gebhart/patrepeval huggingface dataset:
Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery (2015)

The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning approaches can greatly assist in the process and even partly replace expensive laboratory experiments by learning a predictor with existing data or with a smaller amount of data generation. Unfortunately, once the model is learned, selecting peptides having the greatest predicted bioactivity often requires a prohibitive amount of computational time. For this combinatorial problem, heuristics and stochastic optimization methods are not guaranteed to find adequate solutions. We focused on recent advances in kernel methods and machine learning to learn a predictive model with proven success. For this type of model, we propose an efficient algorithm based on graph theory, that is guaranteed to find the peptides for which the model predicts maximal bioactivity. We also present a second algorithm capable of sorting the peptides of maximal bioactivity. Extensive analyses demonstrate how these algorithms can be part of an iterative combinatorial chemistry procedure to speed up the discovery and the validation of peptide leads. Moreover, the proposed approach does not require the use of known ligands for the target protein since it can leverage recent multi-target machine learning predictors where ligands for similar targets can serve as initial training data. Finally, we validated the proposed approach in vitro with the discovery of new cationic antimicrobial peptides. Source code freely available at http://graal.ift.ulaval.ca/peptide-design/.
β-Casomorphin Induces Fos-Like Immunoreactivity in Discrete Brain Regions Relevant to Schizophrenia and Autism (1999)

The induction of Fos-like immunoreactivity (FLI) was used to determine the brain localization affected by b-casomorphin-7 (b-CM7). Peripheral administration of human b-CM7 at different doses (5, 10 and 30 mg/kg, IV for 1 hour) to rats induced moderate to strong FLI in discrete brain regions including the nucleus accumbens, caudate putamen, ventral tegmental and median raphe nucleus, and orbitofrontal, prefrontal, parietal, temporal, occipital and entorhinal cortex. All of the above areas have been shown to be altered either functionally or anatomically in patients with schizophrenia, and most have been shown to be functionally abnormal in autism. Some of these brain areas are originators or components of dopaminergic, serotoninergic and GABA-ergic pathways, suggesting that b-CM7 can affect the function of all of these systems. The role of some other affected areas in emotional and motivated behavior, social adaptation, hallucinations and delusions suggests that b-CM7, which was found in high concentration in the CSF, blood and urine of patients with either schizophrenia or autism, may be relevant to schizophrenia and autism. Induction of FLI in the above brain areas by a moderate dose (10 mg/kg) of b-CM7 was attenuated significantly, or blocked, by pretreatment with naloxone (2 mg/kg, IP). It is concluded that human b-CM7 can cross the blood-brain barrier, activate opioid receptors and affect brain regions similar to those affected by schizophrenia and autism.
Optimal mobile robot pose estimation using geometrical maps (2002)

We propose a weighted least-squares (WLS) algorithm for optimal pose estimation of mobile robots using geometrical maps as environment models. Pose estimation is achieved from feature correspondences in a nonlinear framework without linearization. The proposed WLS approach yields optimal estimates in the least-squares sense, is applicable to heterogeneous geometrical features decomposed in points and lines, and has an O(N) computation time.
Fully integrated lab-on-a-disc for simultaneous analysis of biochemistry and immunoassay from whole blood (2010)

We report a fully integrated device that can perform both multiple biochemical analysis and sandwich type immunoassay simultaneously on a disc. The whole blood is applied directly to the disposable "lab-on-a-disc" containing different kinds of freeze-dried reagents for the blood chemistry analysis as well as reagents required for the immunoassay. The concentrations of different kinds of analytes are reported within 22 min by simply inserting a disc to a portable device. Using the innovative laser irradiated ferrowax microvalves together with the centrifugal microfluidics, the total process of plasma separation, metering, mixing, incubation, washing, and detection is fully automated. The analyzer is equipped with an optical detection module to measure absorbances at 10 different wavelengths to accommodate the various kinds of reaction protocols. Compared to the conventional blood analysis done in clinical laboratories, it is advantageous for point-of-care applications because it requires a smaller amount of blood (350 μL vs. 3 mL), takes less time (22 min vs. several days), does not require specially trained operators or expensive instruments to run biochemical analysis and immunoassay separately.
자궁경부암종 및 상피내종양에서 저위험 및 고위험 인유두종 바이러스 감염에 관한 연구 : 경부도말의 Hybrid Capture 에 의한 연구 (1997)

