gebhart/patrepeval huggingface dataset:
Fully convolutional neural networks for polyp segmentation in colonoscopy (2017)

Colorectal cancer (CRC) is one of the most common and deadliest forms of cancer, accounting for nearly 10% of all forms of cancer in the world. Even though colonoscopy is considered the most effective method for screening and diagnosis, the success of the procedure is highly dependent on the operator skills and level of hand-eye coordination. In this work, we propose to adapt fully convolution neural networks (FCN), to identify and segment polyps in colonoscopy images. We converted three established networks into a fully convolution architecture and fine-tuned their learned representations to the polyp segmentation task. We validate our framework on the 2015 MICCAI polyp detection challenge dataset, surpassing the state-of-the-art in automated polyp detection. Our method obtained high segmentation accuracy and a detection precision and recall of 73.61% and 86.31%, respectively.
Is 1,25-Dihydroxyvitamin D Required for Reproduction? (1989)

The role of 1,25-dihydroxyvitamin D (1,25-(OH)2D) in avian and mammalian reproduction is examined. 1,25-Dihydroxyvitamin D is required, in both the avian and mammalian species, for maintenance of normocalcemia, adequate intestinal calcium absorption, bone turnover, and mineral homeostasis throughout the reproductive cycle— just as it is required in the nonlaying bird or nonpregnant, nonlactating mammal. In the avian species, 1,25-(OH)2D is required for ovulation and shell formation, transfer of calcium from the egg shell across the chorioallantoic membrane to the fetal circulation, and maintenance of fetal serum calcium, bone metabolism, and mineral homeostasis. In the mammalian species, 1,25-(OH)2D is required for normal ovulation, normal fetal and neonatal bone metabolism, milk production, and maintenance of normocalcemia and mineral homeostasis in the neonate. In the absence of 1,25-(OH)2D, however, embryogenesis (rat and chick) and neonatal development (rat) can proceed in such a way as to produce viable, normal appearing offspring. The classical effects of 1,25-(OH)2D deficiency (hypocacemia, inadequate intestinal calcium absorption, and bone mineralization) become increasingly apparent with advancing age but their are no other apparent major developmental abnormalities.
Photochemical organometallic vapor phase epitaxy of mercury cadmium telluride (1986)

Mercury cadmium telluride has been successfully grown by the photolysis of dimethylmercury, dimethylcadmium, and dimethyltelluride, using an ArF excimer laser operating at 193 nm as the radiation source. Growths were accomplished on CdTe substrates at a temperature of 150 °C, with a growth rate of 4 μm per hour. Films are shiny, and x-ray diffraction indicates epitaxial growth. Secondary ion mass spectroscopy and infrared transmission measurements indicate that the composition of the initial films is Hg0.2Cd0.8Te. Details of the growth apparatus and additional data is presented.
Rho protein inactivation induced apoptosis of cultured human endothelial cells (2002)

Small GTP-binding Rho GTPases regulate important signaling pathways in endothelial cells, but little is known about their role in endothelial cell apoptosis. Clostridial cytotoxins specifically inactivate GTPases by glucosylation [Clostridium difficile toxin B-10463 (TcdB-10463), C. difficile toxin B-1470 (TcdB-1470)] or ADP ribosylation (C. botulinum C3 toxin). Exposure of human umbilical cord vein endothelial cells (HUVEC) to TcdB-10463, which inhibits RhoA/Rac1/Cdc42, or to C3 toxin, which inhibits RhoA, -B, -C, resulted in apoptosis, whereas inactivation of Rac1/Cdc42 with TcdB-1470 was without effect, suggesting that Rho inhibition was responsible for endothelial apoptosis. Disruption of endothelial microfilaments as well as inhibition of p160ROCK did not induce endothelial apoptosis. Exposure to TcdB-10463 resulted in activation of caspase-9 and -3 but not caspase-8 in HUVEC. Moreover, Rho inhibition reduced expression of antiapoptotic Bcl-2 and Mcl-1 and increased proapoptotic Bid but had no effect on Bax or FLIP protein levels. Caspase-3 activity and apoptosis induced by TcdB-10463 were abolished by cAMP elevation. In summary, inhibition of Rho in endothelial cells activates caspase-9- and -3-dependent apoptosis, which can be antagonized by cAMP elevation.
Hydrogenated amorphous silicon nitride photonic crystals for improved-performance surface electromagnetic wave biosensors (2012)

