gebhart/patrepeval huggingface dataset:
The LL-100 panel: 100 cell lines for blood cancer studies (2019)

For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and non-inherent virus contamination. Whole exome sequencing and RNA-sequencing of the 100 cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. We show that such comprehensive sequencing data can be used to find lymphoma-subtype-characteristic copy number aberrations, mRNA isoforms, transcription factor activities and expression patterns of NKL homeobox genes. These exemplary studies confirm that the novel LL-100 panel will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
Sustainable production of pharmaceutical, nutraceutical and bioactive compounds from biomass and waste (2021)

The aim of this tutorial review is to provide a general overview of processes, technologies and challenges in the production of pharmaceutical and bioactive compounds from food waste and lignocellulosic residues. Particular attention is given to benign-by-design processes instinctively devoted to environmental sustainability for the recovery of bioactive compounds from food waste as well as for the production of alcohols, acids, polyols, furans and aromatic compounds from lignocellulosic residues. At the same time, novel green synthetic routes for the production of active pharmaceutical ingredients and the development of novel bioactive compounds are discussed. Recent success industrial stories on the use of food waste and lignocellulosic residues for pharmaceutical and nutraceutical applications are also discussed.
Design and development of 77-GHz pair-slot array antenna with single-mode post-wall waveguide for automotive radar (2011)

A 77-GHz slot array antenna with a single-mode post-wall waveguide is presented for automotive radars. First, transmission losses and fabrication costs of various transmission lines in millimeter-wave band are compared. The measured transmission loss in the 77-GHz post-wall waveguide integrated in a PTFE substrate at 77 GHz is shown 0.20 dB/cm, which is less than that of the microstrip line. Then, the design method of one-dimensional slot subarray with the single-mode post-wall waveguide is discussed. Finally, an antenna system composed of four subarrays has been fabricated. The measured gain of the antenna system is 24.4 dBi gain at the designed frequency of 76.5 GHz, and the efficiency for aperture size of 55 mm by 9.2 mm is 67%.
Further Evidence of Immunologic Dissimilarity of Distemper (CD) and Measles (M) Viruses. (1960)

Additional experimental evidence of dissimilarity of canine distemper (CDV) and measles (MV) viruses are presented: 1. Ferrets inoculated with repeated doses of MV-adjuvant mixture and which developed M antibodies proved as susceptible as control animals to challenge with CDV. 2. Paired convalescent sera from measles patients showed significant measles antibody rises, while CD antibodies remained essentially absent. 3. Growth of MV in HeLa cells was not inhibited by presence of CD antiserum or normal serum, while MV antiserum apparently reduced virus multiplication. Presence of measles antiserum did not interfere with propagation of CDV. 4. By 14th day after MV infection, serologically negative monkeys developed high antibody titers for MV but none for CDV. It remains to be determined whether results obtained are attributable to particular virus strains used, or apply also to other isolates of MV and CDV.
Measuring privacy risk in online social networks (2009)

Measuring privacy risk in online social networks is a challenging task. One of the fundamental difficulties is quantifying the amount of information revealed unintentionally. We present PrivAware, a tool to detect and report unintended information loss in online social networks. Our goal is to provide a rudimentary framework to identify privacy risk and provide solutions to reduce information loss. The first instance of the software is focused on information loss attributed to social circles. In subsequent releases we intend to incorporate additional capabilities to capture ancillary threat models. From our initial results, we quantify the privacy risk attributed to friend relationships in Facebook. We show that for each user in our study a majority of their personal attributes can be derived from social contacts. Moreover, we present results denoting the number of friends contributing to a correctly inferred attribute. We also provide similar results for different demographics of users. The intent of PrivAware is to not only report information loss but to recommend user actions to mitigate privacy risk. The actions provide users with the steps necessary to improve their overall privacy measurement. One obvious, but not ideal, solution is to remove risky friends. Another approach is to group risky friends and apply access controls to the group to limit visibility. In summary, our goal is to provide a unique tool to quantify information loss and provide features to reduce privacy risk. 1.
Variable Window for Outlier Detection and Impulsive Noise Recognition in Range Images (2014)

