gebhart/patrepeval huggingface dataset:
An Optimal Adaptive M-PSK Carrier Phase Detector Suitable for Fixed-Point Hardware Implementation within FPGAs and ASICs (2006)

In this paper we shall present an NDA (non data aided) adaptive carrier phase detector for coherent M-PSK receivers operating in AWGN (additive white Gaussian noise). It shall be shown that the detector allows the carrier synchronization PLL (phase locked loop) to achieve optimal performance during both the acquisition and tracking operation modes. The conditions necessary for this optimatity to be achieved will be discussed, and it shall be shown that they are quite reasonable and allow the proposed detector to be implemented in many contemporary M-PSK receivers. The optimal behaviour of the PLL will be shown to bold regardless of the SNR (signal-to-noise ratio) and of the AGC (automatic gain control) circuit behaviour. Moreover, the proposed detector has a simple fixed-point structure that can be feasibly implemented using few hardware resources within contemporary FPGAs (field programmable gate arrays) or ASICs (application specific integrated circuits). Finally, operation of the proposed detector under frequency-flat slow signal fading conditions is also discussed
The Degenerate Primer Design Problem: Theory and Applications (2005)

A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part, or is known in a related species. We prove that various simplified versions of the problem are hard, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant. Based on these algorithms, we implemented a program called HYDEN for designing highly degenerate primers for a set of genomic sequences. We report on the success of the program in several applications, one of which is an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.
Abstract A185: Combined treatment strategies for microtubule interfering agent-resistant tumors (2015)

Abstract Treatment resistances to specific anticancer agents and radiotherapy are often linked to the mutated genetic background of tumor cells. Their activities towards co-targeted tumor microenvironment-related cells are thereby also abrogated but could be reestablished as part of rationally-designed combined treatment modalities. Here we mechanistically investigate in two clinically relevant microtubule-interfering agent (MIA)-refractory tumor models the potency of combined treatment modalities of MIAs, inhibitors of angiogenesis and ionizing radiation to overcome MIA-resistance. Single and combined treatment regimens of ionizing radiation, microtubule stabilizing and de-stabilizing agents and anti-angiogenic compounds (everolimus, bevacizumab) were investigated in genetically defined MIA-sensitive and tubulin-mutated or P-glycoprotein/MDR1-overexpressing MIA-resistant lung and colon adenocarcinoma carcinoma cell systems (A549, SW480) and in the corresponding tumor xenografts. MIAs potently inhibited A549wt and endothelial cell proliferation, while no anti-proliferative effect was observed in the corresponding MIA-resistant tumor cells. More important, MIAs did not downregulate anymore HIF-1α transcriptional activity and subsequent secretion of HIF-1α-mediated growth factors and cytokines from these MIA-resistant tumor cells. Continuous pro-survival auto- and paracrine signaling from these resistant tumor cells resulted in an additional level of treatment resistance towards MIAs and ionizing radiation as determined in tumor xenografts derived from MIA-resistant tumor cells. However rationally-designed combined treatment of MIAs with mTOR-signaling- or VEGF-antagonists strongly re-sensitized treatment-resistant tumors to the corresponding MIA. These data demonstrate that the interaction between the tumor cell compartment and the tumor microenvironment strongly determines the treatment response to different anticancer treatment modalities.A combined treatment modality of MIAs with antiangiogenic agents is potent to overcome tumor cell-linked MIA-resistance and should be considered as clinical strategy for MIA-refractory tumor entities. Citation Format: Angela Broggini-Tenzer, Ashish Sharma, Sabine Bender, Katarzyna Nytko-Karouzakis, Martin Pruschy. Combined treatment strategies for microtubule interfering agent-resistant tumors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A185.
Scale and concurrency of GIGA+: file system directories with millions of files (2011)

We examine the problem of scalable file system directories, motivated by data-intensive applications requiring millions to billions of small files to be ingested in a single directory at rates of hundreds of thousands of file creates every second. We introduce a POSIX-compliant scalable directory design, GIGA+, that distributes directory entries over a cluster of server nodes. For scalability, each server makes only local, independent decisions about migration for load balancing. GIGA+ uses two internal implementation tenets, asynchrony and eventual consistency, to: (1) partition an index among all servers without synchronization or serialization, and (2) gracefully tolerate stale index state at the clients. Applications, however, are provided traditional strong synchronous consistency semantics. We have built and demonstrated that the GIGA+ approach scales better than existing distributed directory implementations, delivers a sustained throughput of more than 98,000 file creates per second on a 32-server cluster, and balances load more efficiently than consistent hashing.
H-Y Antigen and the Genetics of Sex Determination (1977)

