gebhart/patrepeval huggingface dataset:
Escape from Cells: Deep Kd-Networks for the Recognition of 3D Point Cloud Models (2017)

We present a new deep learning architecture (called Kdnetwork) that is designed for 3D model recognition tasks and works with unstructured point clouds. The new architecture performs multiplicative transformations and shares parameters of these transformations according to the subdivisions of the point clouds imposed onto them by kdtrees. Unlike the currently dominant convolutional architectures that usually require rasterization on uniform twodimensional or three-dimensional grids, Kd-networks do not rely on such grids in any way and therefore avoid poor scaling behavior. In a series of experiments with popular shape recognition benchmarks, Kd-networks demonstrate competitive performance in a number of shape recognition tasks such as shape classification, shape retrieval and shape part segmentation.
Expression of the Chemokine Receptor Gene, CCR8, is Associated With DUSP22 Rearrangements in Anaplastic Large Cell Lymphoma (2014)

Anaplastic large cell lymphoma (ALCL) is one of the most common T-cell non-Hodgkin lymphomas and has 2 main subtypes: an anaplastic lymphoma kinase (ALK)-positive subtype characterized by ALK gene rearrangements and an ALK-negative subtype that is poorly understood. We recently identified recurrent rearrangements of the DUSP22 locus on 6p25.3 in both primary cutaneous and systemic ALK-negative ALCLs. This study aimed to determine the relationship between these rearrangements and expression of the chemokine receptor gene, CCR8. CCR8 has skin-homing properties and has been suggested to play a role in limiting extracutaneous spread of primary cutaneous ALCLs. However, overexpression of CCR8 has also been reported in systemic ALK-negative ALCLs. As available antibodies for CCR8 have shown lack of specificity, we examined CCR8 expression using quantitative real-time PCR in frozen tissue and RNA in situ hybridization (ISH) in paraffin tissue. Both approaches showed higher CCR8 expression in ALCLs with DUSP22 rearrangements than in nonrearranged cases (PCR: 19.5-fold increase, P=0.01; ISH: 3.3-fold increase, P=0.0008). CCR8 expression was not associated with cutaneous presentation, cutaneous biopsy site, or cutaneous involvement during the disease course. These findings suggest that CCR8 expression in ALCL is more closely related to the presence of DUSP22 rearrangements than to cutaneous involvement and that the function of CCR8 may extend beyond its skin-homing properties in this disease. This study also underscores the utility of RNA-ISH as a paraffin-based method for investigating gene expression when reliable antibodies for immunohistochemical analysis are not available.
Ultra-thin, two dimensional, multi-element Si pin photodiode array for multipurpose applications (2004)

ABSTRACT The paper discusses opto-electrical properties of a 32x16 (and 16x16) element pin photodiode array built on a 30-µ m thick single silicon die. The element size is ca. 1 mm square or smaller and the gaps between adjacent elements are as small as 100 µ m. The arrays can be tiled facilitating the building of large scale photodetector matrices. The arrays have superior optical and electrical characteristics and are designed to work at zero Volts bias. The internal quantum efficiency is close to 100% within the spectral range 500  800 nm and could be tuned to a maximum value outside that spectral interval. The cross talk is smaller than 0.5% within the spectral range 400 to 1000 nm. The arrays are characterized with very low leakage currents, high shunt resistance, and low capacitance. Some other parameters of the array like the frequency bandwidth and capacitance are also discussed. Keywords : Silicon photodiode, pin photodiode array, quantum efficiency, crosstalk, fast time response 1. INTRODUCTION Recent advances in silicon (Si) photodiode technology provided for design of multi-element photodiode arrays with relatively small element size and narrow gaps between adjacent elements.
A novel recurrent NPM1-TYK2 gene fusion in cutaneous CD30-positive lymphoproliferative disorders (2014)

