gebhart/patrepeval huggingface dataset:
Growth factor-independent activation of protein kinase B contributes to the inherent resistance of vascular endothelium to radiation-induced apoptotic response. (2003)

The phosphatidylinositol 3'-kinase (PI3K)/protein kinase B (Akt) signal transduction pathway plays a critical role in mediating endothelial cell survival during oxidative stress. The role of the PI3K/Akt pathway in promoting cell viability was studied in vascular endothelial cells treated with ionizing radiation. Western blot analysis showed that Akt was phosphorylated rapidly in response to radiation in primary culture human umbilical vein endothelial cells in the absence of serum or growth factors. Akt phosphorylation occurred after doses as low as 1 Gy. PI3K consists of p85 and p110 subunits, which play a central role in Akt activation in response to exogenous stimuli. A mutation within the Src homology region 2 domain of mutant p85 (Deltap85) prevented radiation-induced Akt phosphorylation, when overexpressed in endothelial cells. Vascular endothelial cells transduced with control vector were resistant to radiation-induced apoptosis, whereas endothelial cell transduction with adenovirus encoding the mutated p85 (Ad.Deltap85) reversed this resistance to apoptosis after treatment with intermediate radiation doses (2-6 Gy). Deltap85 overexpression alone had no effect on the viability or apoptosis of endothelial cells. However, irradiated endothelial cells overexpressing Deltap85 released cytochrome c into the cytosol fraction and activated proteolytic cleavage of caspases 3 and 9, thereby inducing the apoptotic response. Inhibition of caspase 3 blocked endothelial apoptosis induced by overexpression of Deltap85 and radiation. These findings suggest that growth factor-independent activation of Akt contributes, in part, to the inherent resistance of irradiated vascular endothelium to the activation of apoptotic response.
Multidimensional Optical Sensing and Imaging System (MOSIS): From Macroscales to Microscales (2017)

Multidimensional optical imaging systems for information processing and visualization technologies have numerous applications in fields such as manufacturing, medical sciences, entertainment, robotics, surveillance, and defense. Among different three-dimensional (3-D) imaging methods, integral imaging is a promising multiperspective sensing and display technique. Compared with other 3-D imaging techniques, integral imaging can capture a scene using an incoherent light source and generate real 3-D images for observation without any special viewing devices. This review paper describes passive multidimensional imaging systems combined with different integral imaging configurations. One example is the integral-imaging-based multidimensional optical sensing and imaging systems (MOSIS), which can be used for 3-D visualization, seeing through obscurations, material inspection, and object recognition from microscales to long range imaging. This system utilizes many degrees of freedom such as time and space multiplexing, depth information, polarimetric, temporal, photon flux and multispectral information based on integral imaging to record and reconstruct the multidimensionally integrated scene. Image fusion may be used to integrate the multidimensional images obtained by polarimetric sensors, multispectral cameras, and various multiplexing techniques. The multidimensional images contain substantially more information compared with two-dimensional (2-D) images or conventional 3-D images. In addition, we present recent progress and applications of 3-D integral imaging including human gesture recognition in the time domain, depth estimation, mid-wave-infrared photon counting, 3-D polarimetric imaging for object shape and material identification, dynamic integral imaging implemented with liquid-crystal devices, and 3-D endoscopy for healthcare applications.
Synthesis of Glycoconjugate Vaccines against Shigella dysenteriae Type 1 (1998)

Syntheses of a hexadecasaccharide and smaller fragments corresponding to one-four repeating units of the O-specific polysaccharide of Shigella dysenteriae type 1 are reported in a reactive aglycon-linked from. Two tetrasaccharide donor/acceptor repeating units were assembled from monosaccharide precursors in a stepwise fashion and used in a linear, iterative manner to construct the higher-membered saccharides using Schmidt's glycosylation technique that proved superior to others tested. Single-point attachment of the saccharides to human serum albumin, using a secondary heterobifunctional spacer, afforded a range of glycoconjugates for a detailed evaluation of their immunological characteristics.
Nucleotide sequence analysis of tetracycline resistance gene tetO from Streptococcus mutans DL5 (1988)