Widespread phylogenetic conservation of H-Y antigen indicates persistence of a vital function. It has been proposed that this function is the primary determination of mammalian sex. According to this proposal, the indifferent embryonic gonad is induced to differentiate as a testis in the presence of H-Y antigen, and as an ovary in the absence of H-Y antigen. But presence of H-Y antigen does not guarantee testicular differentiation. Other factors may be required: a gene that activates the H-Y structural locus, and another gene that codes for specific H-Y antigen receptors.
RSVP-TE Extensions for P2MP-based BIER (2018)

Bit Index Explicit Replication (BIER) is a new architecture that
provides optimal multicast forwarding without requiring intermediate
routers to maintain any per-flow state by using a multicast-specific
BIER header. This document describes extensions to Resource
Reservation Protocol - Traffic Engineering (RSVP-TE) for the set up of
Traffic Engineered (TE) point-to-multipoint (P2MP) Label Switched
Paths (LSPs) with BIER infomation, which is called P2MP based BIER in
[I-D.xie-bier-mvpn-mpls-p2mp].
Robot-Accelerated Perovskite Investigation and Discovery (2020)

Metal halide perovskites are a promising class of materials for next-generation photovoltaic and optoelectronic devices. The discovery and full characterization of new perovskite-derived materials are limited by the difficulty of growing high quality crystals needed for single-crystal X-ray diffraction studies. We present an automated, high-throughput approach for metal halide perovskite single crystal discovery based on inverse temperature crystallization (ITC) as a means to rapidly identify and optimize synthesis conditions for the formation of high quality single crystals. Using this automated approach, a total of 8172 metal halide perovskite synthesis reactions were conducted using 45 organic ammonium cations. This robotic screening increased the number of metal halide perovskite materials accessible by an ITC synthesis route by more than 5-fold and resulted in the formation of two new phases, [C2H7N2][PbI3] and [C7H16N]2[PbI4]. This comprehensive data set allows for a statistical quantification of the total experimental space and of the likelihood of large single crystal formation. Moreover, this data set enables the construction and evaluation of machine learning models for predicting crystal formation conditions. This work is a proof-of-concept that combining high throughput experimentation and machine learning accelerates and enhances the study of metal halide perovskite crystallization. This approach is designed to be generalizable to different synthetic routes for the acceleration of materials discovery.
Children, Youth and Sustainable Cities (2001)

(2001). Children, Youth and Sustainable Cities. Local Environment: Vol. 6, No. 1, pp. 5-12.
CANARY FILES: GENERATING FAKE FILES TO DETECT CRITICAL DATA LOSS FROM COMPLEX COMPUTER NETWORKS (2013)

This paper introduces two concepts: Canary Files and a Canary File management system. A Canary File is a fake computer document that is placed amongst real documents in order to aid in the early detection of unauthorised data access, copying or modification. The name originates from canaries, which were used within coalmines as an early warning to miners. This paper also introduces the Serinus System, a Canary File management system designed to address some of the key challenges associated with operating a cyber deception capability. The Serinus System automates Canary Files generation using content and file statistics drawn from three sources: (1) Internet harvested documents, (2) documents collected from across the entire enterprise environment, and (3) documents within the specific target directory. Each data source is allocated a weighting based on the strength of their relationship to the target directory. The weighting is seeded with a random value to avoid discovery by simple statistical based fake file detection systems. Research is continuing to assess the performance of both Canary Files and the Serinus System.
Multivalent Forms of the Notch Ligand DLL-1 Enhance Antitumor T-cell Immunity in Lung Cancer and Improve Efficacy of EGFR-Targeted Therapy (2015)

Activation of Notch signaling in hematopoietic cells by tumors contributes to immune escape. T-cell defects in tumors can be reversed by treating tumor-bearing mice with multivalent forms of the Notch receptor ligand DLL-1, but the immunologic correlates of this effect have not been elucidated. Here, we report mechanistic insights along with the efficacy of combinational treatments of multivalent DLL-1 with oncoprotein targeting drugs in preclinical mouse models of lung cancer. Systemic DLL-1 administration increased T-cell infiltration into tumors and elevated numbers of CD44(+)CD62L(+)CD8(+) memory T cells while decreasing the number of regulatory T cells and limiting tumor vascularization. This treatment was associated with upregulation of Notch and its ligands in tumor-infiltrating T cells enhanced expression of T-bet and phosphorylation of Stat1/2. Adoptive transfer of T cells from DLL1-treated tumor-bearing immunocompetent hosts into tumor-bearing SCID-NOD immunocompromised mice attenuated tumor growth and extended tumor-free survival in the recipients. When combined with the EGFR-targeted drug erlotinib, DLL-1 significantly improved progression-free survival by inducing robust tumor-specific T-cell immunity. In tissue culture, DLL1 induced proliferation of human peripheral T cells, but lacked proliferative or clonogenic effects on lung cancer cells. Our findings offer preclinical mechanistic support for the development of multivalent DLL1 to stimulate antitumor immunity.
Differentiation of two mouse cell lines is associated with hypomethylation of their genomes. (1984)