To improve comprehensive performance of denoising range images, an impulsive noise (IN) denoising method with variable windows is proposed in this paper. Founded on several discriminant criteria, the principles of dropout IN detection and outlier IN detection are provided. Subsequently, a nearest non-IN neighbors searching process and an Index Distance Weighted Mean filter is combined for IN denoising. As key factors of adapatablity of the proposed denoising method, the sizes of two windows for outlier INs detection and INs denoising are investigated. Originated from a theoretical model of invader occlusion, variable window is presented for adapting window size to dynamic environment of each point, accompanying with practical criteria of adaptive variable window size determination. Experiments on real range images of multi-line surface are proceeded with evaluations in terms of computational complexity and quality assessment with comparison analysis among a few other popular methods. It is indicated that the proposed method can detect the impulsive noises with high accuracy, meanwhile, denoise them with strong adaptability with the help of variable window.
The history of Lyme disease in Italy and its spread in the Italian territory (2023)

Lyme borreliosis (LB) is the most common vector-borne zoonotic inflammatory disease in the Northern Hemisphere. In Italy, the first case was diagnosed in 1985 in a woman in Liguria, while the second, in 1986 in Friuli-Venezia Giulia, documenting the infection in northern Italy. Both diagnoses were confirmed by serological assessment by an indirect immunofluorescence (IFI) technique. <i>Borrelia</i> cultivation from both <i>Ixodes ricinus</i> ticks and human lesions in Trieste (Friuli-Venezia Giulia) identified <i>Borrelia afzelii</i> as the prevalent genospecies; nevertheless, <i>Borrelia garinii</i>, <i>Borrelia burgdorferi</i> (<i>sensu stricto</i>), and <i>Borrelia valaisiana</i> (VS116 Group) were also detected, although less frequently. LB was also documented in other Italian regions: in Tuscany (1991), Trentino-Alto Adige (1995-1996), Emilia-Romagna (1998), Abruzzo (1998), and more recently, Lombardy. Nevertheless, data on LB in other Italian regions, especially in southern Italy and islands, are poor. The aim of this study is to document the spread of LB in Italy through the collection of data from LB patients in eight Italian hospitals located in different Italian regions. Diagnostic criteria for LB diagnosis are as follows: i) the presence of erythema migrans (EM) or ii) a clinical picture suggestive of LB, confirmed by serological tests and/or PCR positivity for <i>Borrelia</i> detection. In addition, data also included the place of residence (town and region) and the place where patients became infected. During the observation period, 1,260 cases were gathered from the participating centers. Although different in extent from northern Italy to central/southern Italy, this study shows that LB is widespread throughout Italy.
Backstop (2008)

The errors that Java programmers are likely to encounter can roughly be categorized into three groups: compile-time (semantic and syntactic), logical, and runtime (exceptions). While much work has focused on the first two, there are very few tools that exist for interpreting the sometimes cryptic messages that result from runtime errors. Novice programmers in particular have difficulty dealing with uncaught exceptions in their code and the resulting stack traces, which are by no means easy to understand. We present Backstop, a tool for debugging runtime errors in Java applications. This tool provides more user-friendly error messages when an uncaught exception occurs, and also provides debugging support by allowing users to watch the execution of the program and the changes to the values of variables. We also present the results of two preliminary studies conducted on introductory-level programmers using the two different features of the tool.
Extracellular lactate cooperates with limited glucose and glutamine to sustain breast cancer cell survival by providing ATP, NADPH, amino acids, and glutathione (2014)

Background Cancer progression occurs upon mutations on regulatory genes that control biological functions including cellular bioenergetics. Such perturbations lead to a metabolic switch that favors aerobic glycolysis and lactate production over oxidative phosphorylation. This process is known as the Warburg effect and results in a lactate-rich tumor microenvironment. The apparently wasteful mechanism has raised the question of why cancer cells switch from the high ATP producing TCA cycle/OXPHOS to glycolysis; and whether lactate serves a biological function in energy metabolism since a high lactate environment correlates with worse patient prognosis in several malignancies including breast cancer. Our goals were to first, determine the fate of carbons from lactate in breast cancer cells; and second, determine the mechanism of lactate metabolism.
Creating RZ data modulation formats using parallel silicon microring modulators for pulse carving in DPSK (2008)

We propose ultra-small silicon microring-based pulse carvers operated at 10 Gb/s. RZ-DPSK transmitter is obtained in chip-size of only tens of mum2 and exhibits lower power-penalty than MZM-based one by 1.7 dB in data transmission.
10-Gb/s All-Optical VPN in WDM-PON Using Injection-Locked Fabry–Pérot Laser Diodes (2014)

