gebhart/patrepeval huggingface dataset:
A 100 Gb/s transimpedance amplifier in 65 nm CMOS technology for optical communications (2014)

A 100 Gb/s CMOS transimpedance amplifier (TIA) for high speed optical communication receivers is presented in this paper. The TIA is based on a differential architecture and composed of a regulated cascode block and a differential amplifier with active feedback. It adopts peaking inductors and a capacitive degeneration scheme to increase the bandwidth. The TIA is designed and laid out in CMOS 65 nm CMOS technology. Post layout simulation results show that the TIA achieves 70 GHz bandwidth, 40 dBO transimpedance gain, ±4.36 ps of the group delay variation, and 31 pA/√Hz of the input referred noise current, and it dissipates 24 mW under 1.2V supply. The proposed TIA increases the bandwidth by more than two times when compared with other existing CMOS TIAs, while achieving comparable performance in other performance metrics.
Distribution and surfactant association of carcinoembryonic cell adhesion molecule 6 in human lung (2011)

Carcinoembryonic cell adhesion molecule 6 (CEACAM6) is a glycosylated, glycophosphatidylinositol-anchored protein expressed in epithelial cells of various primate tissues. It binds gram-negative bacteria and is overexpressed in human cancers. CEACAM6 is associated with lamellar bodies of cultured type II cells of human fetal lung and protects surfactant function in vitro. In this study, we characterized CEACAM6 expression in vivo in human lung. CEACAM6 was present in lung lavage of premature infants at birth and increased progressively in intubated infants with lung disease. Of surfactant-associated CEACAM6, ∼80% was the fully glycosylated, 90-kDa form that contains the glycophosphatidylinositol anchor, and the concentration (3.9% of phospholipid for adult lung) was comparable to that for surfactant proteins (SP)-A/B/C. We examined the affinity of CEACAM6 by purification of surfactant on density gradient centrifugation; concentrations of CEACAM6 and SP-B per phospholipid were unchanged, whereas levels of total protein and SP-A decreased by 60%. CEACAM6 mRNA content decreased progressively from upper trachea to peripheral fetal lung, whereas protein levels were similar in all regions of adult lung, suggesting proximal-to-distal developmental expression in lung epithelium. In adult lung, most type I cells and ∼50% of type II cells were immunopositive. We conclude that CEACAM6 is expressed by alveolar and airway epithelial cells of human lung and is secreted into lung-lining fluid, where fully glycosylated protein binds to surfactant. Production appears to be upregulated during neonatal lung disease, perhaps related to roles of CEACAM6 in surfactant function, cell proliferation, and innate immune defense.
Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum (2005)

Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.
Scaling to very very large corpora for natural language disambiguation (2001)

The amount of readily available on-line text has reached hundreds of billions of words and continues to grow. Yet for most core natural language tasks, algorithms continue to be optimized, tested and compared after training on corpora consisting of only one million words or less. In this paper, we evaluate the performance of different learning methods on a prototypical natural language disambiguation task, confusion set disambiguation, when trained on orders of magnitude more labeled data than has previously been used. We are fortunate that for this particular application, correctly labeled training data is free. Since this will often not be the case, we examine methods for effectively exploiting very large corpora when labeled data comes at a cost.
Evidence-based and consensus clinical practice guidelines for the iron treatment of restless legs syndrome/Willis-Ekbom disease in adults and children: an IRLSSG task force report (2017)

Consensus recommendations based on clinical practice are presented, including when to use oral iron or IV iron, and recommendations on repeated iron treatments. New iron treatment algorithms, based on evidence and consensus opinion have been developed.
Development of scoliosis following pinealectomy in young chickens is not the result of an artifact of the surgical procedure (2001)