자궁경부 상피내종양 및 침유성 편평상피세포암종 환자에서 여러분자생물할적 방법중 안전하고 간편하게 실시하여 단시간내에 결과를 알 수 있는 방법인 hybrid capture system 이 인유두종 바이러스감염 여부와 경부상피내종양 및 침유성 편평상피세포암종의 진단에 유용한지를 구명하기 위하여 경부세포진검사나 조직학적 검사로 자궁경부 상피내 종양으로 진단도니 24명, 침윤성 편평상피세포암조응로 진단된 26명과 정상 자궁경부소견을 보인 대조군28명, 총 78명을 대상으로 hybrid caputere system을 이용하여 저위험성 (6,11,42,43,44)및 고위험성 (16,18,31,33,35,45,51,52,56) 인유두종 바이러스의 감염여부를 조사하고 고위험성 인유두종 바이러스의 감염여부를 조사하고 고위험성 인유두종 바이러스의 감염환장에서는 16 및 18아형의 감염여부를 재검색하고 경부세포진 검사와 조직학적 소견을 비교분석하고 경부세포진 검사와 조직학적 소견을 비교분석하여 다음과 같은 결과를 얻었다. 1. 총 78명중 저위험성 인유두종 바이러스 양성은 6명 (7.7%)이었고 이 중 정상 자궁경부에서 14.3% 상피내종양에서 8.3%이고 편평상피세포암에서는 전원이 음성으로 나타났다. 또한 고위험성 인유두종 바이러스 양성율은 48.7%이었고 이 중 정상경부 7.1%, 상피내종양 70.8% 침윤성 편평상피 세포암종 73.1%로 상피내종양과 침윤성 편평상피암좀에서느 고위험성 인유두종 바이러스 양성율이 현저히 높았다. 2. 정상 장궁경부에서 인유두종 바이러스의 저위험성 및 고 위험성 아형들의 양성율은 각각 14.3% 7.1%로 저위험성 인유두종 바이러스의 양성율이 높았고 상피내종양에서 인유두종 바이러스의 저위험성 및 고위험성 아형의 양성율은 각각 8.3%, 70.8%로 고위험성 인유두종 아형의 빈도가 현저히 높았고 상피내종양의 등급에 따른 차이는 없었다. 3. 침윤성 편평상피세포암종에서는 고위험성 인유두종 바이러스의 양성율은 73.1%이고 저위험성 인유두종 바이러스 감염은 없었다. 4. 경부세포지상 음성판정을 받은 환자에서 인유두종 바이러스의 양성율은 24.2%로 인유두종바이러스의 양성율은 24.2%로 인유두종바이러스의 저위험성 아향이 9.1%, 고위험성 아형이 15.1%이었다. 5. 고위험성 인유두종 바이러스 양성인 38명에서 16및 18아형을 검색한 결과 16 아형은 47.4%, 18아형이 13.2% 양측 모두 양성은 15.7%이고 양측 모두 음성인 경우도 23.7나 되었다. 상피내종양에서는 인유두종 바이러스 16아형은 66.6%, 18아형은 16.7%에서 검출되었고 침윤성 편평상피세포암에서서는 인유두종 바이러스 16아형은 41.7% 189아형은 12.5%, 16/18 모두 검출된 경우는 25%로 총 79.2%에서 16및 18 아형이 검출되어 침윤성 편평상피세포암종의 발생에 깊이 관여하고 있음을 암시하고 있다.
Specificity studies on the heparin lyases from Flavobacterium heparinum (1993)

An understanding of the substrate specificity study of the heparin lyases (heparinase and heparitinases) is crucial for elucidation of the sequence of heparin and heparan sulfate. Four chemically modified heparins have been used to study the substrate specificity of the three heparin lyases. These modified heparins include the N- and O-desulfated and then specifically N-sulfated or N-acetylated derivatives of heparin and a modified heparin containing L-galactopyranosyluronic acid residues. These chemically modified heparins were degraded to various extents by the three heparin lyases. Differences in degree of sulfation have profound impact on the ease of cleavage of glycosidic linkages. Heparin lyase I (EC 4.2.2.7) is selective in cleaving highly sulfated polysaccharide chains containing linkages to 2-O-sulfated alpha-L-idopyranosyluronic acid residues. Heparin lyase III (EC 4.2.2.8) cleaves linkages that have reduced density of sulfation and that contain beta-D-glucopyranosyluronic acid residues. The ability of heparin lyase III to act on linkages to unsulfated alpha-L-idopyranosyluronic acid residues is observed for the first time. Heparin lyase II (no assigned EC number) demonstrates an unparalleled, wide specificity for substrates comprised of linkages containing both alpha-L-idopyranosyluronic and beta-D- glucopyranosyluronic acid residues. Heparin lyase II can also act on substrates containing linkages to unnatural alpha-L-galactopyranosyluronic acid residues. The high level of specificity of heparin lyase I makes it particularly suitable for use in the sequencing of heparin and heparan sulfate, while caution must be exercised in using heparin lyases II and III to sequence heparin and heparan sulfate because of their relatively broad specificity.
Segmentation of Pulmonary Nodules in Thoracic CT Scans: A Region Growing Approach (2008)

