gebhart/patrepeval huggingface dataset:
Systematic Approach to Optimizing Specifically Targeted Antimicrobial Peptides against Streptococcus mutans (2010)

Previously we reported a novel strategy of "targeted killing" through the design of narrow-spectrum molecules known as specifically targeted antimicrobial peptides (STAMPs) (R. Eckert et al., Antimicrob. Agents Chemother. 50:3651-3657, 2006; R. Eckert et al., Antimicrob. Agents Chemother. 50:1480-1488, 2006). Construction of these molecules requires the identification and the subsequent utilization of two conjoined yet functionally independent peptide components: the targeting and killing regions. In this study, we sought to design and synthesize a large number of STAMPs targeting Streptococcus mutans, the primary etiologic agent of human dental caries, in order to identify candidate peptides with increased killing speed and selectivity compared with their unmodified precursor antimicrobial peptides (AMPs). We hypothesized that a combinatorial approach, utilizing a set number of AMP, targeting, and linker regions, would be an effective method for the identification of STAMPs with the desired level of activity. STAMPs composed of the Sm6 S. mutans binding peptide and the PL-135 AMP displayed selectivity at MICs after incubation for 18 to 24 h. A STAMP where PL-135 was replaced by the B-33 killing domain exhibited both selectivity and rapid killing within 1 min of exposure and displayed activity against multispecies biofilms grown in the presence of saliva. These results suggest that potent and selective STAMP molecules can be designed and improved via a tunable "building-block" approach.
Synthesis and Surface Engineering of Complex Nanostructures by Atomic Layer Deposition (2007)

Abstract Atomic layer deposition (ALD) has recently become the method of choice for the semiconductor industry to conformally process extremely thin insulating layers (high‐ k oxides) onto large‐area silicon substrates. ALD is also a key technology for the surface modification of complex nanostructured materials. After briefly introducing ALD, this Review will focus on the various aspects of nanomaterials and their processing by ALD, including nanopores, nanowires and ‐tubes, nanopatterning and nanolaminates as well as low‐temperature ALD for organic nanostructures and biomaterials. Finally, selected examples will be given of device applications, illustrating recent innovative approaches of how ALD can be used in nanotechnology.
PNA-DNA Chimeras Containing 5-Alkynyl-pyrimidine PNA Units. Synthesis, Binding Properties, and Enzymatic Stability (2003)

Three chimeric dimer synthons (oeg_t(NH)T, oeg_up(NH)T and oeg_uh(NH)T) containing thymine (t), 5-(1-propynyl)-uracil (up) and 5-(1-hexyn-1-yl)-uracil (uh) PNA units with N-(2-hydroxyethyl)glycine (oeg) backbone were synthesized in solution and incorporated into T20 oligonucleotide analogues, using standard P-amidite chemistry. Insertion of dimer blocks led to destabilization of duplexes with dA20 target. The smallest Tm drops were found for chimeras containing oeg_up(NH)T dimers. Incorporation of the chimeric synthons into the 3'-end of T20 brought about growing resistance to 3'-exonucleolytic (SV PDE) cleavage in the order of oeg_t(NH)T < oeg_up(NH)T < oeg_uh(NH)T. Due to different endonuclease activities of 3'- and 5'-exonucleases applied, placing of five consecutive dimers at the 5'-terminus resulted in a relatively smaller, but also side-chain dependent, stabilization towards the hydrolysis by 5'-exonuclease (BS PDE). Neither exonucleases (SV and BS PDE) nor an endonuclease (Nuclease P1) could hydrolyse the unnatural phosphodiester bond linking the 3'-OH of thymidine to the terminal OH of N-(2-hydroxyethyl)glycine PNA backbone.
HLA class II restriction specificity of Dermatophagoides spp. reactive T lymphocyte clones that support IgE synthesis (1989)