We exploit the properties of surface electromagnetic waves propagating at the surface of finite one dimensional photonic crystals to improve the performance of optical biosensors with respect to the standard surface plasmon resonance approach. We demonstrate that the hydrogenated amorphous silicon nitride technology is a versatile platform for fabricating one dimensional photonic crystals with any desirable design and operating in a wide wavelength range, from the visible to the near infrared. We prepared sensors based on photonic crystals sustaining either guided modes or surface electromagnetic waves, also known as Bloch surface waves. We carried out for the first time a direct experimental comparison of their sensitivity and figure of merit with surface plasmon polaritons on metal layers, by making use of a commercial surface plasmon resonance instrument that was slightly adapted for the experiments. Our measurements demonstrate that the Bloch surface waves on silicon nitride photonic crystals outperform surface plasmon polaritons by a factor 1.3 in terms of figure of merit.
The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity (2012)

New bioinformatic tools are needed to analyze the growing volume of DNA sequence data. This is especially true in the case of secondary metabolite biosynthesis, where the highly repetitive nature of the associated genes creates major challenges for accurate sequence assembly and analysis. Here we introduce the web tool Natural Product Domain Seeker (NaPDoS), which provides an automated method to assess the secondary metabolite biosynthetic gene diversity and novelty of strains or environments. NaPDoS analyses are based on the phylogenetic relationships of sequence tags derived from polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, respectively. The sequence tags correspond to PKS-derived ketosynthase domains and NRPS-derived condensation domains and are compared to an internal database of experimentally characterized biosynthetic genes. NaPDoS provides a rapid mechanism to extract and classify ketosynthase and condensation domains from PCR products, genomes, and metagenomic datasets. Close database matches provide a mechanism to infer the generalized structures of secondary metabolites while new phylogenetic lineages provide targets for the discovery of new enzyme architectures or mechanisms of secondary metabolite assembly. Here we outline the main features of NaPDoS and test it on four draft genome sequences and two metagenomic datasets. The results provide a rapid method to assess secondary metabolite biosynthetic gene diversity and richness in organisms or environments and a mechanism to identify genes that may be associated with uncharacterized biochemistry.
Automated Lead Optimization of MMP-12 Inhibitors Using a Genetic Algorithm (2010)

Traditional lead optimization projects involve long synthesis and testing cycles, favoring extensive structure-activity relationship (SAR) analysis and molecular design steps, in an attempt to limit the number of cycles that a project must run to optimize a development candidate. Microfluidic-based chemistry and biology platforms, with cycle times of minutes rather than weeks, lend themselves to unattended autonomous operation. The bottleneck in the lead optimization process is therefore shifted from synthesis or test to SAR analysis and design. As such, the way is open to an algorithm-directed process, without the need for detailed user data analysis. Here, we present results of two synthesis and screening experiments, undertaken using traditional methodology, to validate a genetic algorithm optimization process for future application to a microfluidic system. The algorithm has several novel features that are important for the intended application. For example, it is robust to missing data and can suggest compounds for retest to ensure reliability of optimization. The algorithm is first validated on a retrospective analysis of an in-house library embedded in a larger virtual array of presumed inactive compounds. In a second, prospective experiment with MMP-12 as the target protein, 140 compounds are submitted for synthesis over 10 cycles of optimization. Comparison is made to the results from the full combinatorial library that was synthesized manually and tested independently. The results show that compounds selected by the algorithm are heavily biased toward the more active regions of the library, while the algorithm is robust to both missing data (compounds where synthesis failed) and inactive compounds. This publication places the full combinatorial library and biological data into the public domain with the intention of advancing research into algorithm-directed lead optimization methods.
An accurate and adaptive pedometer integrated in mobile health application (2010)