This paper presents an efficient algorithm for segmenting different types of pulmonary nodules including high and low contrast nodules, nodules with vasculature attachment, and nodules in the close vicinity of the lung wall or diaphragm. The algorithm performs an adaptive sphericity oriented contrast region growing on the fuzzy connectivity map of the object of interest. This region growing is operated within a volumetric mask which is created by first applying a local adaptive segmentation algorithm that identifies foreground and background regions within a certain window size. The foreground objects are then filled to remove any holes, and a spatial connectivity map is generated to create a 3-D mask. The mask is then enlarged to contain the background while excluding unwanted foreground regions. Apart from generating a confined search volume, the mask is also used to estimate the parameters for the subsequent region growing, as well as for repositioning the seed point in order to ensure reproducibility. The method was run on 815 pulmonary nodules. By using randomly placed seed points, the approach was shown to be fully reproducible. As for acceptability, the segmentation results were visually inspected by a qualified radiologist to search for any gross miss-segmentation. 84% of the first results of the segmentation were accepted by the radiologist while for the remaining 16% nodules, alternative segmentation solutions that were provided by the method were selected.
An evolution-driven analog circuit topology synthesis (2016)

A design of an analog circuit is often a time consuming, iterative procedure, which strongly depends on designer's knowledge and experience. A designer is facing tough requirements for designing within a time budget and consuming as few resources (both human and material) as possible. We designed a system that can assist and speed-up a design process. Based on a high-level statement describing the circuit functionality, the system evolves both a topology and parameters using a bioinspired evolutionary algorithm. Each circuit within a population is coded as a multidimensional chromosome. Proof of concept is given by a fully-automatic evolution of a 1 KHz low-pass passive filter.
Caspases Are Activated in a Branched Protease Cascade and Control Distinct Downstream Processes in Fas-induced Apoptosis (1998)

Two novel synthetic tetrapeptides, VEID-CHO and DMQD-CHO, could selectively inhibit caspase-6 and caspase-3, respectively. We used these inhibitors to dissect the pathway of caspase activation in Fas-stimulated Jurkat cells and identify the roles of each active caspase in apoptotic processes. Affinity labeling techniques revealed a branched protease cascade in which caspase-8 activates caspase-3 and -7, and caspase-3, in turn, activates caspase-6. Both caspase-6 and -3 have major roles in nuclear apoptosis. Caspase-6 cleaves nuclear mitotic apparatus protein (NuMA) and mediates the shrinkage and fragmentation of nuclei. Caspase-3 cleaves NuMA at sites distinct from caspase-6, and mediates DNA fragmentation and chromatin condensation. It is also involved in extranuclear apoptotic events: cleavage of PAK2, formation of apoptotic bodies, and exposure of phosphatidylserine on the cell surface. In contrast, a caspase(s) distinct from caspase-3 or -6 mediates the disruption of mitochondrial membrane potential (permeability transition) and the shrinkage of cytoplasm. These findings demonstrate that caspases are organized in a protease cascade, and that each activated caspase plays a distinct role(s) in the execution of Fas-induced cell death.
Analysis of the genome structure of tobacco rattle virus strain PSG (1986)

The sequence of the 3'-terminal 2077 nucleotides of genomic RNA 1 and the complete sequence of genomic RNA 2 of tobacco rattle virus (TRV, strain PSG) has been deduced. RNA 2 (1905 nucleotides) contains a single open reading frame for the viral coat protein (209 amino acids), flanked by 5'- and 3'-noncoding regions of 570 and 708 nucleotides, respectively. A subgenomic RNA (RNA 4) was found to lack the 5'-terminal 474 nucleotides of RNA 2 and is the putative messenger for coat protein. The deduced RNA 1 sequence contains the 3'-terminal part of a reading frame that probably corresponds to the TRV 170K protein and reading frames for a 29K protein and a 16K protein. Proteins encoded by the first two reading frames show significant amino acid sequence homology with corresponding proteins encoded by tobacco mosaic virus. Subgenomic RNAs 3 (1.6 kb) and 5 (0.7 kb) were identified as the putative messengers for the 29K and 16K proteins, respectively. At their 3'-termini all PSG-RNAs have an identical sequence of 497 nucleotides; at the 5'-termini homology is limited to 5 to 10 bases.
T‐cell costimulatory pathways in allograft rejection and tolerance (2003)

