gebhart/patrepeval huggingface dataset:
Homologous chromosomes make contact at the sites of double-strand breaks in genes in somatic G <sub>0</sub> /G <sub>1</sub> -phase human cells (2012)

Double-strand DNA breaks (DSBs) are continuously induced in cells by endogenously generated free radicals and exogenous genotoxic agents such as ionizing radiation. DSBs activate the kinase activity in sensor proteins such as ATM and DNA-PK, initiating a complex DNA damage response that coordinates various DNA repair pathways to restore genomic integrity. In this study, we report the unexpected finding that homologous chromosomes contact each other at the sites of DSBs induced by either radiation or the endonuclease I-PpoI in human somatic cells. Contact involves short segments of homologous chromosomes and is centered on a DSB in active genes but does not occur at I-PpoI sites in intergenic DNA. I-PpoI-induced contact between homologous genes is abrogated by the transcriptional inhibitors actinomycin D and α-amanitin and requires the kinase activity of ATM but not DNA-PK. Our findings provide documentation of a common transcription-related and ATM kinase-dependent mechanism that induces contact between allelic regions of homologous chromosomes at sites of DSBs in human somatic cells.
Wind Turbine Placement Optimization by means of the Monte Carlo Simulation Method (2014)

This paper defines a new procedure for optimising wind farm turbine placement by means of Monte Carlo simulation method. To verify the algorithm’s accuracy, an experimental wind farm was tested in a wind tunnel. On the basis of experimental measurements, the error on wind farm power output was less than 4%. The optimization maximises the energy production criterion; wind turbines’ ground positions were used as independent variables. Moreover, the mathematical model takes into account annual wind intensities and directions and wind turbine interaction. The optimization of a wind farm on a real site was carried out using measured wind data, dominant wind direction, and intensity data as inputs to run the Monte Carlo simulations. There were 30 turbines in the wind park, each rated at 20 kW. This choice was based on wind farm economics. The site was proportionally divided into 100 square cells, taking into account a minimum windward and crosswind distance between the turbines. The results highlight that the dominant wind intensity factor tends to overestimate the annual energy production by about 8%. Thus, the proposed method leads to a more precise annual energy evaluation and to a more optimal placement of the wind turbines.
13.56 MHz 1.3 kW resonant converter with GaN FET for wireless power transfer (2015)

This paper presents a 1.3 kW resonant power amplifier using a Gallium Nitride (GaN) device at 13.56 MHz for wireless power transfer (WPT). The power amplifier driving the power transmitting coils is based on a Class Φ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> inverter, a single switch topology with low switch voltage stress and fast transient response. This implementation utilizes a recently available GaN device in a low inductance package that is compatible with operation in the 10's of MHz switching frequency. These power GaN switching devices have low gate resistance RG and low capacitance C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GS</inf> which greatly reduces the power requirements of the gate drive circuitry. This paper shows experimental measurements of the inverter in a WPT application and characterization of the system performance over various distances and operating conditions.
6  Studies of spin-coated polymer films (2005)

Spin-coating is widely employed for the highly reproducible fabrication of thin film coatings over large areas with high structural uniformity. Research in recent years has extended the scope of spin-coating by chemically engineering the interface of support and solution to obtain specific structural order in the resulting supported thin films. This review will discuss both the fundamental physical and chemical processes governing the conventional spin-coating process and describe methodologies for the preparation of spin-coated polymer thin films. Furthermore, a range of advanced applications and recent developments within this field will be reviewed with focus on engineering chemical and topological structure during the coating process.
Knowledge-based Color And Texture Analysis Of Skin Image (2005)

The color and texture of the surface pigmentation pattern of skin-images provides important diagnostic and prognostic features for detection of lethal skin-cancer. Since intensity as well as texture are important in this application, the segmentation algorithm is required to incorporate both of them in the process of region extraction and description. In the multi-channel segmentation scheme, presented in this paper, the intensity-based segmentation is obtained using the modified pyramid-based region extraction algorithm while the texture-based segmentation is obtained by a bi-level shiftedwindow processing algorithm that uses new generalized cooccurrence matrices. The results of each channel, based on individual segmentations, are then analyzed using heuristic rules to obtain the final color and texture based segmentation. The extracted regions are then described through a multilayered neural net for a model-based classification for predicting malignancy.
Supporting dynamic space-sharing on clusters of non-dedicated workstations (2002)

Clusters of workstations are increasingly being viewed as a cost effective alternative to parallel supercomputers. However, resource management and scheduling on workstations clusters is complicated by the fact that the number of idle workstations available for executing parallel applications is constantly fluctuating. We present a case for scheduling parallel applications on non dedicated workstation clusters using dynamic space sharing, a policy under which the number of processors allocated to an application can be changed during its execution. We describe an approach that uses application level checkpointing and data repartitioning for supporting dynamic space sharing and for handling the dynamic reconfiguration triggered when failure or owner activity is detected on a workstation being used by a parallel application. The performance advantages of dynamic space sharing are quantified through a simulation study, and experimental results are presented for the overhead of dynamic reconfiguration of a grid oriented data parallel application using our approach.
Engineering the C-region of human insulin-like growth factor-1: implications for receptor binding (1996)