Pinealectomy in young chickens consistently results in scoliosis, which has many characteristics similar to those seen in adolescent idiopathic scoliosis. The mechanism underlying this phenomenon remains a mystery and it is not yet entirely clear whether some unidentified aspect of the extensive surgery is the major factor rather than the removal of the pineal gland. Four different types of pinealectomy surgery were performed on young chickens as well as deliberate damage to the cerebral cortex which simulated the extreme of any accidental damage that might occur during surgery. Scoliosis was assessed from weekly radiographs. No differences in incidence of scoliosis, degree of severity, or pattern of curve development were observed for any of the experimental groups when compared with controls. In all groups approximately 55% of the chickens developed scoliosis that progressed rapidly. Different pinealectomy procedures and deliberate damage to the cerebral cortex produce scoliosis in young chickens with the same incidence and characteristics. This suggests strongly that the mechanism behind the phenomenon is due to the removal of the pineal gland and not some artifact of the extensive surgery. The pinealectomy model in young chickens is proving to be a good model for studying AIS in humans. An understanding of the mechanism underlying this phenomenon has the potential to provide further insights into the etiology of AIS and can lead to the development of novel treatment methods.
Translation of a Retained Intron in Tyrosinase-related Protein (TRP) 2 mRNA Generates a New Cytotoxic T Lymphocyte (CTL)-defined and Shared Human Melanoma Antigen Not Expressed in Normal Cells of the Melanocytic Lineage (1998)

We report here the identification of a new shared human melanoma antigen recognized by a human leukocyte antigen (HLA)-A*68011-restricted cytotoxic T lymphocyte clone (CTL 128). The cDNA encoding this antigen is composed of a partially spliced form of the melanocyte differentiation antigen tyrosinase-related protein (TRP)-2, containing exons 1-4 with retention of intron 2 and part of intron 4 (TRP-2-INT2). The sequence coding for the antigenic epitope is located at the 5' end of intron 2 and is available for translation in the same open reading frame of the fully spliced TRP-2 mRNA. This peptide is also recognized by CTL 128 when presented by the HLA-A*3301, a member of the HLA-A3-like supertype that includes the HLA-A*68011. Quantitative reverse transcription PCR analysis carried out on total and/or cytoplasmic mRNA demonstrated that, in contrast to the fully spliced TRP-2 mRNA expressed in melanomas, normal skin melanocytes, and retina, the TRP-2-INT2 mRNA could be detected at significant levels in melanomas but not in normal cells of the melanocytic lineage. Instead, in these normal samples, both the spliced and the unspliced transcript of gp100 were expressed at high levels. Absence of endogenous TRP-2-INT2 expression in melanocytes was also confirmed by lack of recognition of HLA-A*68011-transduced, TRP-2(+) melanocyte lines by CTL 128. These results indicate that a partially spliced form of a differentiation antigen mRNA, present in the cytoplasmic compartment of neoplastic but not normal cells of the melanocytic lineage, can be the source of a melanoma-restricted T cell epitope.
A low-cost and low-weight attitude estimation system for an autonomous helicopter (2002)

In this paper a low-cost and low-weight attitude estimation system for an autonomous helicopter is presented. The system is based on an inclinometer and a rate gyro. The data coming from the sensors is fused through a complementary filter. In this way the slow dynamics of the inclinometer can be effectively compensated. Tests have shown that a very effective attitude estimation system can be achieved.
Promiscuous survivin peptide induces robust CD4+ T‐cell responses in the majority of vaccinated cancer patients (2011)

CD4(+) T cells have been shown to be crucial for the induction and maintenance of cytotoxic T cell responses and to be also capable of mediating direct tumor rejection. Therefore, the anticancer therapeutic efficacy of peptide-based vaccines may be improved by addition of HLA class II epitopes to stimulate T helper cells. Survivin is an apoptosis inhibiting protein frequently overexpressed in tumors. Here we describe the first immunological evaluation of a survivin-derived CD4(+) T cell epitope in a multipeptide immunotherapy trial for prostate carcinoma patients. The survivin peptide is promiscuously presented by several human HLA-DRB1 molecules and, most importantly, is naturally processed by dendritic cells. In vaccinated patients, it was able to induce frequent, robust and multifunctional CD4(+) T cell responses, as monitored by IFN-γ ELISPOT and intracellular cytokine staining. Thus, this HLA-DR restricted epitope is broadly immunogenic and should be valuable for stimulating T helper cells in patients suffering from a wide range of tumors.
Detection of Androgen Receptor Mutations in Circulating Tumor Cells in Castration-Resistant Prostate Cancer (2010)