The destiny of activated T cells is critical to the ultimate fate of immune response. After encountering antigen, naïve T cells receive signal 1 through the T-cell receptor (TCR)-major histocompatibility complex (MHC) plus antigenic peptide complex and signal 2 through "positive" costimulatory molecules leading to full activation. "Negative" T-cell costimulatory pathways, on the other hand, function to downregulate immune responses. The purpose of this article is to review the current state of knowledge and recent advances in our understanding of the functions of the positive and negative T-cell costimulatory pathways in alloimmune responses. Specifically, we discuss the functions of the CD28:B7 and the tumor necrosis factor receptor (TNFR):tumor necrosis factor (TNF) family of molecules in allograft rejection and tolerance. We address the following important questions: are T-cell costimulatory pathways merely redundant or do they provide distinct and unique functions? What are the important and unique interactions between the various pathways? And, what are the effects and mechanisms of targeting of these pathways in different types and patterns of allograft rejection and tolerance models?
Dissolution of small diameter single-wall carbon nanotubes in organic solvents? (2001)

The solubility of small diameter single-wall carbon nanotubes in several organic solvents is described, and characterization in 1,2-dichlorobenzene is reported.
UBC9-dependent Association between Calnexin and Protein Tyrosine Phosphatase 1B (PTP1B) at the Endoplasmic Reticulum (2015)

Calnexin is a type I integral endoplasmic reticulum (ER) membrane protein, molecular chaperone, and a component of the translocon. We discovered a novel interaction between the calnexin cytoplasmic domain and UBC9, a SUMOylation E2 ligase, which modified the calnexin cytoplasmic domain by the addition of SUMO. We demonstrated that calnexin interaction with the SUMOylation machinery modulates an interaction with protein tyrosine phosphatase 1B (PTP1B), an ER-associated protein tyrosine phosphatase involved in the negative regulation of insulin and leptin signaling. We showed that calnexin and PTP1B form UBC9-dependent complexes, revealing a previously unrecognized contribution of calnexin to the retention of PTP1B at the ER membrane. This work shows that the SUMOylation machinery links two ER proteins from divergent pathways to potentially affect cellular protein quality control and energy metabolism.
Ultralight Structures for Space Solar Power Satellites (2016)

The design of a deployable spacecraft, measuring 60 m × 60 m, and with an areal density 100 g m -2 , is described.This spacecraft can be packaged into a cylinder measuring 1.5 m in height and 1 m in diameter.It can be deployed to a flat configuration, where it acts as a stiff, lightweight support framework for multifunctional tiles that collect sunlight, generate electric power, and transmit to a ground station on Earth.
HGVbaseG2P: a central genetic association database (2008)

The Human Genome Variation database of Genotype to Phenotype information (HGVbaseG2P) is a new central database for summary-level findings produced by human genetic association studies, both large and small. Such a database is needed so that researchers have an easy way to access all the available association study data relevant to their genes, genome regions or diseases of interest. Such a depository will allow true positive signals to be more readily distinguished from false positives (type I error) that fail to consistently replicate. In this paper we describe how HGVbaseG2P has been constructed, and how its data are gathered and organized. We present a range of user-friendly but powerful website tools for searching, browsing and visualizing G2P study findings. HGVbaseG2P is available at http://www.hgvbaseg2p.org.
Impacts of climate change on distributions and diversity of ungulates on the Tibetan Plateau (2014)