Recombinant wild-type human IGF-1 and a C-region mutant in which residues 28-37 have been replaced by a 4-glycine bridge (4-Gly IGF-1) were secreted and purified from yeast. An IGF-1 analogue in which residues 29-41 of the C-region have been deleted (mini IGF-1) was created by site-directed mutagenesis and also expressed. All three proteins adopted the insulin-fold as determined by circular dichroism. The significantly raised expression levels of mini IGF-1 allowed the recording of two-dimensional NMR spectra. The affinity of 4-Gly IGF-1 for the IGF-1 receptor was approximately 100-fold lower than that of wild-type IGF-1 and the affinity for the insulin receptor was approximately 10-fold lower. Mini IGF-1 showed no affinity for either receptor. Not only does the C-region of IGF-1 contribute directly to the free energy of binding to the IGF-1 receptor, but also the absence of flexibility in this region eliminates binding altogether. As postulated for the binding of insulin to its own receptor, it is proposed that binding of IGF-1 to the IGF-1 receptor also involves a conformational change in which the C-terminal B-region residues detach from the body of the molecule to expose the underlying A-region residues.
True three-dimensional nuclear magnetic resonance neuro-imaging in ischemic stroke: correlation of NMR, X-ray CT and pathology. (1983)

True three-dimensional proton nuclear magnetic resonance (NMR) imaging was performed on an 84-year-old man following a recent cerebral embolic infarction. NMR data obtained using different pulse sequences were inter-correlated, stressing the significance of image appearance in terms of the NMR tissue parameters. Planes selected for display from the three-dimensional data set allowed optimal visualization of the pathology. Accurate correlations of the NMR data with X-ray computerized tomography scans and with subsequent autopsy findings indicate that NMR may play an important role in the detection and diagnosis of ischemic stroke.
Therapeutic effect of intracolonically administered nuclear factor<i>κ</i>B (p65) antisense oligonucleotide on mouse dextran sulphate sodium (DSS)-induced colitis (2000)

Cytokines such as IL-1, tumour necrosis factor-alpha (TNF-alpha), IL-6 and IL-8 are increased in inflamed colonic mucosa after administration of mouse DSS. Nuclear factor kappaB (NF-kappaB) is a transcription factor which regulates the expression of these cytokine genes. The effect of intracolonically administered NF-kappaB (p65) antisense phosphorothioate oligonucleotide was examined in mouse DSS-induced colitis using drinking water containing 5% DSS. When antisense oligonucleotide was given on day 0, the disease activity index (DAI) representing clinical symptoms improved and the histological score decreased; furthermore, IL-1, IL-6, and TNF-alpha concentrations in rectal mucosa were lower compared with the control group. Clinical and histological improvement was also observed when antisense oligonucleotide was begun on day 2 but not on day 7. In addition, the distribution of antisense oligonucleotides was investigated by confocal laser microscopy. In colonic mucosa, oligonucleotides were predominantly localized to cells in the lamina propria, but also in the epithelium. Western blot analysis using homogenized rectal mucosa showed the decreased expression of NF-kappaB p65 in the antisense oligonucleotide-treated group, although it was increased in the colitis group. These results suggest that intracolonic administration of NF-kappaB antisense oligonucleotide may be effective in ulcerative colitis.
FlowPic: Encrypted Internet Traffic Classification is as Easy as Image Recognition (2019)

Identifying the type of a network flow or a specific application has many advantages, but become harder in recent years due to the use of encryption, e.g., by VPN and Tor. Current solutions rely mostly on handcrafted features and then apply supervised learning techniques for the classification. We introduce a novel approach for encrypted Internet traffic classification by transforming basic flow data into a picture, a FlowPic, and then using known image classification deep learning techniques, Convolutional Neural Networks (CNNs), to identify the flow category (browsing, chat, video, etc.) and the application in use. We show using the UNB ISCX datasets that our approach can classify traffic with high accuracy. We can identify a category with very high accuracy even for VPN and Tor traffic. We classified with high success VPN traffic when the training was done for a non-VPN traffic. Our categorization can identify with good success new applications that were not part of the training phase. We can also use the same CNN to classify applications with an accuracy of 99.7%. Overall, our approach achieves significant better performance than previous work, and can handle classification problems that were not studied in the past.
Retrovirus-Mediated Herpes Simplex Virus Thymidine Kinase Gene Transduction Renders Human Thyroid Carcinoma Cell Lines Sensitive to Ganciclovir and Radiation in Vitro and in Vivo (1997)