AR mutations can be identified in CTC-enriched peripheral blood samples from CRPC patients. This approach has the potential to open new perspectives in understanding CTCs and the mechanisms for tumor progression and metastasis in CRPC.
The Mode of Action of Vitamin K (1974)

Abstract An unusual tryptic peptide isolated from the protein, prothrombin, has recently been shown to contain at least a portion of the vitamin K-dependent region of this protein (Nelsestuen, G. L., and Suttie, J. W. (1973) Proc. Nat. Acad. Sci. U. S. A. 70, 3366–3370). A modified glutamylserine dipeptide has been isolated from proteolytic digests of this vitamin K-dependent peptide and has been characterized. It has been unambiguously demonstrated that the glutamic acid of the glutamylserine has been substituted by carboxylation of the γ carbon atom so that the dipeptide structure is: [see PDF for equation] Presumably, the incorporation of the second γ-carboxyl group is dependent on vitamin K.
Fast packet switching for broadband ISDN (1989)

The paper is designed to serve as a brief introduction to the subject of fast packet switching with particular emphasis on designs of fast packet switch that have been proposed for use in the asynchronous transfer mode (ATM) of broadband ISDN. A simple classification of existing fast packet switch designs is introduced and examples of switch designs belonging to each class are described. Some elementary performance comparisons are also drawn between the various classes of switch design. >
Regulation of AID expression in the immune response (2007)

The B cell-specific enzyme activation-induced cytidine deaminase (AID) has been shown to be essential for isotype switching and affinity maturation of antibody genes during the immune response. Conversely, AID activity has also been linked to autoimmunity and tumorigenesis. Determining how AID expression is regulated in vivo is therefore central to understanding its role in health and disease. Here we use phylogenetic footprinting and high-resolution histone acetylation mapping to accurately demarcate AID gene regulatory boundaries. Based on this strategy, we identify a novel, positive regulatory element required for AID transcription. Furthermore, we generate two AID indicator mouse strains using bacterial artificial chromosomes that faithfully recapitulate endogenous AID expression. The first strain uses a green fluorescent protein reporter to identify B cells that actively express AID during the immune response. In the second strain, AID transcription affects the permanent expression of a yellow fluorescent protein reporter in post-germinal center and terminally differentiated lymphocytes. We demonstrate the usefulness of these novel strains by resolving recent contradictory observations on AID expression during B cell ontogeny.
The Iterative Protein Redesign and Optimization (IPRO) suite of programs (2014)

Proteins are an important class of biomolecules with applications spanning across biotechnology and medicine. In many cases, native proteins must be redesigned to improve various performance metrics by changing their amino acid sequences. Algorithms can help sharpen protein library design by focusing the library on sequences that optimize computationally accessible proxies. The Iterative Protein Redesign and Optimization (IPRO) suite of programs offers an integrated environment for (1) altering protein binding affinity and specificity, (2) grafting a binding pocket into an existing protein scaffold, (3) predicting an antibody's tertiary structure based on its sequence, (4) enhancing enzymatic activity, and (5) assessing the structure and binding energetics for a specific mutant. This manuscript provides an overview of the methods involved in IPRO, input language terminology, algorithmic details, software implementation specifics and application highlights. IPRO can be downloaded at http://maranas.che.psu.edu.
Amnesia-reversal activity of a series of N-[(disubstituted-amino)alkyl]-2-oxo-1-pyrrolidineacetamides, including pramiracetam (1984)