Climate change has significant impacts on species' distributions and diversity patterns. Understanding range shifts and changes in richness gradients under climate change is crucial for conservation. The Tibetan Plateau, home to wild yak, chiru, and kiang, contains a biome with many endemic ungulates. It is highly sensitive to climate change and a region that merits particular attention with regard to the impacts of global climate change on its biomes. Maximum entropy approaches were used to estimate current and future potential distributions, in response to climate change, for 22 ungulate species. We used three general circulation (MK3, HADCM3, MIROC3_2-MED) and three emissions scenarios (Bl, A1B, A2) to derive estimated future measurements of 14 environmental variables over three time periods (2020, 2050, 2080), and then modeled species distributions using these predicted environmental measurements for each time period under two dispersal hypotheses (full and zero, respectively). This resulted in a total of 6160 prediction models. We found that these ungulates, on average, may lose 30-50% of their distributional areas, depending on the dispersal scenarios. In addition, 55-68% of the ungulate species were predicted to become locally endangered under the different dispersal assumptions, 23-32% to become locally critically endangered, and 4-7 endemic species to become globally endangered. Furthermore, ungulate species ranges may experience average poleward shifts of ~300 km. We also predict west-to-east reductions in species richness: southeastern mountainous areas currently have the highest species richness, but are predicted to face the greatest diversity losses, whereas the northern areas are predicted to see increasing numbers of ungulate species in the 21st century. Our study indicates much more severe range reductions of ungulates on the Tibetan Plateau than those anticipated elsewhere in the world, and species richness patterns will change dramatically with climate change. For conservation, we suggest (1) securing existing protected areas, and (2) establishing new nature reserves to counterbalance climate change impacts.
Boron-loaded silicone rubber scintillators (2004)

Silicone rubber has received attention as an alternative to polyvinyltoluene in applications in which the scintillator is exposed to high doses of radiation because of the increased resistance of the rubber to the formation of blue-absorbing color centers. Work by Bowen, et al., and Harmon, et al., has demonstrated their properties under gamma/X-ray irradiation, and Bell, et al. have shown their response to thermal neutrons. This last work, however, provides an example of a silicone in which both the boron and the scintillator are contained in the rubber as solutes, a formulation which leads to the precipitation of solids and sublimation of the boron component. In the present work we describe a scintillator in which the boron is chemically bonded to the siloxane and so avoids the problem of precipitation and loss of boron to sublimation. Material containing up to 18% boron, by weight, was prepared, mounted on photomultipliers, and exposed to both neutron and gamma fluxes. Pulse height spectra showing the neutron and photon response were obtained, and although the light output was found to be much poorer than from samples in which boron was dissolved, the higher boron concentrations enabled essentially 100% neutron absorption in only a few millimeters of rubber.
The ClpE protein involved in biogenesis of the CS31A capsule-like antigen is a member of a periplasmic chaperone family in Gram-negative bacteria (1993)

The putative chaperone-like protein ClpE, required for biogenesis of the Escherichia coli capsule-like antigen CS31A, was compared with ten known periplasmic chaperones from E. coli, Klebsiella pneumoniae, Bordetella pertussis, Haemophilus influenzae and Yersinia pestis. The amino acid sequence alignment was superimposed onto the three-dimensional structure of the PapD chaperone of uropathogenic E. coli, and amino acid residues involved in maintaining the structure integrity of the suggested binding site were found identical in most of the 11 chaperones. Construction of a phylogenetic tree to investigate the relationship within the chaperone family has revealed interesting degrees of relatedness between the different proteins.
COMPREHENSIVE XML FOR CONTACT CENTER (2006)

W3C languages, VoiceXML and CCXML all play an important role in contact centers (CC) by simplifying the creation of CC applications. However, they cover only a subset of contact center functions, such as simple call control and interactive voice response (IVR) with automatic speech recognition. We discuss ways to complement VoiceXML and CCXML in order to cover all necessary contact center functions required to script end-to-end interactions in a consistent and seamless way. For this purpose we introduce an XML forms-based framework called XContact comprising the CC platform and applications, multi-script and multi-browsing, and interaction data processing.
Genetics of somatic mammalian cells: genetic, immunologic, and biochemical analysis with Chinese hamster cell hybrids containing selected human chromosomes. (1976)

Through hybridization of specific Chinese hamster cell auxotrophs with human cells and selection in media lacking the nutritional supplements required by the former cells, a series of stable hybrid clones can be prepared. These hybrids have genomes consisting of a common part--the complete or almost complete set of Chinese hamster chromosomes, plus a variable part--one or a few human chromosomes. The identity of the human chromosomes can be varied by utilizing different Chinese hamster auxotrophs and the appropriate selective media. The human chromosomes present can be determined by a combination of cytogenetic analysis with chromosome banding and testing for specific human marker genes. Hybrids containing single human chromosomes 11 and 12 and the combination of both 11 and 12 are described. The system appears to lend itself to various studies such as identification of human cell surface antigens, determination of their chromosomal loci, measurement of their distribution among cells of normal human tissues, study of interrelations among syntenic and asyntenic genes, and mutational analysis of the human genome.