A 10-Gb/s reconfigurable all-optical virtual private network (VPN) scheme in wavelength-division-multiplexed passive optical networks is proposed. The upstream VPN optical signal from the source optical network unit (ONU) is wavelength converted by mutual injection locking of a Fabry-Pérot laser diode at the optical line terminal to a different wavelength and then transmitted to the target ONU. The proposed scheme is power efficient and reconfigurable. In the experiment, the power penalty at a bit error rate of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> is 1.4 dB after transmission in 25 km of optical fiber. The impact of detunes and powers of the injected light on the system performance are also studied. The experimental results show that the wavelength detunes and signal powers should be selected appropriately to achieve optimal system performance.
Bone Mineral Density in Children With Neurofibromatosis Type 1 (2008)

Stevenson, David A.*†; Murray, Mary*; Viskochil, David H.*†; Carey, John C.*†; Moyer-Mileur, Laurie J.* Author Information
High-Performance Plug-and-Perf Completions in Unconventional Wells (2015)

Abstract An innovative new design of a perforating system for plug-and-perf completions in unconventional wells demonstrates that operations can be made more efficient, safe and reliable. Results from extensive modeling, testing and field tests demonstrate that the entire perforating process, including gun loading, arming, running, perforating, maintenance and disposal, is made more robust by eliminating traditional approaches to selective perforating, detonators, gun hardware and accessory equipment. The new system optimizes perforating operations with fully assembled and ready-to-shoot gun modules delivered to the base or to the wellsite. An innovative integrated switch-detonator design replaces all wiring and crimping to eliminate human error and to significantly reduce the risk of inadvertent ignition or detonation. Arming a gun is now as efficient, safe and reliable as placing a battery in a flashlight. True intrinsically safe microprocessor switch-detonators require no wiring so they achieve measurably higher reliability than standard separate switch-detonator combinations, and they are immune to potential hazards that can impact standard selective perforating equipment in use today. Surface test equipment detects any malfunctions before running in hole, and the software allows continuous monitoring of all downhole components until initiation and in between shots. All wellsite operations can continue without interruption, and full selectivity, communication to all detonators, stage-skipping and gun redundancy are enabled for the most complex completions. Gun length, shot phasing, shot density and charge type are fully customizable with injection-molded gun parts that do not create unwanted debris after perforation. The system design targets a 10X improvement in reliability over existing plug-and-perf equipment. Wireline service companies traditionally experience reliability in unconventional well perforating ranging from 30 runs/misrun to 100 runs/misrun. Early results suggest the new system may exceed 1,000 runs/misrun. By reducing the risk of mishaps, misruns and misfires, rig time is saved, frack costs are lowered, and every stage can be perforated to contribute to higher well productivity. Field tests of the new design demonstrate the advantages of a fully integrated perforating gun system. The new technology leverages innovative component-level features and a system design approach to produce a perforating system that eliminates many of the causes for misruns, increases simplicity and safety of operations, and delivers higher well productivity.
Transcatheter Aortic Valve Implantation in Surgically Repaired Double Outlet Right Ventricle (2013)

A 52-year-old male patient, with a medical history of surgically repaired double outlet right ventricle presented with severe aortic stenosis (AS) and hepatitis C with cirrhosis, presented with New York Heart Association Class IV heart failure. During evaluation for a liver transplant, he was deemed a poor surgical candidate due to his aortic valve disease and cirrhosis with model for end-stage liver disease score of 14. Transthoracic echocardiogram showed severe AS with a mean gradient of 62 mm Hg and calculated aortic valve area of 0.74 cm(2) with a normal ejection fraction of 65%. The patient underwent transfemoral implantation of a 23-mm Edwards Sapien commercial heart valve with significant mean gradient reduction across the aortic valve from 62 to 13 mm Hg. The patient was observed in the coronary care unit and discharged home 2 days postprocedure with his clinical symptoms greatly improved.
Targeted editing of the PSIP1 gene encoding LEDGF/p75 protects cells against HIV infection (2019)