Streptococcus mutans DL5, isolated from the dental plaque of a pig, was resistant to high levels of streptomycin (Sm, 20 mg/ml), erythromycin (Em, 1 mg/ml), and tetracycline (Tc, greater than 100 micrograms/ml), but contained no detectable plasmid DNA. The Smr and Emr determinants were cloned from cellular DNA on the self-replicating 5-kilobase-pair (kbp) EcoRI fragment of pAM beta 1 and the 4.2-kbp cryptic plasmid pVA380-1, respectively, by transformation of Streptococcus sanguis Challis. Helper plasmid cloning, with a Challis host containing pVA380-1, was required to clone the Tcr determinant of strain DL5 on this vector. A single-colony isolate of the original Tcr clone contained a hybrid plasmid, pDL421, composed of 2.6 kbp of vector DNA and 11.4 kbp of S. mutans DNA. Plasmid pDL421 did not hybridize to plasmids containing the streptococcal Tcr determinants tetL, tetM, and tetN. A shortened derivative of this hybrid plasmid, pDL422, missing a 4.9-kbp HincII fragment from the S. mutans DNA but still encoding Tcr, was obtained by subcloning in S. sanguis Challis. The Tcr gene was located in a 1,917-base-pair open reading frame (ORF) corresponding to a 72-kilodalton protein. The ORF exhibited 99.4% sequence identity with the 1,917-base-pair tetO gene from a strain of Campylobacter coli (W. Sougakoff, B. Papadopoulou, P. Nordmann, and P. Courvalin, FEMS Microbiol. Lett. 44:153-160, 1987). A 1.67-kbp NdeI fragment, internal to the ORF from strain DL5, as well as pDL421 hybridized under stringent conditions to DNA from 10 of 10 Tcr strains of C. coli and Campylobacter jejuni from human and animal sources, but not to DNA from Tcs isolates of these two species.
Estimating kinetic parameters from dynamic contrast-enhanced t1-weighted MRI of a diffusable tracer: Standardized quantities and symbols (1999)

We describe a standard set of quantity names and symbols related to the estimation of kinetic parameters from dynamic contrast-enhanced T(1)-weighted magnetic resonance imaging data, using diffusable agents such as gadopentetate dimeglumine (Gd-DTPA). These include a) the volume transfer constant K(trans) (min(-1)); b) the volume of extravascular extracellular space (EES) per unit volume of tissue v(e) (0 < v(e) < 1); and c) the flux rate constant between EES and plasma k(ep) (min(-1)). The rate constant is the ratio of the transfer constant to the EES (k(ep) = K(trans)/v(e)). Under flow-limited conditions K(trans) equals the blood plasma flow per unit volume of tissue; under permeability-limited conditions K(trans) equals the permeability surface area product per unit volume of tissue. We relate these quantities to previously published work from our groups; our future publications will refer to these standardized terms, and we propose that these be adopted as international standards.
New and Emerging Therapies for Sepsis (2002)

With the recent approval of drotrecogin alfa, there is renewed optimism that we can effectively reduce sepsis-associated mortality.
A physically-based haptic rendering for telemanipulation with visual information: Macro and micro applications (2008)

This paper presents a haptic rendering technique for a telemanipulation system of deformable objects using image processing techniques and physically based modeling. The interaction forces between an instrument driven by a haptic device and a deformable object are inferred in real time based on a continuum mechanics model of the object, which consists of a boundary element model and a prior knowledge of the object’s mechanical properties. These models allow users to feel reaction forces during manipulation tasks through a haptic device. Macro- and micro-scale experimental systems, equipped with a telemanipulation system and a commercial haptic display, were developed and tested using silicone (macro-scale) and zebrafish embryos (micro-scale). The developed algorithm can be used with a needle operation robot or a cellular injection system.
High incidence of chromosome 13 deletion in multiple myeloma detected by multiprobe interphase FISH (2000)