The spectrum of cutaneous CD30-positive lymphoproliferative disorders (LPDs) includes lymphomatoid papulosis and primary cutaneous anaplastic large cell lymphoma. Chromosomal translocations targeting tyrosine kinases in CD30-positive LPDs have not been described. Using whole-transcriptome sequencing, we identified a chimeric fusion involving NPM1 (5q35) and TYK2 (19p13) that encodes an NPM1-TYK2 protein containing the oligomerization domain of NPM1 and an intact catalytic domain in TYK2. Fluorescence in situ hybridization revealed NPM1-TYK2 fusions in 2 of 47 (4%) primary cases of CD30-positive LPDs and was absent in other mature T-cell neoplasms (n = 151). Functionally, NPM1-TYK2 induced constitutive TYK2, signal transducer and activator of transcription 1 (STAT1), STAT3, and STAT5 activation. Conversely, a kinase-defective NPM1-TYK2 mutant abrogated STAT1/3/5 signaling. Finally, short hairpin RNA-mediated silencing of TYK2 abrogated lymphoma cell growth. This is the first report of recurrent translocations involving TYK2, and it highlights the novel therapeutic opportunities in the treatment of CD30-positive LPDs with TYK2 translocations.
Carbonyl reductase as a significant predictor of survival and lymph node metastasis in epithelial ovarian cancer (2001)

We have recently reported a novel function for carbonyl reductase (CR), namely, its ability to modulate the metastatic potential of malignant mouse cells. Because there are currently no data addressing a similar function for CR in human cancers, the aim of this study was to assess a correlation between survival and metastasis, and CR level in epithelial ovarian cancer. Using anti-CR antibody, immunohistochemical staining was performed on 73 epithelial ovarian cancers, 13 borderline malignant tumours, and 25 benign ovarian tumours for a total of 111 specimens. The combined rate for strongly and weakly positive reactions for CR was 32.0% for benign tumours, 38.5% for borderline malignant tumours, and 61.6% for ovarian cancers. The CR-positive rate was 35.7% (weakly positive alone) for ovarian cancers with retroperitoneal lymph node (RLN) metastasis and 67.8% for those without RLN metastasis (P< 0.05). The 5-year survival rate was 62.7% for the patients with CR-negative cancer and 86.1% for those with CR-positive cancer (P< 0.05). The present results indicate that decreased CR expression in epithelial ovarian cancer is associated with RLN metastasis and poor survival.
Utilization of Substitutable Carbon and Phosphorus Sources by the Mixotrophic Chrysophyte Ochromonas Sp (1996)

In laboratory experiments, I studied the influences of bacterial density and light on the ingestion and growth rates, pigment contents, and the carbon and phosphorus turnover rates of the mixotrophic flagellate Ochromonas sp. The investigated strain is a bacterivorous flagellate that can enhance its photosynthetic apparatus and grow phototrophically when bacterial densities are low. This was also evident from significantly higher chlorophyll $a$ contents during active photosynthetic growth phases. Moderate phototrophic growth should be possible even if bacteria were absent. Bacterial ingestion rates increased hyperbolically with bacterial density, and there was no difference between light— and dark—adapted cells. Ochromonas released soluble reactive phosphorus (SRP) when growth was predominantly phagotrophic, but it took up SRP when growth was phototrophic. The mixotrophic strategy in Ochromonas appears to be bound up with costs and trade—offs: Ochromonas needs high bacterial densities to reach maximum growth rates, its basic metabolic costs are higher than for obligately phagotrophic flagellates, and its phototrophic growth rates are lower than for obligately phototrophic phytoplankton of comparable size.
(.+-.)-(Aminoalkyl)benzazepine Analogs: Novel Dopamine D1 Receptor Antagonists (1995)

(+/-)-(N-Alkylamino)benzazepine analogs were prepared as novel dopamine D1 receptor antagonists to further elucidate the role of these receptor subtypes in the pharmacology and toxicology of cocaine. In the first series of compounds, (+/-)-7-chloro-8-hydroxy-3- [6-(N,N-dimethylamino)-hexyl]-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepi ne (15) showed the highest affinity (Ki = 49.3 nM) and subtype-selectivity for dopamine D1 over dopamine D2, 5-HT2a, and 5-HT2c receptors. Compounds 7a [(+/-)-7-Chloro-8-hydroxy-3-[4-(N,N-dimethylamino)butyl]-1-phenyl- 2,3,4,5-tetrahydro-1H-3-benzazepine], 11 [(+/-)-7-chloro-8-hydroxy-3-[6-[(N,N-dimethylamino)hexyl]-1- phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-cyanoborane], and 15 were moderately potent dopamine D1 receptor antagonists as evidenced by their ability to block dopamine-stimulated adenylyl cyclase activity in rat caudate (predicted Ki values = 60, 34, and 21 nM, respectively). Compound 7a appears to be unique in that, despite its relatively potent inhibition of dopamine stimulated adenylyl cyclase, it demonstrated relatively weak binding affinity at the dopamine D1 receptors (Ki = 811 nM). Unlike previously reported N-alkylbenzazepines, where a significant loss in dopamine D1 receptor binding affinity was observed when successive increases in the alkyl side chain size at the benzazepine nitrogen were made, several of these novel N-alkylamino analogs demonstrated high-affinity binding with an optimal chain length of six carbons. This initial series of compounds appears to be identifying another binding domain on the dopamine D1 receptor protein that has not previously been characterized and that accepts an amino function. Further, these compounds may serve as templates for the design of peripherally active dopamine D1 receptor antagonists.
In-plane-gated quantum wire transistor fabricated with directly written focused ion beams (1990)