The results of recent experiments investigating the restriction specificity of cross-reactive, or Dermatophagoides farinae-specific, T cell clones isolated from an atopic individual with perennial rhinitis are reviewed. The restriction specificity was examined using serological inhibition, allogeneic presenting cells and murine fibroblasts expressing HLA-D region products. Although serological inhibition studies suggested that DR class II proteins were the major restriction elements used, the patterns of recognition observed with the allogeneic cell panel were complex, generally failing to correlate with the serologically defined MHC class II specificities. Analysis of the restriction patterns indicated that the majority of the T cell clones were restricted by DR beta III gene products and this was confirmed using murine fibroblasts expressing DRw52. DR beta I gene products functioned as restriction elements in the recognition of house dust mite allergen by the other clones. In an in-vitro model of allergen-dependent IgE synthesis, both DR beta I and DR beta III class II restricted T cells could be shown to provide functional help for IgE synthesized by autologous B cell-enriched populations.
Side Effects of Chemotherapy and Combined Chemohormonal Therapy in Women With Early-Stage Breast Cancer (2001)

The decision to receive chemotherapy or chemohormonal therapy involves careful consideration of both the potential benefits and possible risks of therapy. There are substantial short- and long-term side effects from chemotherapy. By convention, short-term side effects include those toxic effects encountered during chemotherapy, while long-term side effects include later complications of treatment arising after the conclusion of adjuvant chemotherapy. These side effects vary, depending on the specific agents used in the adjuvant regimen as well as on the dose used and the duration of treatment. There is also considerable variability in side effect profile across individuals. This review will focus on the short- and long-term toxicity seen with the most commonly used adjuvant chemotherapy and chemohormonal therapy regimens.
PROVIDING ADVANCED AND REAL-TIME TRAVEL/TRAFFIC INFORMATION TO TOURISTS (1998)

Advanced traveler information systems (ATIS) analyze and communicate information that can enhance travel efficiency, alleviate congestion, and increase safety. In Texas, tourists (i.e., tripmakers unacquainted with the state) constitute an important user group for ATIS. Given that tourism represents a sizable industry and, consequently, has an enormous impact on the state's economy, technology that enhances the tourist's experience can help sustain this sizable industry. However, such enhancement requires that traveler guidance be adequately provided. While tourists provide the principal users for this study, the development of ATIS is best accomplished by a comprehensive ATIS development approach that considers all possible user types. In this study, a synthesis of pertinent ATIS implementation and field tests, including methodologies for evaluating systems/technologies, was performed. Interviews with district-level staff in Texas were conducted to define the focus issues and the target users within each locality. On-location surveys were conducted and statistically analyzed according to the specific information needs of users. The study identified candidate systems/technologies that match the information needs, technical regulations, legal constraints, and compatibility with Intelligent Transportation Systems (ITS) standards and systems in Texas. Possible public and private sector roles and cost/benefit analyses were performed to identify the leading candidate system/technology alternatives. The study provides recommendations for developing the identified systems and for making necessary guidelines that could facilitate implementation.
Fast accurate fish detection and recognition of underwater images with Fast R-CNN (2015)

This paper aims at detecting and recognizing fish species from underwater images by means of Fast R-CNN (Regions with Convolutional Neural and Networks) features. Encouraged by powerful recognition results achieved by Convolutional Neural Networks (CNNs) on generic VOC and ImageNet dataset, we apply this popular deep ConvNets to domain-specific underwater environment which is more complicated than overland situation, using a new dataset of 24277 ImageCLEF fish images belonging to 12 classes. The experimental results demonstrate the promising performance of our networks. Fast R-CNN improves mean average precision (mAP) by 11.2% relative to Deformable Parts Model (DPM) baseline-achieving a mAP of 81.4%, and detects 80× faster than previous R-CNN on a single fish image.
Reaktionen von 1‐Phenyl‐1‐cyan‐2‐aminoäthen mit substituierten Acetaldehyden 21. Mitt über Untersuchungen an Acyl‐enaminen (1971)

Abstract Aus 1‐Phenyl‐1‐cyan‐2‐aminoäthen (2) und substituierten Acetaldehyden (3a, b, c) wurden die 3‐Azapenta‐1.4‐dien‐Derivate 4a, b und c dargestellt. Katalytisches Hydrieren führte zu 3‐Azapenten‐1‐bzw. ‐4‐Derivaten (5, 7, 13, 15) , deren Struktur durch unabhängige Synthese oder durch Hydrolyse sichergestellt wurde.
Low-power monolithic RF peak detector analysis (1995)

