gebhart/patrepeval huggingface dataset:
Suppression of Interleukin-11-mediated bone resorption by cyclooxygenases inhibitors (1998)

We previously found that human melanoma (A375M) and human breast cancer (MDA-MB-231) cells formed osteolytic bone metastasis in vivo. These cancer cells produced interleukin-11 (IL-11) by themselves and stimulated its production from osteoblasts. Interleukin-11 could increase the number of osteoclasts and raise the calcium concentration in the medium of neonatal murine calvaria organ culture, indicating bone resorption in vitro. Therefore, IL-11 could play an important role in the promotion of osteolysis at the site of bone metastasis. In the present study, we used the calvaria culture system to try to clarify the mechanisms of IL-11–mediated bone resorption. The murine calvaria expressed both the specificity-determining α subunit and the signal–transducing β subunit (gp130) of the IL-11 receptor. When IL-11 was added to the calvaria culture, the concentrations of prostaglandin E2 (PGE2) was elevated. Pretreatment of calvaria with cyclooxygenases inhibitors (e.g., indomethacin, NS-398, and dexamethasone) suppressed the production of PGE2 and the bone resorption induced by IL-11. Addition of exogenous PGE2 overcame the inhibitory effect of cyclooxygenases inhibitors and promoted bone resorption. These results indicate that IL-11 promotes bone resorption through a PGE2 synthesis–dependent mechanism and that cyclooxygenases inhibitors could be interesting drugs to suppress IL-11–mediated osteolytic bone metastasis of cancer cells. J. Cell. Physiol. 175:247–254, 1998. © 1998 Wiley-Liss, Inc.
Development of Working Life Competencies in a Project Course for Master Students at Aalto University (2019)

Education programmes are expected to fulfil many requirements in the uncertain environment that constitutes the beginning of the 21st century. Whilst the transmission of content, the development of comprehension and analytical skills, and specific skills related to a particular discipline are still valid, it is vital to equip students for working in groups that may be diverse, situations that may be challenging, and in a work environment that is changing at an increasing rate. Attempting to rise to these challenges, this article focuses on team and multicultural working life skills, utilising a survey and group interviews of masters students in the Department of Electrical Engineering and Automation at Aalto University, who are required to participate in a recently introduced 10 ECTS project-based course. The groups were formed in terms of their suitability to perform project tasks given by research groups in the department. The efficacy of such purposive grouping of students is assessed in terms of 26 skills, adapted from the national-level TEK (Academic Engineers and Architects in Finland) feedback survey for engineering 2016 graduates, with a deeper focus on two of these competencies, skills related to the international work environment and team working.
Altun Khan (1967)

Though the linguistic interest for Indo-Iranian predominates in the study of the texts from Gostana-dea (Khotan), the contents offer also considerable materials for closer understanding of pre-Muslim Chinese Turkistan in Central Asia.
Student Performance Data and Research Tools to Ensure Aboriginal Student Success (2004)

What Kind of Data Does the Ministry of Education Collect?The Ministry of Education collects data and compiles it into K-12 standard reports that are made available to the public.These data include demographic information, Foundation Skills Assessment results, Grade 12 graduation rates and satisfaction results.The Ministry uses student-level data to produce a report entitled How Are We Doing? which focuses specifically on Aboriginal student performance for those students enrolled in public schools
Proteomics beyond trypsin (2015)

Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome.
Computational Design of Durable Spherical Nanoparticles with Optimal Material, Shape, and Size for Ultrafast Plasmon-Enhanced Nanocavitation (2016)

Photons interaction with metallic nanoparticles can excite a resonant plasmon that concentrates energy at the nanoscale. At high intensity, this quasi-particle decays into a photoexcited nanoplasma that triggers the generation of nanobubbles, which can be used for imaging and therapeutic purposes. This highly nonlinear wavelength-dependent process is controlled by the nanoparticle material, shape, and size in intricate ways, which justifies the need for a systematic design approach that currently lacks in the field. To palliate to this, we developed in this work a computational framework that enables the efficient in silico screening of large libraries of spherically symmetric structures and metallic materials. Using this framework, we have investigated the nanocavitation performance of spherical nanoparticles with more than 14 million combinations of materials, shapes, sizes, and irradiation conditions, from which we could distill general principles for the design of durable nanoantennas. In the near-infrared, our work suggests that Cu, TiN, Ag, and Au nanoparticles offer similar performance, with optimal diameters of ∼λ/5. In contrast, only Ag and Al are appropriate for irradiation in the UV–visible, cavitation being associated with structural damage for all other tested materials at these wavelengths. We also demonstrate that silica-metal nanoshell structures have the potential to reduce the cavitation threshold at all wavelengths compared to homogeneous nanoparticles due to their extensive spectral tunability. However, designing more complex layered systems seems to bring no benefit. Our work provides important physical insight on the influence of materials on nanocavitation and simulation-based design guidelines that should be broadly useful for the engineering of nonlinear nanoplasmonic materials for biological applications.
Dimer crystallization of chiral proteoids (2017)