Methyl-accepting assays and a sensitive method for labeling specific CpG sites have been used to show that the DNA of F9 embryonal carcinoma cells decreases in 5-methylcytosine content by ca. 9% during retinoic acid-induced differentiation, whereas the DNA of dimethyl sulfoxide-induced Friend murine erythroleukemia (MEL) cells loses ca. 3.8% of its methyl groups. These values correspond to the demethylation of 2.2 X 10(6) and 0.9 X 10(6) 5'-CpG-3' sites per haploid genome in differentiating F9 and MEL cells, respectively. Fluorography of DNA restriction fragments methylated in vitro and displayed on agarose gels showed that demethylation occurred throughout the genome. In uninduced F9 cells, the sequence TCGA tended to be more heavily methylated than did the sequence CCGG, whereas this tendency was reversed in MEL cells. The kinetics of in vitro DNA methylation reactions catalyzed by MEL cell DNA methyltransferase showed that substantial numbers of hemimethylated sites accumulate in the DNA of terminally differentiating F9 and MEL cells, implying that a partial loss of DNA-methylating activity may accompany terminal differentiation in these two cell types.
The Retinoic Acid Receptors (2015)

Three retinoic acid receptors (RAR), structurally homologous to steroid and thyroid hormone nuclear receptors, have recently been cloned. Analysis of the tissue distribution of RARs mRNAs have demonstrated a distinct expression pattern of the receptors' transcripts. Moreover, the RAR beta gene specifically, is autoregulated by RA. These findings suggest that the retinoic acid receptors differentially contribute retinoic acid physiology.
The Multifaceted Role of Commensal Microbiota in Homeostasis and Gastrointestinal Diseases (2015)

The gastrointestinal tract houses a complex and diverse community of microbes. In recent years, an increased understanding of the importance of intestinal microbiota for human physiology has been gained. In the steady state, commensal microorganisms have a symbiotic relationship with the host and possess critical and distinct functions, including directly influencing immunity. This means that recognition of commensal antigens is necessary for the development of complete immune responses. Therefore, the immune system must face the challenge of maintaining mucosal homeostasis while dealing with undue passage of commensal or pathogenic microbes, as well as the host nutritional status or drug use. Disruption of this fine balance has been associated with the development of several intestinal inflammatory diseases. In this review, we discuss the mechanisms involved in the modulation of host-microbe interactions and how the breakdown of this homeostatic association can lead to intestinal inflammation and pathology.
Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies (2016)

The enormous diversity created by gene recombination and somatic hypermutation makes de novo protein sequencing of monoclonal antibodies a uniquely challenging problem. Modern mass spectrometry-based sequencing will rarely, if ever, provide a single unambiguous sequence for the variable domains. A more likely outcome is computation of an ensemble of highly similar sequences that can satisfy the experimental data. This outcome can result in the need for empirical testing of many candidate sequences, sometimes iteratively, to identity one which can replicate the activity of the parental antibody. Here we describe an improved approach to antibody protein sequencing by using phage display technology to generate a combinatorial library of sequences that satisfy the mass spectrometry data, and selecting for functional candidates that bind antigen. This approach was used to reverse engineer 2 commercially-obtained monoclonal antibodies against murine CD137. Proteomic data enabled us to assign the majority of the variable domain sequences, with the exception of 3-5% of the sequence located within or adjacent to complementarity-determining regions. To efficiently resolve the sequence in these regions, small phage-displayed libraries were generated and subjected to antigen binding selection. Following enrichment of antigen-binding clones, 2 clones were selected for each antibody and recombinantly expressed as antigen-binding fragments (Fabs). In both cases, the reverse-engineered Fabs exhibited identical antigen binding affinity, within error, as Fabs produced from the commercial IgGs. This combination of proteomic and protein engineering techniques provides a useful approach to simplifying the technically challenging process of reverse engineering monoclonal antibodies from protein material.
Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium (2015)