Closed-form expressions are derived for the transfer characteristic of a low-power monolithic RF peak detector. These are compared with computer simulation and experimental measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ocean Acidification: Present Conditions and Future Changes in a High-CO2 World (2009)

Author Posting. © Oceanography Society, 2009. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 22 no. 4 (2009): 36-47.
INCA: synonymous codon usage analysis and clustering by means of self-organizing map (2004)

Software is accompanied with a user manual and a short tutorial.
CT Diagnosis of Breast Cancer (2003)

Objective To study the value of CT in diagnosis of breast cancer. Methods Forty six pathologically proved breast cancer patients underwent plain and contrast enhancement CT. The imaging features were compared with gross pathological results. Results All the 46 patients demonstrated masses on the CT images. Forty of them protruded irregularly, with lobular and spiculate boundary. Whereas 6 of them bore smooth boundary without capsule. Forty three ones were solid masses with great enhancement (more than 45Hu), and the other 3 cases were cystic masses with little enhancement. Lymph node metastasis of axilla were detected in fourteen patients, as well as chest wall invasion in 3 patients, lung metastasis in 4 patients, skin adherence in 9 cases and nipple depression in 5 patients. Conclusion CT is useful in the diagnosis and staging of breast cancer. [
Multicolour Single Molecule Imaging in Cells with Near Infra-Red Dyes (2012)

We have demonstrated that near infra-red dyes can be used to avoid autofluorescence background in samples where restricting the illumination volume of visible light fails or is inappropriate. We have also shown that supercontinuum sources are suited to single molecule multicolour imaging throughout the 470-1000 nm range. Our measurements of near infra-red dye properties will enable others to select optimal dyes for single molecule imaging.
Mutated Ras Peptides as Vaccines in Immunotherapy of Cancer (1998)

Mutations in codon 12 and 13 of K-RAS are frequently found in human cancer, including pancreatic- and colorectal adenocarcinomas. T cell responses specific for individual RAS mutations can be elicited in vitro by stimulation with synthetic peptides and in vivo following vaccination with antigen presenting cells pulsed ex vivo with synthetic peptides. The peptide-responding T cells are capable of responding to intact p21 ras, and can recognise and kill tumour cell lines and isolated tumour cells harbouring the corresponding RAS mutation. The responding cells can be of both CD4+ and CD8+ phenotype, and these T cell subsets recognise nested epitopes within the vaccine peptides. Mutant ras peptides are therefore possibly an important vaccine for specific immunotherapy in patients with pancreatic and colorectal carcinomas, and are currently being tested in vivo together with GM-CSF as an adjuvant in these cancer patients.
A Comprehensive View of Nuclear Receptor Cancer Cistromes (2011)

Nuclear receptors comprise a superfamily of ligand-activated transcription factors that play important roles in both physiology and diseases including cancer. The technologies of chromatin immunoprecipitation followed by array hybridization (ChIP-chip) or massively parallel sequencing (ChIP-seq) has been used to map, at an unprecedented rate, the in vivo genome-wide binding (cistrome) of nuclear receptors in both normal and cancer cells. We developed a curated database of 88 nuclear receptor cistrome data sets and other associated high-throughput data sets including 121 collaborating factor cistromes, 94 epigenomes, and 319 transcriptomes. Through integrative analysis of the curated nuclear receptor ChIP-chip/seq data sets, we discovered novel factor-specific noncanonical motifs that may have important regulatory roles. We also revealed a common feature of nuclear receptor pioneering factors to recognize relatively short and AT-rich motifs. Most nuclear receptors bind predominantly to introns and distal intergenetic regions, and binding sites closer to transcription start sites were found to be neither stronger nor more evolutionarily conserved. Interestingly, while most nuclear receptors appear to be predominantly transcriptional activators, our analysis suggests that the binding of ESR1, RARA, and RARG has both activating and repressive effects. Through meta-analysis of different omic data of the same cancer cell line model from multiple studies, we generated consensus cistrome and expression profiles. We further made probabilistic predictions of the nuclear receptor target genes by integrating cistrome and transcriptome data and validated the predictions using expression data from tumor samples. The final database, with comprehensive cistrome, epigenome, and transcriptome data sets and downstream analysis results, constitutes a valuable resource for the nuclear receptor and cancer community.
Transcription and transcript processing in the sdh CDAB-sucABCD operon of Escherichia coli (1998)