An interesting and valuable application in sensor network technology is Personalised Rehabilitation. In particular, through the combination of a smart phone and wearable sensors, patients can follow and have feedback on their exercise programmes, while enhancing the medical monitoring. In this paper, we design a system to measure the patient's activity by estimating his walking habits. The system, ready to be integrated in a mobile health application, consists of an inertial sensor with a tri-axial orthogonal accelerometer attached to patient's foot, while the sensor is connected to a smart phone for data processing. Additionally, we propose an algorithm for step detection and gait state estimation. The challenge is to provide reliable and accurate detection when pacers are in different gait states. Also, the algorithm will reduce error drifts at start moment when sensor signals are very unstable. Extensive experiment results will demonstrate that the algorithm provides good performance in terms of accuracy, adaptability and memory use.
Axial-cones (2010)

Catadioptric imaging systems are commonly used for wide-angle imaging, but lead to multi-perspective images which do not allow algorithms designed for perspective cameras to be used. Efficient use of such systems requires accurate geometric ray modeling as well as fast algorithms. We present accurate geometric modeling of the multi-perspective photo captured with a spherical catadioptric imaging system using axial-cone cameras: multiple perspective cameras lying on an axis each with a different viewpoint and a different cone of rays. This modeling avoids geometric approximations and allows several algorithms developed for perspective cameras to be applied to multi-perspective catadioptric cameras. We demonstrate axial-cone modeling in the context of rendering wide-angle light fields, captured using a spherical mirror array. We present several applications such as spherical distortion correction, digital refocusing for artistic depth of field effects in wide-angle scenes, and wide-angle dense depth estimation. Our GPU implementation using axial-cone modeling achieves up to three orders of magnitude speed up over ray tracing for these applications.
GPU-accelerated high-quality hidden surface removal (2005)

High-quality off-line rendering requires many features not natively supported by current commodity graphics hardware: wide smooth filters, high sampling rates, order-independent transparency, spectral opacity, motion blur, depth of field. We present a GPU-based hidden-surface algorithm that implements all these features. The algorithm is Reyes-like but uses regular sampling and multiple passes. Transparency is implemented by depth peeling, made more efficient by opacity thresholding and a new method called z batches. We discuss performance and some design trade-offs. At high spatial sampling rates, our implementation is substantially faster than a CPU-only renderer for typical scenes.
Interface Design of Man-Machine Engineering System Based on SkinMagic (2010)

Interfaces of man-machine engineering system are not ideal, one method is proposed: interface design method of man-machine engineering system based on SkinMagic. First, a common design method is introduced briefly. Then, the implementation principle of the SkinMagic method is given depth analysis, and the correct guidance of using it is given. Finally, its advantages and disadvantages are discussed, and its feasibility is verified in the practical application.
Combating Friend Spam Using Social Rejections (2015)

Unwanted friend requests in online social networks (OSNs), also known as friend spam, are among the most evasive malicious activities. Friend spam can result in OSN links that do not correspond to social relationship among users, thus pollute the underlying social graph upon which core OSN functionalities are built, including social search engine, ad targeting, and OSN defense systems. To effectively detect the fake accounts that act as friend spammers, we propose a system called Rejecto. It stems from the observation on social rejections in OSNs, i.e., Even well-maintained fake accounts inevitably have their friend requests rejected or they are reported by legitimate users. Our key insight is to partition the social graph into two regions such that the aggregate acceptance rate of friend requests from one region to the other is minimized. This design leads to reliable detection of a region that comprises friend spammers, regardless of the request collusion among the spammers. Meanwhile, it is resilient to other strategic manipulations. To efficiently obtain the graph cut, we extend the Kernighan-Lin heuristic and use it to iteratively detect the fake accounts that send out friend spam. Our evaluation shows that Rejecto can discern friend spammers under a broad range of scenarios and that it is computationally practical.
Human Immunodeficiency Virus Type 1 (HIV-1) and Herpes Simplex Virus Type 2 (HSV-2) Can Coinfect and Simultaneously Replicate in the Same Human CD4 <sup>+</sup> Cell: Effect of Coinfection on Infectious HSV-2 and HIV-1 Replication (1990)