In an attempt to develop gene therapy for thyroid carcinomas, the present studies were undertaken to evaluate in vitro and in vivo therapeutic efficacy and toxicity of herpes simplex virus thymidine kinase (HSV-tk) gene and ganciclovir (GCV) treatment, a widely used prodrug/suicide gene therapy, in human thyroid carcinoma cell lines, FRO and WRO cells, using a means of retrovirus-mediated gene transduction. In vitro experiments demonstrated dose- and time-dependent cell killing by transduction of the HSV-tk gene followed by GCV treatment. The IC50 (the concentration required to elicit 50% growth inhibition) shifted from 250 to 0.5 mg/liter in FRO cells, and from 3,000 to 0.09 mg/liter in WRO cells with therapeutic indexes of 500 and 33,000, respectively. Treatment with 30 mg/liter GCV for 4 days led to complete cell death in HSV-tk tumor cells. Nontransduced cells mixed with transduced cells were also effectively killed by GCV (bystander effect). Low concentrations of GCV, which alone showed little cytotoxicity, enhanced radiation-induced cytotoxicity (radiosensitization). In vivo sc FRO-tk tumor models in nude mice also showed dose- and time-dependent tumor regression. The IC50 was less than 2 mg/kg, and treatment with 100 mg/kg GCV for 2 weeks completely eradicated all tumors. The bystander effect and radiosensitization were also obtained in vivo. These results suggest that the HSV-tk/GCV approach to human thyroid carcinoma cells appears to be very efficacious, with a wide therapeutic range, and exerts a bystander effect and radiosensitization both in vitro and in vivo. Thus, HSV-tk/GCV system, alone or in combination with radiotherapy, may be a promising suicide gene therapy for thyroid carcinomas.
Thermal Expansion of Synthetic β‐Spodumene and β‐Spodumene—Silica Solid Solutions (1968)

Synthetic β‐Spodumene and several β‐Spodumene‐silica solid solutions were prepared, and their thermal expansion behavior was studied using high‐temperature X‐ray diffraction techniques. Data indicate that all β‐Spodumenes are characterized by a pronounced anisotropy of thermal expansion much the same as that of the silica polymorph keatite. Anisotropy increases slightly and the volume expansion decreases as the compositions become richer in SiO 2 . Specimens with more than 80.8 wt% SiO 2 at 130O°C and 1 atm contain P‐cristobalite along with β‐Spodumene. The lattice parameters of β‐Spodumene compositions throughout the solid solution range were determined. The structural aspects of the anisotropy of thermal expansion are discussed.
Identification of CTX-M-Type Extended-Spectrum-β-Lactamase Genes Using Real-Time PCR and Pyrosequencing (2006)

CTX-M extended-spectrum beta-lactamases (ESBLs) are increasingly prevalent worldwide among Escherichia coli bacteria, mostly in community-acquired urinary tract infections. Finding a fast and reliable technique for identification of CTX-M enzymes is becoming a challenge for the microbiology laboratory. A fast real-time PCR amplification technique, using degenerated primers specific for all the bla(CTX-M) alleles, coupled to real-time pyrosequencing was developed. The five CTX-M groups were unambiguously identified by pyrosequencing a 13-bp DNA region. Further sequencing of an additional 16-bp region allowed further division into subgroups. Phylogenetic trees constructed with the entire bla(CTX-M) genes and with both pyrosequenced regions (29 bp) gave similar results, suggesting that this technique, termed the real-time detection and sequencing method, has a powerful discriminatory ability. This high-throughput technique has been evaluated by screening 48 ESBL-producing E. coli isolates recovered from the Bicêtre hospital (France) in 2004. Forty-four of these strains were CTX-M positive by real-time PCR detection and direct pyrosequencing of the PCR products, which identified CTX-M-15 as the main CTX-M-type beta-lactamase. Pulsed-field gel electrophoresis analysis of these strains revealed that several clones, of which one CTX-M-15-positive clone was predominant (60%), were identified both in nosocomial and in community-acquired isolates. The combination of real-time PCR with pyrosequencing represents a powerful tool for epidemiological studies of CTX-M producers. This assay has the potential to be used in a diagnostic laboratory since up to 96 bacterial isolates may be screened in less than 3 h.
Lysine Sulfonamides as Novel HIV‐Protease Inhibitors: Nε‐Acyl Aromatic α‐Amino Acids. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Relative Potencies of Antagonists of the Luteinizing Hormone Releasing Hormone with Lys<sup>8</sup> and Arg<sup>8</sup> and Substitutions in Positions 3 ,5 ,6 ,7 and 8 (1986)