Multiple myeloma (MM) is a hypoproliferative malignancy yielding informative karyotypes in no more than 30% of newly diagnosed cases. Although cytogenetic and molecular deletion of chromosome 13 is associated with poor prognosis, a MM tumor suppressor gene (TSG) has not been identified. To localize a minimal deleted region of chromosome 13, clonotypic plasma cells from 50 consecutive patients with MM were subjected to interphase fluorescence in situ hybridization (FISH) analysis using a panel of 11 probes spanning the entire long arm of chromosome 13. Whereas chromosome 13 abnormalities were absent in plasma cells from 25 normal donors, 86% of patients with MM demonstrated such aberrations. Heterogeneity, both in deletion frequency and extent, was confirmed by simultaneous FISH with 2 chromosome 13 probes. Deletion hot spots were noted at D13S272 (70%) and D13S31 (64%), 2 unlinked loci at 13q14. Homozygous deletions at these loci occurred in 12% (simultaneously in 8%) of the cases. Molecular deletions were found in all 14 patients with morphologic deletions, in 21 of 24 with uninformative karyotypes, and 8 of 12 patients with karyotype abnormalities lacking chromosome 13 deletion. Homozygous deletion of any marker was noted in 4% with low and in 36% with higher plasma cell labeling index greater than 0.4% (P = .01). The absence of increasing deletion incidence and extent with therapy duration suggests that the observed lesions are not induced by treatment. The high incidence and extent of chromosome 13 deletions require the correlation of specific deletion(s) with poor prognosis. These analyses will provide valuable guidance toward cloning of an MM-TSG.
AFRAID: a frequently redundant array of independent disks (1996)

Disk arrays are commonly designed to ensure that stored data will always be able to withstand a disk failure, but meeting this goal comes at a significant cost in performance. We show that this is unnecessary. By trading away a fraction of the enormous reliability provided by disk arrays, it is possible to achieve performance that is almost as good as a non-parityprotected set of disks. In particular, our AFRAID design eliminates the smallupdate penalty that plagues traditional RAID 5 disk arrays. It does this by applying the data update immediately, but delaying the parity update to the next quiet period between bursts of client activity. That is, AFRAID makes sure that the array is frequently redundant, even if it isn’t always so. By regulating the parity update policy, AFRAID allows a smooth trade-off between performance and availability. Under real-life workloads, the AFRAID design can provide close to the full performance of an array of unprotected disks, and data availability comparable to a traditional RAID 5. Our results show that AFRAID offers 42 % better performance for only 10 % less availability, 97 % better for 23 % less, and as much as a factor of 4.1 times better performance for giving up less than half RAID 5’s availability. We explore here the detailed availability and performance implications of the AFRAID approach. 1.
Self-Organization of a Mesoscale Bristle into Ordered, Hierarchical Helical Assemblies (2009)

Mesoscale hierarchical helical structures with diverse functions are abundant in nature. Here we show how spontaneous helicity can be induced in a synthetic polymeric nanobristle assembling in an evaporating liquid. We use a simple theoretical model to characterize the geometry, stiffness, and surface properties of the pillars that favor the adhesive self-organization of bundles with pillars wound around each other. The process can be controlled to yield highly ordered helical clusters with a unique structural hierarchy that arises from the sequential assembly of self-similar coiled building blocks over multiple length scales. We demonstrate their function in the context of self-assembly into previously unseen structures with uniform, periodic patterns and controlled handedness and as an efficient particle-trapping and adhesive system.
The biology of skin grafts. Skin grafts as pharmacologic agents (1993)

<h3>† Background.—</h3> Skin grafting is commonly used to treat nonhealing wounds. However, how skin grafts help to heal wounds is not entirely known. Why epithelium from grafted skin is able to migrate and cover these wounds, while epithelium at the edge of nonhealing wounds is unable to, is a long unanswered biologic question. <h3>Observations.—</h3> The recent use of cultured epithelial allografts has rekindled interest in the biology of skin grafts. Replaced, even in chronic wounds, by recipient epithelium, cultured epithelial allografts appear to work by providing a potent stimulus to healing imparted by the graft itself. Based on this, we have reassessed how skin autografts help to heal wounds and hypothesize that, in a similar fashion, autografts may work not only by replacing tissue but also by providing a stimulus for healing. <h3>Conclusions.—</h3> We suggest that skin grafts may work not only as tissue replacement but as pharmacologic agents that provide a stimulus for healing. We believe that, someday, it may be possible to augment the stimulatory properties of donor skin to speed healing of the recipient wound. (<i>Arch Dermatol.</i>1993;129:481-483)
Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes. (1990)