Proteins can self-assemble into a variety of exquisitely organized structures through hierarchical reaction pathways. To examine how different core shapes of proteins and entropy combine to influence self-assembly, we create systems of lithographically fabricated proteomimetic colloids, or 'proteoids', and explore how Brownian monolayers of mobile proteoids, which have hard interactions, self-assemble as they are slowly crowded. Remarkably, chiral C-shaped proteoids having circular heads on only one side form enantiopure lock-and-key chiral dimers; these dimers have corrugated, shape-complementary perimeters, so they, in turn, form lock-and-key arrangements into chiral dimer crystals. Time-lapse video microscopy reveals the expulsion of monomers from the growing dimer crystals through tautomerization translocation reactions which expedite the crystallization kinetics. By lithographically mutating proteoids, we also tune the types and structures of the resulting dimer crystals. Thus, rational design of sub-particle features in hard-core colloidal shapes can be used to sterically select desired self-assembly pathways without introducing any site-specific attractions, thereby generating a striking degree of hierarchical self-ordering, reminiscent of protein crystallization.
In situ-grown carbon nanotube array with excellent field emission characteristics (2000)

In situ catalytic thermal decomposition method was used for producing aligned multiwalled carbon nanotubes (MWNTs) in bulk quantities on stable and electrically conducting substrates. Very low turn-on electric fields of 0.75 V/μm and low threshold fields of ∼1.6 V/μm (for current density of 10 mA/cm2) were obtained from the MWNT arrays grown on TiN substrate. Furthermore, large emission current densities of 1–3 A/cm2 were obtained at reasonably low fields of less than ∼8 V/μm. These enhanced emission properties are tentatively attributed to the oriented and high-density nature of the emitting carbon nanotube structure and the high-conductivity, stable nature of the TiN substrate onto which the nanotubes are attached.
Subclinical impairment of dynamic left ventricular systolic and diastolic function in patients with obstructive sleep apnea and preserved left ventricular ejection fraction (2020)

Evaluation of diastolic function and myocardial deformation during exercise is feasible through stress echocardiography. OSA patients with preserved LVEF show subclinical LV systolic dysfunction, impaired LV systolic and diastolic reserve, reduced exercise tolerance, and increased peripheral levels of OB. Therapy aimed at increasing LV diastolic function reserve might improve the quality of life and exercise tolerability in OSA patients.
Plane-based Accurate Registration of Real-world Point Clouds (2021)

Traditional 3D point clouds registration algorithms, based on Iterative Closest Point (ICP), rely on point matching of large point clouds. In well-structured environments, such as buildings, planes can be segmented and used for registration, similarly to the classical point-based ICP approach. Using planes tremendously reduces the number of inputs.In this article, an efficient plane-based registration algorithm is presented. The optimal transformation is estimated through a two-step approach, successively performing robust plane-to-plane minimization and non-linear robust point-to-plane registration. Experiments on the Autonomous Systems Lab (ASL) benchmark dataset show that the proposed method enables to successfully register 100% of the scans from the three indoor sequences. Experiments also show that the proposed method is robust in large motion scenarios and more accurate than other state-of-the-art algorithms. Moreover, a new challenging dataset, LOOP’IN, is provided. It is composed of two loops in real-world indoor scenes, with a large number of scans captured with a 3D LiDAR. Tests led on this dataset show that the algorithm is able to register long sequences, to close loops and to build an incremental map of the explored environment.
Distance Closures: Unifying Search- and Lookup-based Shortest Path Speedup Techniques (2022)

Most popular speed-up techniques for shortest path queries in road networks are based either on pruned graph search or clever lookup schemes and allow for answering of shortest path distance queries within continent-sized road networks in less than a milli-(search-based) or even microsecond (lookup-based) compared to several seconds of a normal Dijkstra run. While both paradigms previously have been considered mostly separately, we present a framework that unifies these seemingly different views on shortest path computations. Apart from the conceptual novelty, this allows for new and (practically very attractive) space-time tradeoffs for shortest-path computation. To our knowledge we are also the first to report on computational results for the largest connected component of the Open-StreetMap planet road network with more than half a billion nodes.
SKIN ALLOGRAFT REJECTION BY L3/t4+ AND LYT-2+ T CELL SUBESTS (1986)