A series of N-[(dialkylamino)alkyl]-2-oxo-1- pyrrolidineacetamides was synthesized. The title compounds reversed electroconvulsive shock (ECS) induced amnesia in mice when administered subsequent to the ECS treatment and were inactive in a general observational test for central nervous system (CNS) activity. Active compounds exhibited an inverted U-shaped dose-response curve. Among the compounds with the broadest dose-response curve, as well as the most potent, were those with the N-[2-[bis(1-methylethyl)amino] ethyl] or 2,6- dimethylpiperidinoethyl residues as amide substituent. The N-(dialkylamino) substituent markedly enhances amnesia-reversal activity, with ethylene providing the optimal chain length. N-[2-[Bis(1-methylethyl)amino]ethyl] -2-oxo-1- pyrrolidineacetamide N-(dialkylamino) substituent was selected for preclinical toxicological evaluation, assigned the investigational number CI-879 and the U.S. adopted name ( USAN ) pramiracetam . Pramiracetam demonstrated a wide margin of safety in animals and was well tolerated in normal human volunteers. It has shown encouraging activity in an open label trial in patients with primary degenerative dementia (PDD or senile dementia of the Alzheimer's type).
Epidermal Growth Factor Receptor Inhibition and Non-Small Cell Lung cancer (2006)

The majority of non-small cell (NSC) lung cancers express epidermal growth factor receptor (EGFR). Many studies have evaluated the clinical effect from targeted therapy achieved by blocking EGFR in patients with NSC lung cancer. Treatment of biologically unselected patients with NSC lung cancer with two reversible quinazole EGFR inhibitors, gefitinib and erlotinib, gave negative results in all controlled trials but one. Ten percent to 20% of patients with NSC lung cancers have somatic mutations in EGFR, and these patients have a significantly higher response rate (73%) to treatment with EGFR inhibitors than patients with wild-type EGFR (10%). Patients with Asian background, women, non-smokers, and patients with adenocarcinoma had higher response rates than other patients, and the differences may be due to an association between the clinical characteristics and EGFR mutations. Further studies are needed to fully evaluate the effect of EGFR inhibitor-treatment for subgroups of patients with NSC lung cancer with favorable biological and clinical characteristics.
Mechanisms controlling human endothelial lumen formation and tube assembly in three‐dimensional extracellular matrices (2007)

Recent data have revealed new mechanisms that underlie endothelial cell (EC) lumen formation during vascular morphogenic events in development, wound repair, and other disease states. It is apparent that EC interactions with extracellular matrices (ECMs) establish signaling cascades downstream of integrin ligation leading to activation of the Rho GTPases, Cdc42 and Rac1, which are required for lumen formation. In large part, this process is driven by intracellular vacuole formation and coalescence, which rapidly leads to the creation of fluid-filled matrix-free spaces that are then interconnected via EC-EC interactions to create multicellular tube structures. EC vacuoles markedly accumulate in a polarized fashion directly adjacent to the centrosome in a region that strongly accumulates Cdc42 protein as indicated by green fluorescent protein (GFP)-Cdc42 during the lumen formation process. Downstream of Cdc42-mediated signaling, key molecules that have been identified to be required for EC lumen formation include Pak2, Pak4, Par3, Par6, and the protein kinase C (PKC) isoforms zeta and epsilon. Together, these molecules coordinately regulate the critical EC lumen formation process in three-dimensional (3D) collagen matrices. These events also require cell surface proteolysis mediated through membrane type 1 matrix metalloproteinase (MT1-MMP), which is necessary to create vascular guidance tunnels within the 3D matrix environment. These tunnels represent physical spaces within the ECM that are necessary to regulate vascular morphogenic events, including the establishment of interconnected vascular tube networks as well as the recruitment of pericytes to initiate vascular tube maturation (via basement membrane matrix assembly) and stabilization. Current research continues to analyze how specific molecules integrate signaling information in concert to catalyze EC lumen formation, pericyte recruitment, and stabilization processes to control vascular morphogenesis in 3D extracellular matrices.
Defending against denial of service attacks in Scout (1999)