A new unipolar electronic device with a quasi-one-dimensional (1D) tunable carrier channel defined by directly written focused ion beams has been fabricated and characterized. Special features of the device are simple and rapid fabrication in one single technology step, inherent self-alignment, and linear instead of planar gates with very low capacitances. High integration as well as ultrahigh speed operation in logical and linear applications are feasible. The striking new aspect of this in-plane-gate structure is that the confining electric field is parallel to the two-dimensional electron gas, and the distorted, insulating region serves as a dielectric. Ballistic 1D transport is observed at low temperatures, and field-effect transistor operation of the device is demonstrated up to room temperature.
The Automation of a Sulphur Mine (1991)

ABSTRACT In December of 1988 a joint venture led by Freeport Sulphur Company discovered a major brimstone deposit of 67,000,000 long tons twenty miles offshore in the Gulf of Mexico. At a production of 2 million tons of sulphur per year this facility will be in operation for the next 30 years. This paper will cover the process of automating the frasch sulphur mine including design and planning, redundancy, reliability, training and configuration. A description of system architecture which allows information for production to be gathered and handled at the facility from process control, production and drilling will be presented. The ability to monitor and control the offshore platform from an onshore facility via satellite communications and the ability to network the process control system with a local area network of host and personal computers will be discussed. INTRODUCTION Main Pass Block 299, is located (Fig. 1) in 210 feet of water, 20 miles east of the mouth of the Mississippi River in the Gulf of Mexico. The production facilities will incorporate the latest technology based upon previous applications, the company's expertise in offshore sulphur mining and on proprietary mining techniques that use seawater in sulphur mining. The offshore production facility will be installed on a series of offshore platforms (Fig. 2) linked together by more than a mile of bridges. The Main Pass facilities are scheduled for completion in late 1991 with sulphur production beginning soon thereafter. One of the greatest tools in assisting operations achieve high safety and efficiency goals is through production automation. Improved productivity as well as improved management of production information can be realized from a modern process control system. Through automation and remote monitoring, operating costs can be reduced and production revenues increased. The strategy was to implement a completely integrated information system - one that gives the association of the process operations data with management and business systems data. AUTOMATION PROCESS Planning There are a great number of factors to consider when developing a plan for plantwide process control and flow of information. The needs and requirements of production planning, engineering, maintenance, material handling, scheduling and overall management are unique when it comes to process control data and business information systems. The first step in the planning of the control system was assembling a team of people from the various areas listed above. The company had to make a decision to make available the best that the company has to offer in the areas of production, maintenance and engineering to be a part of the team. Because of their other responsibilities in construction of this facility as well as running existing facilities it is almost impossible for them to spend a majority of their time on process automation alone. Once a team was established then the next step was to set the criteria for controlling the process and the handling of production data.
Determination of Δ1‐tetrahydrocannabinol in human fat biopsies from marihuana users by gas chromatography–mass spectrometry (1989)