The L3/T4+ and Lyt-2+ T-cell subsets can be depleted from mice, using selected monoclonal antibodies in vivo, at different times during rejection of, or priming to, allogeneic skin grafts. Although L3/T4+ cells are sufficient to reject skin grafts in naive Lyt-2-depleted mice, we show that Lyt-2+ cells can become involved, after an initial delay, in intact mice. Furthermore, these Lyt-2+ cells are primed to dominate the accelerated rejection of a normal secondary response. Mice depleted of L3/T4+ cells cannot be primed in this way, suggesting that priming of Lyt-2+ cells is dependent on help from L3/T4+ cells. However, in mice depleted of Lyt-2+ cells, priming for rapid rejection can be achieved, presumably via the L3/T4+ population. This suggests that the rejection of skin allografts in a given situation reflects different contributions of multiple effector mechanisms.
Robot-Assisted Partial Nephrectomy in Obese Patients (2011)

RAPN is safe and feasible in obese patients. Obese patients had a higher estimated blood loss and a trend toward greater operative time and warm ischemia time, which did not achieve statistical significance.
Protocol for a clinical trial of text messaging in addition to standard care versus standard care alone in prevention of type 2 diabetes through lifestyle modification in India and the UK (2018)

ClinicalTrials.gov ; NCT01570946 , 4<sup>th</sup> April 2012 (India); NCT01795833 , 21<sup>st</sup> February 2013 (UK).
BitTorrent vulnerability to free riders: Root causes analysis (2014)

BitTorrent has gained popularity as a file sharing environment. The concept of sharing assumes that every peer in the environment contributes. However, the action of not sharing negates the fundamental concepts of BitTorrent. In this paper, we investigate the free riding phenomenon in BitTorrent. Through simulation experiments, we study in detail BitTorrent's vulnerability to free riders.
LiDAR point-cloud processing based on projection methods: a comparison (2020)

An accurate and rapid-response perception system is fundamental for autonomous vehicles to operate safely. 3D object detection methods handle point clouds given by LiDAR sensors to provide accurate depth and position information for each detection, together with its dimensions and classification. The information is then used to track vehicles and other obstacles in the surroundings of the autonomous vehicle, and also to feed control units that guarantee collision avoidance and motion planning. Nowadays, object detection systems can be divided into two main categories. The first ones are the geometric based, which retrieve the obstacles using geometric and morphological operations on the 3D points. The seconds are the deep learning-based, which process the 3D points, or an elaboration of the 3D point-cloud, with deep learning techniques to retrieve a set of obstacles. This paper presents a comparison between those two approaches, presenting one implementation of each class on a real autonomous vehicle. Accuracy of the estimates of the algorithms has been evaluated with experimental tests carried in the Monza ENI circuit. The position of the ego vehicle and the obstacle is given by GPS sensors with RTK correction, which guarantees an accurate ground truth for the comparison. Both algorithms have been implemented on ROS and run on a consumer laptop.
A humanized anti-CEACAM6 monoclonal antibody targeting pancreatic adenocarcinoma demonstrates potent in vitro and in vivo activity. (2004)

2180 CEACAM6 (carcinoembryonic antigen cell adhesion molecule 6, CD66c), is a cell surface oncogene, which is composed of immunoglobulin-like (Ig-like) domains capable of homophilic and heterophilic interactions. It is a 320 amino acid long cell surface GPI-linked glycoprotein comprised of 3 Ig-like C2 domains with a short C-terminal cytoplasmic tail of Mr ∼35.2 kD. The expression profile of CEACAM6 in normal human tissues shows moderate expression in a variety of epithelial tissue and myeloid cells. However, deregulated cell surface expression of CEACAM6 is observed in ∼50% of human cancers, including colorectal and pancreatic cancer. Further, it has been demonstrated that de-regulated over-expression of CEACAM6 inhibits differentiation and apoptosis of cells when deprived of their anchorage to the extracellular matrix, a process known as anoikis, which accompanies malignant transformation. An immunohistochemical analysis of a human pancreatic cancer tissue array demonstrated that >80% patients had cell surface expression of CEACAM6 with no expression on surrounding normal cells. Of the 11 human pancreatic cancer cell lines evaluated by western blots using a murine monoclonal antibody (13-1) only CFPAC-1, ASPC-1, CaPan-1, BXPC-3 and HPAF-2 showed expression. For the five pancreatic cancer cell lines evaluated, the mouse monoclonal antibody (13-1) promoted pancreatic cancer cell apoptosis with an IC50 = 1-10μg/ml and therefore is an effective agent in killing pancreatic cancer cells. Consequently, we have humanized the murine monoclonal antibody using a structure based design algorithm. The crystal structure of 1MCP, a mouse monoclonal antibody against phosphorylcholine was identified as the best structure for molecular modeling using ICM software. A glycine-serine linker was constructed linking the VL C-terminus to VH N-terminus (distance c 33° A) with a cysteine residue in the following order (GGGGSGGGGS (cys) GGGGS). Humanization was based on careful searching through the sequence databases using the program fasta with analysis of the modeled structure utilizing the program QUANTA. The original murine and 9 humanized ScFv versions were constructed by gene synthesis. The murine and version 8 of the humanized ScFv antibody fragments were expressed, purified and evaluated for cellular cytotoxicity utilizing the above human pancreatic cancer cell lines. All showed cell killing with IC50 in the range 0.1-0.5 μg/ml. Currently, we are evaluating the efficacy and potency of the murine monoclonal antibody 13.1 in a SCID mouse xenograft of human pancreatic cancer using the above cell lines with promising early results. These data will be presented at the meeting.
Mechanisms of Topoisomerase I (TOP1) Gene Copy Number Increase in a Stage III Colorectal Cancer Patient Cohort (2013)