We describe a two-dimensional architecture for defending against denial of service attacks. In one dimension, the architecture accounts for all resources consumed by each I/O path in the system; this accounting mechanism is implemented as an extension to the path object in the Scout operating system. In the second dimension, the various modules that define each path can be configured in separate protection domains; we implement hardware enforced protection domains, although other implementations are possible. The resulting system-which we call Escort-is the first example of a system that simultaneously does end-to-end resource accounting (thereby protecting against resource based denial of service attacks where principals can be identified) and supports multiple protection domains (thereby allowing untrusted modules to be isolated from each other). The paper describes the Escort architecture and its implementation in Scout, and reports a collection of experiments that measure the costs and benefits of using Escort to protect a web server from denial of service attacks.
CD4‐mediated functional activation of human CD4+CD25+ regulatory T cells (2007)

Naturally occurring CD4(+)CD25(+)FoxP3(+) regulatory T cells (CD25(+) Tregs) constitute a specialized population of T cells that is essential for the maintenance of peripheral self-tolerance. The immune regulatory function of CD25(+) Tregs depends upon their activation. We found that anti-CD4 antibodies activate the suppressive function of human CD25(+) Tregs in a dose-dependent manner. We demonstrate that CD4-activated CD25(+) Tregs suppress the proliferation of CD4(+) and CD8(+) T cells, their IL-2 and IFN-gamma production as well as the capacity of CD8(+) T cells to re-express CD25. By contrast, anti-CD4 stimulation did not induce suppressive activity in conventional CD4(+) T cells. These results identify CD4 as a trigger for the suppressive function of CD25(+) Tregs and suggest a possible CD4-mediated exploitation of these cells.
Comparative genomics on SLIT1, SLIT2, and SLIT3 orthologs (2005)

SLIT1 gene at human chromosome 10q24.1, SLIT2 gene at 4p15.31, and SLIT3 gene at 5q34-q35.1 encode large secreted proteins functioning as ligands for Roundabout (Robo) receptors. SLIT-ROBO signaling pathway is implicated in neurogenesis, angiogenesis, and immune response through the regulation of axonal guidance, endothelial cell migration, and denderitic cell migration, respectively. GREMLIN (CKTSF1B1 or GREM1) and DANTE (CKTSF1B3 or GREM3) are secreted antagonists for BMPs and SLITs. Here, comparative integromics analyses on SLIT1, SLIT2, and SLIT3 orthologs were performed by using bioinformatics. Rat Slit2 gene, consisting of 36 exons, was located within rat genome sequences AC098362.4 and AC111627.6. Mouse Slit3 complete coding sequence was determined by assembling BB634238 EST, AF144629 cDNA, and AK129223 cDNA. Leucine-rich repeats with nine conserved cysteine (LRRCC) domains and SLIT C-terminal cysteine-rich (SLITCCR) domain were identified in this study. CPxxCxCxxxxVxCxxxxLxxxPxxxPx(10~58) Nx(19,20)LxxNx(9)Fx(8)LxLxxNxxxCxxxxxFxxLxxx xxLxLxxNx(9)Fx(13)NxxxCxCxxxWLx(15)CxxPx(17)C was the consensus sequence of LRRCC domain. Mammalian SLIT1, SLIT2 and SLIT3 orthologs were large secreted proteins with four LRRCC domains, nine EGF domains, Laminin G (LamG) domain, and SLITCCR domain. SLIT1 mRNA was expressed in fetal brain, infant brain, anaplastic oligodendroglioma, and Jurkat T cells. SLIT2 and SLIT3 mRNAs were co-expressed in embryonic stem (ES) cells with embryoid body formation, and diffuse type gastric cancer with signet ring cell features. Double TCF/LEF and bHLH-binding sites were conserved among mammalian SLIT1 promoters. FOXJ2, E47, ETS1, and FOXA2-binding sites and CCAAT box were conserved among mammalian SLIT3 promoters. Mammalian SLIT1 orthologs were identified as evolutionarily conserved targets of the WNT/beta-catenin signaling pathway.