Abstract A gas chromatographic–mass spectrometric (GC/MS) method for analysis of Δ 1 ‐tetrahydrocannabinol (Δ 1 ‐THC) in human fat samples is described. The fat sample, obtained from heavy marihuana users 1 week before and 4 weeks after smoking, is homogenized in hexane + 2‐propanol, centrifuged, and the supernatant mixed with Lipidex 5000. The solvent is evaporated and the dried gel is packed in a glass column. Δ 1 ‐THC is eluted from the column with methanol + water + acetic acid, diluted with water and the eluent is passed through a bed of Octadecylsilanebonded silica. After washing and drying, the retained Δ 1 ‐THC is eluted with hexane, derivatized with N‐methyl‐N‐( t ‐butyl‐dimethysilyl)trifluoroacetamide (MTBSTFA) and finally purified by HPLC on an Octadecyl SI 100 column in methanol. The amount of Δ 1 ‐THC is determined by GC/MS, using selected ion monitoring, and a deuterated internal standard. The recovery of Δ 1 ‐THC is about 80%, and the concentration of Δ 1 ‐THC in the fat samples analysed ranged between 0.4 and 193 ng/g wet tissue.
Cutting Edge: FcR-Like 5 on Innate B Cells Is Targeted by a Poxvirus MHC Class I-Like Immunoevasin (2010)

Under selective pressure from host immunity, viruses have retained genes encoding immunoevasins, molecules interfering with host viral recognition and clearance. Due to their binding specificities, immunoevasins can be exploited as affinity labels to identify host-encoded molecules of previously unsuspected importance in defense against the relevant class of virus. We previously described an orthopoxvirus MHC class I-like protein (OMCP) that binds with high affinity to the activating receptor NKG2D on NK and T cell subsets, implicating NKG2D in antiorthopoxvirus immunity. In this study, we report that OMCP also binds in an NKG2D-independent manner to B cells and monocytes/macrophages. We identify murine FcR-like 5 (FCRL5), an orphan immunoregulatory protein highly expressed by innate B lymphocytes, as a specific receptor for OMCP. The three N-terminal Ig domains of FCRL5 are required for OMCP binding. The targeting of FCRL5 by an orthopoxvirus immunoevasin strongly implicates it in contributing to host defense against zoonotic orthopoxviruses.
Passive snubber energy recovery for a GTO thyristor inverter bridge leg (2000)

This paper presents a turn-on and turn-off passive energy recovery snubber circuit suitable for high-voltage high-power gate-turn-off thyristor inverter bridge configurations. The circuit recovers not only inductive turn-on and capacitive turn-off snubber energies, but also energies associated with freewheel diode reverse recovery. Energy is transferred back to the DC supply via a high-frequency transformer, that is fully reset. A method for reducing the transformer secondary diode voltage stress is presented. The performance of the circuit is supported by PSpice simulation, mathematical analysis, and practical results.
Adaptation of Methicillin-Resistant Staphylococcus aureus in the Face of Vancomycin Therapy (2005)

For the past 2 decades, vancomycin has served as the cornerstone of therapy against serious methicillin-resistant Staphylococcus aureus infections. This role is increasingly challenged by questions of efficacy, including reduced efficacy against infections caused by glycopeptide-intermediate S. aureus strains. In an evaluation of clinical glycopeptide-intermediate S. aureus isolates and serial, clinical methicillin-resistant S. aureus isolates obtained from patients receiving vancomycin for the treatment of bacteremia, we found that loss of function of the accessory gene regulator operon may confer a survival advantage to S. aureus under vancomycin selection pressure, particularly in strains with the accessory gene regulator group II genotype. Other advantages in a nosocomial setting may include enhancement of biofilm formation and promotion of physiologic changes supporting colonization. We conclude that loss of accessory gene regulator function in methicillin-resistant S. aureus might, in part, explain the decreased efficacy of vancomycin in the therapy of methicillin-resistant S. aureus bacteremia, thus highlighting the need to reevaluate the criteria of susceptibility to vancomycin.
Self-peptide released from class II HLA-DR1 exhibits a hydrophobic two-residue contact motif. (1992)

Peptide fragments of foreign and self-proteins are of great immunologic importance as their binding to major histocompatibility complex (MHC) class I or II molecules makes an interaction with a corresponding T cell receptor possible. Recently, allele-specific peptide sequence motifs proved to be responsible for MHC binding, no matter whether self- or non-self-antigens were involved. Up to now, all investigated human class II-associated peptides were derived from foreign antigenic proteins. Therefore, we undertook sequence and binding analyses with a 16-mer self-peptide (SP3) that has been eluted from HLA-DR1. Here we demonstrate, by synthetic polyalanine-based 13-mer analogues of SP3, that two bulky hydrophobic anchor residues with relative spacing i, i + 8 are sufficient for high affinity binding. This is consistent with the hydrophobic i, i + 8 binding pattern recently found for DR-restricted T cell epitopes. Nevertheless, highly helical alanine-based design peptides with anchor spacing i, i + 9 exhibit maximal affinity, whereas replacement of alanine by helix destabilizing proline abrogates binding. Thus, a two-residue contact motif is the common minimal requirement of self- and foreign peptides for high affinity anchoring to HLA-DR1. In contrast to class I, the anchor spacing of DR1-associated peptides seems to bear some variability due to conformational diversity.
(S,S)-trans-Cyclopentane-Constrained Peptide Nucleic Acids. A General Backbone Modification that Improves Binding Affinity and Sequence Specificity (2004)