Antagonists of the luteinizing hormone releasing hormone (LHRH) of increased potency is a goal for control of ovulation. In the design and synthesis of 26 decapeptides, emphasis was given to analogs with Lys8 and Arg8 and with various substitutions in positions 3, 5, 6, 7 and 8. Two antagonists, [N-Ac-D-2-Nal1,D-pClPhe2,D-3-Pal3,Ser4,Tyr5,D-Ar g6,Leu7,Lys8, Pro9,D-Ala10]-NH2 and [N-Ac-D-2-Nal1,D-pClPhe2,D-3-Pal3,Ser4,Arg5++ +,D-3-Pal6,Leu7,Arg8,Pro9, D-Ala10]-NH2 showed 80-85% antiovulatory activity (AOA) at 0.25 micrograms in the rat. The latter antagonist showed 60% AOA at 0.125 micrograms. Of four pairs of analogs with Arg8 and Lys8, respectively, two pairs favored Lys8 over Arg8 for potency. One pair showed negligible difference and another pair favored Arg8 over Lys8. There is specificity of substitution for potency. In other antagonists, D-3-Pal3, Tyr5 or Phe5, D-Arg6 and Leu7 or Nle7 or Val7 and Arg8 were variously effective substitutions for increase of potency and reduction of histamine release.
Superhydrophobic Copper Tubes with Possible Flow Enhancement and Drag Reduction (2009)

The transport of a Newtonian liquid through a smooth pipe or tube is dominated by the frictional drag on the liquid against the walls. The resistance to flow against a solid can, however, be reduced by introducing a layer of gas at or near the boundary between the solid and liquid. This can occur by the vaporization of liquid at a surface at a temperature above the Leidenfrost point, by a cushion of air (e.g. below a hovercraft), or by producing bubbles at the interface. These methods require a continuous energy input, but a more recent discovery is the possibility of using a superhydrophobic surface. Most reported research uses small sections of lithographically patterned surfaces and rarely considers pressure differences or varying flow rates. In this work we present a method for creating a uniform superhydrophobic nanoribbon layer on the inside of round copper tubes of millimetric internal radius. Two types of experiments are described, with the first involving a simultaneous comparison of four tubes with different surface finishes (as received, as received with hydrophobic coating, nanoribbon, and nanoribbon with a hydrophobic coating) under constant flow rate conditions using water and water-glycerol mixtures. The results show that the superhydrophobic nanoribbon with a hydrophobic coating surface finish allows greater flow at low pressure differences but that the effect disappears as the pressure at the inlet of the tube is increased. The second experiment is a simple visual demonstration of the low-pressure behavior using two nominally identical tubes in terms of length and cross-section, but with one tube possessing a superhydrophobic internal surface finish. In this experiment a reservoir is allowed to feed the two tubes with open ends via a T-piece and it is observed that, once flow commences, it preferentially occurs down the superhydrophobic tube.
Predicting Disease Transmission from Geo-Tagged Micro-Blog Data (2021)

Researchers have begun to mine social network data in order to predict a variety of social, economic, and health related phenomena. While previous work has focused on predicting aggregate properties, such as the prevalence of seasonal influenza in a given country, we consider the task of fine-grained prediction of the health of specific people from noisy and incomplete data. We construct a probabilistic model that can predict if and when an individual will fall ill with high precision and good recall on the basis of his social ties and co-locations with other people, as revealed by their Twitter posts. Our model is highly scalable and can be used to predict general dynamic properties of individuals in large real-world social networks. These results provide a foundation for research on fundamental questions of public health, including the identification of non-cooperative disease carriers ("Typhoid Marys"), adaptive vaccination policies, and our understanding of the emergence of global epidemics from day-to-day interpersonal interactions.
Enhancements of Trapdoor Permutations. (2011)

We take a closer look at several enhancements of the notion of trapdoor permutations. Specifically, we consider the notions of enhanced trapdoor permutation (Goldreich 2004) and doubly enhanced trapdoor permutation (Goldreich 2008) as well as intermediate notions (Rothblum 2010). These enhancements arose in the study of Oblivious Transfer and NIZK, but they address natural concerns that may arise also in other applications of trapdoor permutations. We clarify why these enhancements are needed in such applications, and show that they actually suffice for these needs. Keywords:
Associative Embedding: End-to-End Learning for Joint Detection and Grouping (2016)

We introduce associative embedding, a novel method for supervising convolutional neural networks for the task of detection and grouping. A number of computer vision problems can be framed in this manner including multi-person pose estimation, instance segmentation, and multi-object tracking. Usually the grouping of detections is achieved with multi-stage pipelines, instead we propose an approach that teaches a network to simultaneously output detections and group assignments. This technique can be easily integrated into any state-of-the-art network architecture that produces pixel-wise predictions. We show how to apply this method to both multi-person pose estimation and instance segmentation and report state-of-the-art performance for multi-person pose on the MPII and MS-COCO datasets.