TOP1 gene copy number increase occurs frequently in stage III CRC in a mechanism that often includes CEN-20. Using CEN-2 as a measurement for tumor ploidy levels, we were able to discriminate between different mechanisms of gene gain, which appeared to differ in prognostic impact. TOP1 FISH guidelines have been updated.
Improved stability and tumor targeting of 5‐fluorouracil by conjugation with hyaluronan (2013)

To circumvent the rapid clearance in vivo and consequent low tumor targeting of 5‐fluorouracil (5‐Fu), hyaluronan‐5‐fluorouracil conjugate (HA‐5‐Fu) was firstly synthesized and characterized. The stability of HA‐5‐Fu in vitro was evaluated by incubation with phosphate buffered saline, hyaluronidase solution, and mice plasma, respectively. The tumor targeting was tested by in vitro cytotoxicity evaluation and in vivo pharmacokinetics study in plasma and tumor. HA‐5‐Fu with drug loading of 87.674 mg/g was successfully obtained and confirmed. HA‐5‐Fu showed high stability in acidic environment and moderate stability under enzymatic cleavage. The enhanced cytotoxicity of HA‐5‐Fu over 5‐Fu depended on drug concentration, incubation time, and cell lines type. The t 1/2 of HA‐5‐Fu in plasma after injection of prodrug was extended up to 10 times compared with that of 5‐Fu. Notably, AUC 0– t in tumors of HA‐5‐Fu was 3.6 times higher than 5‐Fu, demonstrating its excellent tumor targeting and quite promising prospect in anti‐cancer therapy. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 927‐932, 2013
Repeated Inhalation of Low Doses of Cat Allergen That Do Not Induce Clinical Symptoms Increases Bronchial Hyperresponsiveness and Eosinophil Cationic Protein Levels (1999)

The aim of this study was to investigate whether repeated exposure to subclinical doses of cat allergens, not inducing asthma symptoms, could affect eosinophil cationic protein (ECP) levels in bronchoalveolar lavage (BAL) or in peripheral blood, without the appearance of clinical symptoms. Twelve patients with mild asthma, all sensitized to cats and not exposed to cat allergen at home, underwent a series of inhalations of cat allergen or placebo for 8 days over 2 weeks. A methacholine challenge was performed before and after the allergen and saline exposures, and BAL and blood were sampled for ECP measurements and eosinophil counts. No patients experienced asthma symptoms. However, PD20 methacholine (geometric mean) decreased significantly from 263 microg before to 126 microg after inhalation of allergen. Inhalation of saline did not induce any significant change in PD20. The change in log PD20 before and after cat allergen exposure was statistically different from the change in log PD20 before and after saline. Median ECP levels in BAL and serum increased significantly after allergen exposure, from 0.8 to 3.1 microg/l (p<0.02) and from 15.9 to 31.4 microg/l (p<0.05), respectively. No change was observed after saline inhalations. The change in BAL and serum ECP levels was statistically significant compared to that in the control group. The number of eosinophils did not change, however, nor did IL-5 and RANTES levels in BAL and serum. In conclusion, our results show that (1) exposure of asthma patients to repeated low doses of allergen, which did not provoke any clinical symptoms, is capable of inducing a local eosinophil activation associated with an increase in nonspecific bronchial hyperresponsiveness and (2) the increase in serum ECP levels due to eosinophil activation precedes the occurrence of asthma symptoms and may thus be a marker of allergen exposure in allergic asthma.
Snapshot 3D imaging with a gigapixel-scale multi-aperture microscope (2021)

We present a gigapixel-scale multi-aperture microscope capable of measuring a sample’s 3D height profile over multi-centimeter-scale fields of view with a series of single synchronized camera snapshots. Exploiting the overlap redundancy in our multi-aperture camera array microscope, we developed a novel, end-to-end photogrammetric reconstruction algorithm that simultaneously calibrates the cameras’ 3D positions and poses, stitches the acquired images, and generates a coregistered, pixel-wise 3D height map of the sample. Our work opens the door to video-rate 3D monitoring of dynamic scenes at micrometer-scale resolutions and centimeter-scale fields of view.