crystals at low temperature in atomic scale, flowing liquid He specimen cooling holder has been constructed. It was aimed to achieve the low temperature without giving any effects to the resolution and analytical function of JEM-4000EX such as X-ray detection system and goniometer functions. The pole piece of electron lens used in this experiment has the following functions, i.e. Cs=2.88mm Cc=2.69mm f=3.55mm and the resolution is 0.34nm. The present specimen stage can be tilted ±20 degrees to X- and Y-directions inside of this pole piece. In connection of double tilt mechanism and protection of heat loss, double layered bellows are fabricated at the entrance of driving mechanism. At this point every vibrations from outside of the microscope such as from pumping out system of introduced liquid helium (the pipe A in Fig. 1) would be extinguished. This mechanism is fabricated in the vacuum box (marked by B in Fig.1).
Molecular epidemiology of adenoviruses: alternating appearance of two different genome types of adenovirus 7 during epidemic outbreaks in Europe from 1958 to 1980 (1981)

Four genome types of adenovirus serotype 7 (Ad7, Ad7a, Ad7b, and Ad7c) were identified by use of DNA restriction enzymes BamHI, EcoRI, and SmaI. We obtained information on the distribution of the four Ad7 genome types by typing 68 Ad7 isolates obtained in the Netherlands from 1958 to 1979 and 36 Ad7 isolates obtained in Sweden from 1964 to 1980. The Ad7 prototype was never detected, and only seven isolates were genome-typed Ad7a. Ad7b and Ad7c accounted for 94% of the genome-typed isolates obtained from patients. Ad7c was isolated in the Netherlands during 1958 to 1969, but only Ad7b has been detected there since 1970. In Sweden, Ad7c was recovered between 1964 to 1972, but only Ad7b has been isolated there since 1973. In conclusion, the newly recognized Ad7b and Ad7c genome types, which in the Netherlands and Sweden represent virtually all genome-typed isolates from patients, show a mutually exclusive appearance.
Targeting AKT elicits tumor suppressive functions of FOXO transcription factors and GSK3 kinase in Multiple Myeloma (2019)

ABSTRACT The phosphatidylinositide-3 kinases (PI3K) and the downstream mediator AKT drive survival and proliferation of multiple myeloma (MM) cells and several AKT inhibitors are currently being tested in clinical trials for MM patients. AKT inhibition has pleiotropic effects, and the key aspects that determine therapeutic efficacy are not fully clear. Therefore, we investigated the antimyeloma mechanism(s) of AKT inhibition. Among the various downstream AKT targets are Forkhead box O (FOXO) transcription factors, and we demonstrate that they are crucial for changes in gene expression upon AKT inhibition. Based on gene expression profiling we defined an AKT-induced FOXO-dependent gene set that has prognostic significance in a large cohort of MM patients, where low FOXO activity correlates with inferior survival. We show that cell cycle exit and cell death of MM cells after AKT inhibition required FOXO. In addition, glycogen synthase kinase 3 (GSK3), a negatively regulated AKT substrate, proved to be pivotal to induce cell death and to inhibit cell cycle progression after AKT inhibition. Finally, we demonstrate that FOXO and GSK3 induced cell death by increasing the turnover of the myeloid cell leukemia 1 (MCL1) protein. In concordance, the AKT inhibitor MK2206 greatly sensitized MM cells for the MCL1 inhibitor S63845. Thus, our results indicate that FOXO and GSK3 are crucial mediators of the antimyeloma effects of AKT inhibition, and suggest combination therapies that may have therapeutic potential in MM. KEYPOINTS FOXO transcription factors and the GSK3 kinase are pivotal tumor suppressors downstream of AKT inhibition in MM cells. FOXO and GSK3 activation after AKT inhibition leads to a decrease in MCL1 levels in MM cells resulting in cell death.
Dependency Networks for Relational Data (2005)

Instance independence is a critical assumption of traditional machine learning methods contradicted by many relational datasets. For example, in scientific literature datasets, there are dependencies among the references of a paper. Recent work on graphical models for relational data has demonstrated significant performance gains for models that exploit the dependencies among instances. In this paper, we present relational dependency networks (RDNs), a new form of graphical model capable of reasoning with such dependencies in a relational setting. We describe the details of RDN models and outline their strengths, most notably the ability to learn and reason with cyclic relational dependencies. We present RDN models learned on a number of real-world datasets, and evaluate the models in a classification context, showing significant performance improvements. In addition, we use synthetic data to evaluate the quality of model learning and inference procedures.
Inhibition of the Defense System Stimulating Interleukin-12 Interferon-γ Pathway During Critical Illness (1997)