Replacing the ethylenediamine portion of aminoethylglycine peptide nucleic acids (aegPNAs) with one or more (S,S)-trans-cyclopentane diamine units significantly increases binding affinity and sequence specificity to complementary DNA, making these modified PNAs ideal for use as nucleic acid probes in genomic analysis. The synthesis and study of this new class of PNAs (tcypPNAs) is described in which trans-cyclopentane diamine has been incorporated into several positions, and in varying number, within PNA backbones of mixed-base sequences.
Synthesis, characterization and pharmacological screening of some isatinoid compounds (2002)

Schiff bases and hydrazones of substituted isatins have been prepared by reacting isatin and the appropriate aromatic primary amine / hydrazines and characterized by spectral and elementary analysis. The compounds have been screened for analgesic, antiinflammatory and antipyretic activity. 3[(4-Bromo phenylidene)-1-amino] isatin is the only compound to exhibit all the activities. 3[(4-Bromo phenylidene)-1-amino] isatin and 3[(4-Bromo phenylidene)-1-amino]-5-methyl isatin possesses analgesic activity equipotent to paracetamol. 3(4-Phenylhydrazino) isatin and 3(thiosemicarbazino) isatin exhibit marked reduction of acetic acid induced inflammation. 3[(4-Methyl phenylidene)-1-amino] isatin at 200 mg/kg exhibits pronounced antipyretic activity comparable to paracetamol.
FISH analysis of 107 prostate cancers shows that PTEN genomic deletion is associated with poor clinical outcome (2007)

This study examines the clinical impact of PTEN genomic deletions using fluorescence in situ hybridisation (FISH) analysis of 107 prostate cancers, with follow-up information covering a period of up to 10 years. Tissue microarray analysis using interphase FISH indicated that hemizygous PTEN losses were present in 42/107 (39%) of prostatic adenocarcinomas, with a homozygous PTEN deletion observed in 5/107 (5%) tumours. FISH analysis using closely linked probes centromeric and telomeric to the PTEN indicated that subband microdeletions accounted for approximately 70% genomic losses. Kaplan-Meier survival analysis of PTEN genomic losses (hemizygous and homozygous deletion vs not deleted) identified subgroups with different prognosis based on their time to biochemical relapse after surgery, and demonstrated significant association between PTEN deletion and an earlier onset of disease recurrence (as determined by prostate-specific antigen levels). Homozygous PTEN deletion was associated with a much earlier onset of biochemical recurrence (P=0.002). Furthermore, PTEN loss at the time of prostatectomy correlated with clinical parameters of more advanced disease, such as extraprostatic extension and seminal vesicle invasion. Collectively, our data indicates that haploinsufficiency or PTEN genomic loss is an indicator of more advanced disease at surgery, and is predictive of a shorter time to biochemical recurrence of disease.
Host-Pathogen Interactions: Redefining the Basic Concepts of Virulence and Pathogenicity (1999)

While preparing to teach the Microbial Pathogenesis graduate course at our institution, we found ourselves struggling to find basic definitions of virulence and pathogenicity that incorporated the contributions of both the host and the pathogen. The generally used definition of a pathogen as a microbe that causes disease in a host (Table 1) seemed inadequate, because some microbes do not cause clinically evident disease in all hosts. As we investigated the origins of the modern concepts of microbial pathogenesis, we found that while the importance of a host’s susceptibility for a microbe’s virulence was often recognized, the existing definitions did not account for the contributions of both pathogen and host. Historical definitions of pathogens were based on their ability to cause disease as an invariant trait. An integrated view of microbial pathogenesis accounting for the contributions of both host and pathogen has not been developed. In this article, we review historical concepts of microbial pathogenicity and virulence, propose new definitions, and suggest a classification system for microbial pathogens based on their ability to cause damage as a function of the host’s immune response.