The genes encoding succinate dehydrogenase (sdhCDAB), the specific components of the 2-oxoglutarate dehydrogenase complex (ODH, E1o and E2o; sucAB) and succinyl-CoA synthetase (sucCD) form a cluster containing two promoters at 16.3 min in the chromosome of Escherichia coli: Psdh sdhCDAB-Psuc sucAB-sucCD. The gene encoding the lipoamide dehydrogenase component of both the 2-oxoglutarate and pyruvate dehydrogenase complexes (E3; lpdA) is the distal gene of another cluster containing two promoters located at 2.7 min: Ppdh pdhR-aceEF-Plpd lpdA. The responses of the suc and lpd promoters to different environmental conditions and to regulator defects were investigated with appropriate lacZ fusions, in order to understand how expression of the sucAB genes is co-regulated with other genes in the sdhCDAB-sucABCD cluster and with lpdA expression. Expression from the suc promoter was repressed by IHF and partially activated by sigma 38 but it was not regulated by ArcA, FNR, CRP, FruR or Fis, and not repressed by glucose or anaerobiosis, indicating that the well-established catabolite and anaerobic repression of ODH synthesis is imposed elsewhere. In contrast, the lpd promoter was repressed by both glucose (via a CRP-independent mechanism) and anaerobiosis (mediated by ArcA), and activated by Fis, but it was not regulated by FNR, FruR, IHF or sigma 38. These observations support the view that transcription of the sucABCD genes is primarily initiated and regulated at the upstream sdh promoter, and that the lpd promoter is independently co-regulated with Psdh (primarily by ArcA-mediated repression) rather than with Psuc. Direct evidence for co-transcription of the entire sdhCDAB-sucABCD region from Psdh was obtained by detecting a 10 kb transcript in rnc and rne mutants, but not in the parental strains. Three RNaseIII-specific processing sites, which contribute to the extreme instability of the readthrough transcript, were identified in the sdhCDAB-sucABCD intergenic region. Other sites of endonuclease processing were located by interpreting the patterns of transcript subfragments observed in Northern blotting.
MED1: A central molecule for maintenance of genome integrity and response to DNA damage (2003)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Dynamic deformation of solid primitives with constraints (1992)

This paper develops a systematic approach to deriving dynamic models from pammetrically dejined solid primitives, g!obal geometric deformations and local jiniteelement deformations.
Modern use of clomiphene citrate in induction of ovulation (1997)

Clomiphene citrate is the treatment of first choice in the management of infertility in normally oestrogenized, anovulatory women (WHO group II). The majority of women with 'pure' anovulatory infertility respond to treatment with clomiphene citrate. The rates of pregnancy and miscarriage are close to those expected in a normal fertile population. Basal hormone concentrations do not predict outcome. An increased body mass index is the only factor which is consistently associated with a decreased response to clomiphene citrate; it follows therefore, that weight reduction should be an important part of therapy in anovulatory women. According to our data, only an increased luteinizing hormone value immediately post clomiphene citrate predicted an adverse pregnancy outcome in women who conceived. Clomiphene citrate, along with other ovulation induction therapies, can cause multiple follicular development, with a risk of ovarian hyperstimulation and multiple pregnancy. Ultrasound monitoring of treatment is important in order to choose the appropriate dose of clomiphene citrate in subsequent cycles and to minimize the risks of hyperstimulation and multiple pregnancy. When couples with other factors contributing to subfertility are excluded, the cumulative conception rate continues to rise after 6 months of treatment with clomiphene citrate, reaches a plateau by treatment cycle 12 and approaches that of the normal population. It has been reported that prolonged use of clomiphene citrate may be associated with an increased risk of a borderline or invasive ovarian tumour. Taking into consideration these observations, we recommend that anovulatory women responsive to clomiphene citrate should be treated for at least 6 cycles before considering more complex or invasive methods of ovulation induction, and that treatment should probably be limited to a maximum of 12 cycles.
Cell-specified expression of a selectable hybrid gene. (1984)