Experiments were designed to determine whether HIV-1 and herpes simplex virus type 2 (HSV-2) coinfection leads to simultaneous replication of both viruses in the same human CD4+ cell (MT-4 cell line) and the possible effects of coinfection on infectious virus production. Results from transmission electron microscopy analysis revealed replication of typical HSV-2 nucleocapsids in the nucleus and budding of HIV-1 particles through the plasma membrane and through intracytoplasmic vacuoles containing enveloped HSV-2 particles in the same coinfected cell. Coinfection of HIV-1 persistently infected H9IIIB or promonocytic U1 cells with HSV-2 did not alter total production of infectious HSV-2 or the percentage of HSV-2 infectious centers compared with control H9 and U937 cells infected with HSV-2 alone. However, in coinfected promonocytic U1 cells HSV-2 induced infectious HIV-1 production measured by syncytial plaque assay. In summary, both HIV-1 and HSV-2 can coinfect and simultaneously replicate in the same human CD4+ cell. Interactions between HIV-1 and HSV-2 appear to be unidirectional, resulting in accelerated replication of HIV-1 as reported by Albrecht et al. (J Virol 1989;63:1861-1868), but not HSV-2 as shown by us.
Transforming Growth Factor-β Mediates Astrocyte-Specific Regulation of Brain Endothelial Anticoagulant Factors (1999)

These data indicate that TGF-beta mediates astrocyte regulation of brain capillary endothelial expression of tPA and TM.
Intrastriatal Grafts from Multiple Donors do not Result in a Proportional Increase in Survival of Dopamine Neurons in Nonhuman Primates (1998)

We examined the potential for “double grafts,” i.e., grafts from two donors in each recipient, to enhance the total number of ventral mesencephalic dopamine neurons that survive grafting in adult African green monkeys. Because dopamine cell survival in grafts represents a small percentage of the total number of neurons grafted, several human clinical trials recently have employed grafts of tissue from multiple donors (e.g., from two to eight embryos per host recipient) in attempts to increase the total number of dopamine neurons that survive in grafts. Presumably, this is intended to elevate dopamine levels by providing more dopamine neurons to the damaged brain to alleviate the symptoms of parkinsonism. While well-developed grafts with several thousand dopamine neurons were found in most recipient animals, we observed a reduced total number of tyrosine hydroxylase positive neurons in the grafts in spite of the presence of some double grafts that were larger than normal. The overall growth of the grafts was impressive; some grafts were so large that they spanned the full dorsoventral extent of the caudate nucleus, probably reflecting the fact that twice as much tissue was implanted in each drop site in comparison to our standard protocol. However, some animals revealed atypical patterns of neurite outgrowth that appeared limited to the grafted tissue, and at least one monkey revealed “amorphous” grafts generally lacking in cellular structure, which suggests a possible rejection phenomenon. These findings raise questions about the use of multiple donors and suggest that the likelihood of rejection and/or cell death may be enhanced, which is of potential importance in the design of grafting strategies for clinical applications.
Stimulation and inhibition of gastrointestinal propulsion induced by substance P and substance K in the rat (1985)