Interleukin-12 (IL-12) and interferon-γ (IFN-γ) exert protective effects during experimental endotoxemia through upregulation of cellular immunity and phagocytic functions. They are part of a positive regulatory feedback loop that enhances the production of the other. Because critically ill patients show a marked suppression of T-cell and macrophage functions with a high susceptibility to infection, potential defects in the immunity/inflammation upregulating IL-12 IFN-γ pathway were studied. As an ex vivo model of endotoxemia, lipopolysaccharide (LPS) stimulated whole blood from 25 critically ill patients and 12 healthy individuals was incubated with either recombinant human (rh) IL-12 or rhIFN-γ, respectively. IFN-γ dose-dependently (P &lt; .05) increased the release of IL-12 p40 and p70 into LPS-stimulated whole blood from healthy humans without effect in whole blood from critically ill patients. RhIL-12 p70 enhanced (P &lt; .05) the secretion of IFN-γ in controls, while it was ineffective in LPS-stimulated whole blood from critically ill patients. The observed inhibition of the IL-12 IFN-γ pathway is not specific to LPS, since Staphylococcus aureus Cowan strain I (SAC)-stimulated whole blood from critically ill patients showed similar suppression. The secretion of IL-12 and IFN-γ was less reduced in critically ill patients when using isolated cultures of adherent cells or lymphocytes. Although preculture of whole blood from healthy humans with IL-10, but not with IL-4, mimicked suppression of the IL-12 IFN-γ pathway similar to that observed during critical illness, the release of antiinflammatory reacting cytokines (IL-4, IL-10, transforming growth factor [TGF]-β1 ) was decreased into LPS-stimulated whole blood from critically ill patients. These results indicate at least two mechanisms responsible for dramatic disturbances of the IL-12 IFN-γ pathway during critical illness: (1) deactivation of IL-12 and IFN-γ producing leukocytes in vivo early after the primary insult, and (2) presence of serum suppressive factors different from IL-4, IL-10, or TGF-β1 . Because IL-12 and IFN-γ upregulate essential immune functions, the marked inhibition of IL-12 and IFN-γ release may be pivotal for high susceptibility of critically ill patients to infection.
Blueprint for the Intercloud - Protocols and Formats for Cloud Computing Interoperability (2009)

Cloud computing is a term applied to large, hosted datacenters, usually geographically distributed, which offer various computational services on a ldquoutilityrdquo basis. Most typically the configuration and provisioning of these datacenters, as far as the services for the subscribers go, is highly automated, to the point of the service being delivered within seconds of the subscriber request. Additionally, the datacenters typically use hypervisor based virtualization as a technique to deliver these services. The concept of a cloud operated by one service provider or enterprise interoperating with a clouds operated by another is a powerful idea. So far that is limited to use cases where code running on one cloud explicitly references a service on another cloud. There is no implicit and transparent interoperability. Use cases for interoperability, as well as work-in-progress around inter-cloud protocols and formats for enabling those use cases, are discussed in this paper.
Abstract S02-02: Covid-19 treatment candidate hydroxychloroquine impairs tumor response to anti-PD1 (2020)

Abstract Background and Aims: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a worldwide health crisis. As of now, only one treatment has been established for the coronavirus infection disease 2019 (Covid-19), which has disproportionally affected patients with comorbidities such as cancer. Hydroxychloroquine (HCQ) has been studied as a potential treatment for Covid-19. Here we studied whether HCQ treatment could influence the effect of immunotherapy against colorectal and liver cancer. Methods: In vitro studies were conducted to assess the effect of HCQ on lymphocyte activation and proliferation as well as cell growth and antigen presentation. Mouse cell lines used included MC38, CT26, RIL-175, SB1, and LD1 while human tumor cell lines used were TFK-1 and EGI-1. Mice bearing subcutaneous MC38, CT26, and RIL-175 tumors were treated with HCQ, anti-PD1, or both. Tumor volume was measured over 19 days. Systemic and tumor-infiltrating immune cells were analyzed by flow cytometry. Results: HCQ treatment impairs T-cell production of TNF-α and IFNγ in vitro and in vivo. Whereas cell growth was decreased in all tumor cell lines, in vitro treatment of tumor cells with HCQ revealed an upregulation of MHC-1 in CT26, SB1, LD1, TFK-1, and EGI-1 but not in MC38 and RIL-175. HCQ treatment impaired response to anti-PD1 treatment in all subcutaneous models. Compared to control, HCQ treatment led to increased tumor growth in MC38 tumors. Flow cytometry analysis revealed an impaired activation of CD4+ T cells as well as tumor-infiltrating cytotoxic antigen-specific CD8+ T cells. Conclusion: This study shows that HCQ treatment can result in immunotherapy failure due to a systematic immunosuppressive effect that overcomes the increased MHC expression on tumor cells. Citation Format: Simon Wabitsch, Jack C McVey, Chi Ma, Benjamin Ruf, Laurence Diggs, Bernd Heinrich, Tim F Greten. Covid-19 treatment candidate hydroxychloroquine impairs tumor response to anti-PD1 [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr S02-02.
Coaggregation between and among human intestinal and oral bacteria (2008)

Coaggregation is believed to facilitate the integration of new bacterial species into polymicrobial communities. The aim of this study was to investigate coaggregation between and among human oral and enteric bacteria. Stationary phase cultures of 10 oral and 10 enteric species, chosen on the basis of numerical and ecological significance in their respective environments together with their ease of cultivation, were tested using a quantitative spectrophotometric coaggregation assay in all possible pairwise combinations to provide quantitative coaggregation scores. While 40% of possible partnerships coaggregated strongly for oral strains, strong interactions between oral and gut strains were considerably less common (4% incidence). Coaggregation scores were also weak between members of the intestinal microbiota (7% incidence), apart from Bacteroides fragilis with Clostridium perfringens, and Bifidobacterium adolescentis with C. perfringens. Oral and intestinal bacteria did not strongly interact, apart from B. adolescentis with Fusobacterium nucleatum, Actinomyces naeslundii with C. perfringens and F. nucleatum with Lactobacillus paracasei. Heating and sugar-addition experiments indicated that similar to oral microorganisms, interactions within intestinal bacteria and between intestinal and oral strains were mediated by lectin-carbohydrate interactions. © 2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.