The gene for ricin toxin A chain was modified by site-specific mutagenesis to change arginine 180 to alanine, glutamine, methionine, lysine, or histidine. Separately, glutamic acid 177 was changed to alanine and glutamic acid 208 was changed to aspartic acid. Both the wild-type and mutant proteins were expressed in Escherichia coli and, when soluble, purified and tested quantitatively for enzyme activity. A positive charge at position 180 was found necessary for solubility of the protein and for enzyme activity. Similarly, a negative charge with a proper geometry in the vicinity of position 177 was critical for ricin toxin A chain catalysis. When glutamic acid 177 was converted to alanine, nearby glutamic acid 208 could largely substitute for it. This observation provided valuable structural information concerning the nature of second-site mutations.
A Petri-Net-Based Scheduling Strategy for Dual-Arm Cluster Tools With Wafer Revisiting (2013)

There are wafer fabrication processes in cluster tools that require wafer revisiting. The adoption of a swap strategy for such tools forms a 3-wafer cyclic (3-WC) period with three wafers completed in each period. It has been shown that, by such a scheduling strategy, the minimal cycle time cannot be reached for some cases. This raises a question of whether there is a scheduling method such that the performance can be improved. To answer this question, a dual-arm cluster tool with wafer revisiting is modeled by a Petri net. Based on the model, the dynamical behavior of the process is analyzed. Then, a 2-wafer cyclic (2-WC) scheduling strategy is revealed for the first time. Cycle time analysis is conducted for the proposed strategy to evaluate its performance. It shows that, for some cases, the performance obtained by a 2-WC schedule is better than that obtained by any existing 3-WC ones. Thus, they can be used to complement each other in scheduling dual-arm cluster tools with wafer revisiting. Illustrative examples are given.
Controllable Work Function of Li:Al Alloy Nanolayers for Organic Light‐Emitting Devices (2005)

The surface of Li:Al nanolayers that were deposited by thermal evaporation of Li:Al alloy sources has been measured by ultraviolet photoelectron spectroscopy, which exhibited huge variation with the Li:Al nanolayer thickness. The hybrid organic light‐emitting devices with the controlled Li:Al nanolayer surface contacts as an electron‐injecting layer showed linearly varied charge transport and turn‐on voltages with the work function of the nanolayer surfaces.
Prevalence of Vibrio cholerae O1 El Tor variant in a cholera-endemic zone of Kenya (2014)

Since 2007, Kenya has experienced an increase in cholera outbreaks characterized by a high fatality rate. In this study, we characterized 81 Vibrio cholerae isolates from diarrhoeal stool samples in Nyanza, a cholera-endemic lake region of Kenya, for virulence properties, clonality and antibiotic susceptibility. Eighty of these isolates were V. cholerae O1 El Tor variants carrying the classical ctxB gene sequence, while one isolate was V. cholerae non-O1/O139. All of the El Tor variants were of clonal origin, as revealed by PFGE, and were susceptible to ampicillin, tetracycline, ciprofloxacin, fosfomycin, kanamycin and norfloxacin. However, the isolates showed resistance to sulfamethoxazole/trimethoprim and streptomycin, and intermediate resistance to nalidixic acid, chloramphenicol and imipenem. The non-O1/O139 isolate carried the cholix toxin II gene (chxA II) and was susceptible to all antimicrobials tested except ampicillin. We propose that an El Tor variant clone caused the Nyanza cholera outbreak of 2007-2008.
An unusual atrial tachycardia in a patient with Friedreich ataxia (2011)