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.
[Prokaryotic expression and bioreactivity analysis of a major epitope region of 2C with 3AB within non-structural protein of foot-and-mouth disease virus]. (2009)

In recent years, the potential value of nonstructural protein (NSP) 2C was well documented for distinguishing foot-and-mouth disease virus (FMDV) in infected animals and vaccinated animals. In order to develop a more sensitive approach to detect natural infected FMDV while there is no interact with vaccinated FMDV, we incorporated a major epitope region of 2C with whole 3AB coding region within NSP and expressed in Escherichia coli. We got a 47.6 kD fusion protein named 2C'3AB. The product showed a specific reactivity with FMDV from serum of infected animal by using Western blotting analysis. This suggests that this protein could be applied to distinguish infected FMDV and vaccinated FMDV. We further compared 2C'3AB protein with 3ABC fusion protein, another available protein used for detecting infected FMDV, using indirect ELISA assay. The results showed that 2C'3AB-ELISA had higher sensitivity than that of 3ABC-ELISA for distinguishing infected FMDV and vaccinated FMDV of sera from epidemic region. Therefore, this recombinant protein 2C'3AB is a good candidate protein to develop more sensitive method to differentiate infected FMDV and vaccinated FMDV from vaccinated animals. This finding will increase our capability to check the infectious virus carrier and finally improve FMDV infection control.
Portugal (1999)

The main purpose of this chapter is to analyse intra-industry trade and adjustment in the Portuguese economy.1 Portugal has traditionally been quite open to international trade — having been referred to already by Ricardo in his famous example of the theory of comparative advantage. It is still a moot point among economic historians, however, whether free trade was a priority of Portuguese policy in the postwar years. Salazar's political ideology would have favoured a more inward-looking approach, but the realization of its external economic dependency as a small nation led Portugal to follow the main integration movements. Portugal was a founder member of the OEEC and EFTA, joined the GATT in 1962, signed wide-ranging free-trade agreements with the EEC in 1972 and 1976 and joined the Community in 1986.2
Thermal Ablation of Colorectal Lung Metastases: Retrospective Comparison Among Laser-Induced Thermotherapy, Radiofrequency Ablation, and Microwave Ablation (2016)

LITT, RFA, and MWA can be used as therapeutic options for lung metastases resulting from colorectal cancer. Statistically significant differences in local tumor control revealed a potential advantage in using MWA. No differences in time to tumor progression or survival rates were detected when the three different ablation methods were compared.
Double blind, randomised, placebo controlled, crossover, multicentre study to determine the efficacy of a 0.1% (w/v) sodium hyaluronate solution (Fermavisc) in the treatment of dry eye syndrome (1999)

The study demonstrates a clear benefit of hyaluronan over saline, in both subjective and objective assessments of dry eye syndrome. Hyaluronan was shown to be well tolerated.
The legumin gene family: structure of a B type gene of<i>Vicia faba</i>and a possible legumin gene specific regulatory element (1986)

The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid residues, an acidic, very hydrophilic alpha-chain of 281 residues and a basic, somewhat hydrophobic beta-chain of 181 residues. The latter two coding regions are immediately contiguous, but each is interrupted by a short intron. Type A legumin genes from soybean and pea are known to have introns in the same two positions, in addition to an extra intron (within the alpha-coding sequence). Sequence comparisons of legumin genes from these three plants revealed a highly conserved sequence element of at least 28 bp, centered at approximately 100 bp upstream of each cap site. The element is absent from the equivalent position of all non-legumin and other plant and fungal genes examined. We tentatively name this element "legumin box" and suggest that it may have a function in the regulation of legumin gene expression.
DNA-uptake in the naturally competent cyanobacterium,<i>Synechocystis sp.</i>PCC 6803 (1995)

Uptake of DNA has been examined in the naturally competent cyanobacterium, Synechocystis sp. Pasteur Culture Collection (PCC) 6803. This bacterium is easily transformed by exogenously offered, homologous as well as heterologous DNA. During uptake, the DNA is converted from double stranded to single stranded form. A Ca-dependent nuclease, located in the cytoplasmic membrane, probably processes the DNA offered for uptake and converts it into single stranded form. The cyanobacterial DNA-uptake process is discussed in comparison to respective phenomena in other bacteria.
Sarilumab versus standard of care for the early treatment of COVID-19 pneumonia in hospitalized patients: SARTRE: a structured summary of a study protocol for a randomised controlled trial (2020)

The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this letter serves as a summary of the key elements of the full protocol. The study protocol has been reported in accordance with the Standard Protocol Items: Recommendations for Clinical Interventional Trials (SPIRIT) guidelines (Additional file 2).