To fulfill a productive infection cycle the human immunodeficiency virus (HIV) relies on host-cell factors. Interference with these co-factors holds great promise in protecting cells against HIV infection. LEDGF/p75, encoded by the PSIP1 gene, is used by the integrase (IN) protein in the pre-integration complex of HIV to bind host-cell chromatin facilitating proviral integration. LEDGF/p75 depletion results in defective HIV replication. However, as part of its cellular function LEDGF/p75 tethers cellular proteins to the host-cell genome. We used site-specific editing of the PSIP1 locus using CRISPR/Cas to target the aspartic acid residue in position 366 and mutated it to asparagine (D366N) to disrupt the interaction with HIV IN but retain LEDGF/p75 cellular function. The resulting cell lines demonstrated successful disruption of the LEDGF/p75 HIV-IN interface without affecting interaction with cellular binding partners. In line with LEDGF/p75 depleted cells, D366N cells did not support HIV replication, in part due to decreased integration efficiency. In addition, we confirm the remaining integrated provirus is more silent. Taken together, these results support the potential of site-directed CRISPR/Cas9 mediated knock-in to render cells more resistant to HIV infection and provides an additional strategy to protect patient-derived T-cells against HIV-1 infection as part of cell-based therapy.
Flt3 ligand treatment modulates parasitemia during infection with rodent malaria parasites via MyD88‐ and IFN‐γ‐dependent mechanisms (2013)

We previously showed that treatment of mice with the Flt3 ligand (Flt3L) prevents development of lethal experimental cerebral malaria and inhibits parasitemia during Plasmodium berghei ANKA (PbA) infection. In this study, we investigated the mechanisms underlying the reduction of parasitemia in Flt3L-treated mice. Studies using gene knockout mice and antibody treatment indicated that the anti-parasitemia effect of Flt3L was mediated by innate immune system and was dependent on MyD88, IFN-γ, IL-12 and natural killer (NK) cells. The number of NK cells and their ability to produce IFN-γ was enhanced in Flt3L-treated mice. Phagocytic activity of splenocytes was increased in Flt3L-treated mice after PbA infection when compared with that in untreated mice, and this activity was mainly mediated by the accumulation of F4/80(mid) CD11b(+) cells in the spleen. In both MyD88(-/-) and IFN-γ(-/-) mice, the proportion of F4/80(mid) CD11b(+) cells was not increased in the spleen of Flt3L-treated mice after infection. These correlations suggest that NK cells produce IFN-γ in Flt3L-treated mice, and accumulation of F4/80(mid) CD11b(+) cells in the spleen is promoted by an IFN-γ -dependent manner, culminating in the inhibition of parasitemia. These findings imply that Flt3L promotes effective innate immunity against malaria infection mediated by interplay among varieties of innate immune cells.
Balen, Petrus van (1643–90) (2003)

Balen, Petrus van Cocceius (Coccejus), Johannes Petrus van Balen, born in 1643 in Utrecht, University of Utrecht, studied theology at the University of Utrecht and was appointed as a Reformed preacher to the Dutch Embassy in Madrid. He was called back when it became clear that he had shown sympathy
Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation (2021)

The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%-70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. Fifteen of 45 of the translated lncRNA-smORFs exhibit sequence conservation within <i>Hominidea</i>, suggesting they are under strong selective constraint in this clade. The profiling of publicly available data sets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development, and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is <i>LINC01116</i>, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localizes to neurites. Knockdown of <i>LINC01116</i> results in a significant reduction of neurite length in differentiated cells, indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a noncanonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for <i>LINC01116</i> during human neuronal differentiation.
Magnetic resonance perfusion imaging for assessment of correlation between myocardial activity and endothelin in acute myocardial infarction (2013)

Objective To determine the correlation between myocardial activity and endothelin by conducting magnetic resonance perfusion imaging in patients with clinically diagnosed acute myocardial infarction (AMI). Methods Nineteen patients with AMI were allocated to be subjected to magnetic resonance perfusion imaging for assessment of myocardial activity. Changes in myocardial activity were determined by comparison on the magnetic resonance perfusion imaging conducted at days 3-5 preoperatively and 13 months postoperatively in patients scheduled for percutaneous coronary intervention (PCI). This was accompanied by sampling of the venous blood that entailed subse quent assessment of the level of ET, thus allowing analysis on the correlation with the results derived from magnetic resonance perfusion imaging. Results Of 19 patients with myocardial infarction, treatment with PCI resulted in markedly reduced level of ET at month 13 preoperatively (P0.01). Meanwhile, the treatment group yielded a significant improvement (P0.05) in left ventricular ejection fraction (LVEF). Conclusion Detection of plasma ET may shed light on predicting the myocardial activity, disease severity and prognosis. Magnetic resonance perfusion imaging may effectively discriminate the survived and mortal myocardium as well as the extent and size of infarction.