We present the unusual association of an atrial tachycardia with Friedreich ataxia. The arrhythmia was initially suspected to be focal in origin; however, use of a three-dimensional mapping system demonstrated that the tachycardia was macro-reentrant. This was subsequently treated successfully by linear ablation.
Probiotics: their role in the treatment and prevention of disease (2006)

A probiotic is a "live microbial food ingredients that, when ingested in sufficient quantities, exerts health benefits on the consumer". Probiotics exert their benefits through several mechanisms; they prevent colonization, cellular adhesion and invasion by pathogenic organisms, they have direct antimicrobial activity and they modulate the host immune response. The strongest evidence for the clinical effectiveness of probiotics has been in their use for the prevention of symptoms of lactose intolerance, treatment of acute diarrhea, attenuation of antibiotic-associated gastrointestinal side effects and the prevention and treatment of allergy manifestations. More research needs to be carried out to clarify conflicting findings on the use of probiotics for prevention of travelers' diarrhea, infections in children in daycare and dental caries, and elimination of nasal colonization with potentially pathogenic bacteria. Promising ongoing research is being conducted on the use of probiotics for the treatment of Clostridium difficile colitis, treatment of Helicobacter pylori infection, treatment of inflammatory bowel disease and prevention of relapse, treatment of irritable bowel syndrome, treatment of intestinal inflammation in cystic fibrosis patients, and prevention of necrotizing enterocolitis in premature infants. Finally, areas of future research include the use of probiotics for the treatment of rheumatoid arthritis, prevention of cancer and the treatment of graft-versus-host disease in bone marrow transplant recipients.
Structure and expression of neutrophil gelatinase cDNA. Identity with type IV collagenase from HT1080 cells. (1992)

Neutrophils synthesize and store intracellularly a 92-kDa type IV collagenase (gelatinase), the primary structure of which is unknown. We designed a primer based on the highly conserved cysteine-switch region of metalloproteinases and employed the polymerase chain reaction to generate a probe of the human neutrophil gelatinase (HNG) gene. This probe was used to clone the cDNA encoding HNG by screening a chronic granulocytic leukemia cDNA library. In vitro translation of the cDNA-derived HNG mRNA yielded a major product of 78 kDa and smaller autolytically activated or degraded products, all of which were recognized by anti-HNG antibody. The HNG cDNA sequence is nearly identical to that encoding a 92-kDa gelatinase secreted by HT1080 cells. In addition, primer extension and S1 analysis reveal that the above two gelatinase transcripts have similar initiation sites. The HNG cDNA hybridized to a 2.8-kilobase mRNA from chronic granulocytic leukemia cells. HNG mRNA expression was absent from uninduced HL60 cells and from HL60 cells induced to granulocytic maturation with Me2SO. However, unlike other neutrophil secondary granule genes, HNG mRNA was detected in HL60 cells induced to monocytic maturation with 12-O-tetradecanoylphorbol 13-acetate. This suggests that the HNG gene may be subject to differential control pathways in two related but distinct hematopoietic lineages.
DeepDriving: Learning Affordance for Direct Perception in Autonomous Driving (2015)

Today, there are two major paradigms for vision-based autonomous driving systems: mediated perception approaches that parse an entire scene to make a driving decision, and behavior reflex approaches that directly map an input image to a driving action by a regressor. In this paper, we propose a third paradigm: a direct perception approach to estimate the affordance for driving. We propose to map an input image to a small number of key perception indicators that directly relate to the affordance of a road/traffic state for driving. Our representation provides a set of compact yet complete descriptions of the scene to enable a simple controller to drive autonomously. Falling in between the two extremes of mediated perception and behavior reflex, we argue that our direct perception representation provides the right level of abstraction. To demonstrate this, we train a deep Convolutional Neural Network using recording from 12 hours of human driving in a video game and show that our model can work well to drive a car in a very diverse set of virtual environments. We also train a model for car distance estimation on the KITTI dataset. Results show that our direct perception approach can generalize well to real driving images. Source code and data are available on our project website.