We have inserted into a retroviral vector the structural information encoding the selectable bacterial genes neo and gpt linked, respectively, to the promoters of the herpesvirus thymidine kinase gene and the rat preproinsulin II gene. We have used this recombinant retrovirus construction to transduce insulinoma cell lines that are positive or negative for insulin expression. Selection of the transductants for neo yielded resistant colonies from all of the cell lines, while selection for gpt yielded resistant transductants in relatively high frequency only from insulin-producing cells. The 5' end of the gpt transcripts maps to the authentic preproinsulin capping site of the construction.
SOP: What Is It and Why? A New Microsystem-Integration Technology Paradigm-Moore's Law for System Integration of Miniaturized Convergent Systems of the Next Decade (2004)

In the past, microsystems packaging played two roles: 1) it provided I/O connections to and from integrated circuits (ICs) or wafer-level packaging (WLP), and 2) it interconnected both active and passive components on system level boards, referred to as systems packaging. Both were accomplished by interconnections or multilayer wiring at the package or board level. More recently, the IC devices have begun to integrate not only more and more transistors, but also active and passive components on an individual chip, leading the community to believe that someday there may be a single-chip complete system, referred to as system-on-chip (SOC). This can be called horizontal or two-dimensional (2-D) integration of IC blocks in a single-chip toward end-product systems. The community began to realize, however, that such an approach presents fundamental, engineering, and investment limits, as well as computing and communication limits for wireless and wired systems over the long run. This led to 3-D packaging approaches, often referred to as system-in-package (SIP). The SIP, while providing major opportunities in both miniaturization and integration for advanced and portable electronic products, is a subsystem, limited by the CMOS process just like the SOC. Some existing and emerging applications, however, include sensors, memory modules and embedded processors with DRAMs. More recent 3-D solutions, which incorporate stacked package approaches, offer solutions toward faster time-to-market and business impediments that have plagued MCM deployment for the past decade. There is a new emerging concept called system-on-package (SOP). With SOP, the package, not the board, is the system. As such, SOP is beginning to address the shortcomings of both SOC and SIP, as well as traditional packaging which is bulky, costly, and lower in performance and reliability than ICs, in two ways: 1) It uses CMOS-based silicon for what it is good for, namely, for transistor integration, and the package, for what it is good for, namely, RF, optical, and digital integration by means of IC-package-system codesign. The SOP package, therefore, overcomes both the computing limitations and integration limitations of SOC, SIP, MCM, and traditional system packaging. It does this by having global wiring as well as RF, digital, and optical component integration in the package, not in the chip. The SOP, therefore, includes both active and passive components in thin-film form, in contrast with indiscrete or thick-film form, including embedded digital, RF, and optical components, and functions in a microminiaturized package or board.
Psychosocial Work Stress: Stock-taking and Reflection (2001)

There is an emerging trend that stress, anxiety and depression will become the leading causes of disability in the workplace over the next 20 years. In this paper, a number of causes of work-related psychosocial stresses are examined, based on various theories and research findings. Reflection on how occupational therapy could be proactive in responding to this emerging issue will be explored to encourage further discussion about possible actions that could be taken by the occupational therapists.
Fragment‐Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition (2010)

Fragment-based drug discovery has gained a foothold in today's lead identification processes. We present the application of in silico fragment-based screening for the discovery of novel lead compounds for the metalloendoproteinase thermolysin. We have chosen thermolysin to validate our screening approach as it is a well-studied enzyme and serves as a model system for other proteases. A protein-targeted virtual library was designed and screening was carried out using the program AutoDock. Two fragment hits could be identified. For one of them, the crystal structure in complex with thermolysin is presented. This compound was selected for structure-based optimization of binding affinity and improvement of ligand efficiency, while concomitantly keeping the fragment-like properties of the initial hit. Redesigning the zinc coordination group revealed a novel class of fragments possessing K(i) values as low as 128 microM, thus they provide a good starting point for further hit evolution in a tailored lead design.