Substance P and substance K (neurokinin A) (dose range: 0.08-80 nmol kg-1) were tested for their effects on gastrointestinal propulsion in the rat. The peptides were given by intraperitoneal injection concurrently with the intragastric administration of a test meal containing charcoal and 51Cr. Examination 3 min after the test meal showed that high doses of substance P (greater than 0.74 nmol kg-1) and substance K (greater than 8.8 nmol kg-1) inhibited gastric emptying and gastrointestinal transit. This inhibitory effect was changed to a stimulant effect by pretreatment of the rats with atropine (3.5 mumol kg-1). Guanethidine pretreatment (67 mumol kg-1) revealed a facilitatory effect of low doses of the two tachykinins (about 1 nmol kg-1) on gastrointestinal propulsion. Examination 15 min after the test meal demonstrated that substance P (greater than 0.74 nmol kg-1) dose-dependently enhanced gastrointestinal propulsion, an effect that was also seen after atropine pretreatment. Low doses of substance K (about 1 nmol kg-1) also stimulated gastrointestinal propulsion but this effect was abolished by atropine. In addition, atropine pretreatment revealed a stimulant effect of high doses of substance K (88 nmol kg-1) on gastric emptying. These results show that the effects of substance P and substance K on gastrointestinal propulsion vary with dose and time and involve, at least partly, activation of the autonomic nervous system.
Discovery, Isolation, and Structure Elucidation of a Family of Structurally Unique, Fermentation-Derived Tetracyclic Macrolides (1992)

Screening of fermentation broths for mosquito larvicidal activity yielded an active culture denoted as A83543. Nine active, structurally-related factors were isolated and purified by extractive and chromatographic procedures. Their structures were elucidated by a combination of spectroscopic (NMR, MS, UV, IR) and X-ray crystallographic methods. Each factor possessed the core structure of a 5,6,5-cis-anti-trans-tricyclic ring system fused to a 12-membered lactone. In addition, an aminosugar (forosamine) and a neutral sugar (2,3,4-tri-O-methylrhamnose) were glycosidically linked to the tetracyclic framework. Absolute stereochemistry was established by comparing samples of forosamine obtained from acidic hydrolyses of A83543A and spiramycin. The novel tetracyclic structure of A83543 suggests that unique features are involved in its biosynthesis. The purified factors exhibited potent mosquito larvicidal activity, but lacked antibiotic activity.
Power allocation for secrecy diversity in MISOME wiretap channels (2013)

We consider secure beamforming with artificial noise in a multiple-input single-output multiple-eavesdropper (MISOME) wiretap channel, where a transmitter has access to full channel state information (CSI) of a legitimate channel but only partial CSI of eavesdropper channels. In this paper, we first put forth a notion of symbol error probability (SEP) for confidential information—called the δ-secrecy SEP—to connect the reliability and confidentiality of the legitimate communication in MISOME wiretap channels. For single-antenna colluding and non-colluding eavesdroppers, we determine the optimal power allocation between the information-bearing signal and artificial noise to minimize the δ-secrecy SEP in the presence of weak or strong eavesdroppers, and further develop the switched power allocation for general eavesdropping attacks.
Multistage pH‐Responsive Liposomes for Mitochondrial‐Targeted Anticancer Drug Delivery (2012)

Zwitterionic oligopeptide liposomes (HHG2C(18)-L) containing a smart lipid (1,5-dioctadecyl-L-glutamyl 2-histidyl-hexahydrobenzoic acid, HHG2C(18)) are developed to overcome the barriers faced by anticancer drugs on the route from the site of injection into the body to the final antitumor target within transport steps with multiple physiological and biological barriers. HHG2C(18)-L show the multistage pH-responsive to the tumor cell (the mitochondria in this case). Their multistage pH response leads to more effective entry of the tumor cell, improved escape from the endolysosomes, and accumulation at the mitochondria (see picture).
OMRE OPERATING EXPERIENCE (1959)

Atherosclerosis, the leading cause of death in western countries, is a multifactiorial condition in which a local and low-grade inflammatory response plays an important role. Elevation in markers of inflammation prospectively defines risk of atherosclerotic complications and predicts all-cause mortality. Alcohol consumption has been related with all-cause mortality and cardiovascular risk with a J-shaped relationship, suggesting that alcohol consumption might have an antiinflammatory effect. This review assesses the current state of knowledge regarding the immunomodulatory effect of moderate alcohol consumption.