gebhart/patrepeval huggingface dataset:
A comparison of sample and total census data for a population of the Eastern Longneck Turtle Chelodina longicollis in a farm dam north-west of Sydney, New South Wales (1999)

Interpretation of trap bias in sampling freshwater turtles has previously relied on indirect methods. The data presented here provides the first comparison of a sample and total census of a waterbody. Eastern Longneck Turtles Chelodina longicollis Shaw were sampled in a 0.1 ha farm dam for three days immediately prior to drainage and a population census was subsequently carried out. Fyke nets proved to be an effective method of sampling the population. During the sampling phase 78% of males (n = 11) and 81% of females (n = 21) were captured, and there was no significant difference between the sample and the census in terms of population size structure (χ23 = 1.12, excluding juveniles) or sex ratio (χ21 = 0.008). None of the three resident hatchlings were captured despite a high probability of capture (p = 0.67). Hatchlings and juveniles combined made up 19.4% of the population and there were no immature resident females and few immature males. Based on the population profile, recruitment was intermittent and apparently infrequent with the greatest cohort being mature females, although there were no immature females. Mature males were present in larger numbers than immature males.
The structural basis of Janus kinase 2 inhibition by a potent and specific pan-Janus kinase inhibitor (2005)

JAK2, a member of the Janus kinase (JAK) family of protein tyrosine kinases (PTKs), is an important intracellular mediator of cytokine signaling. Mutations of the JAK2 gene are associated with hematologic cancers, and aberrant JAK activity is also associated with a number of immune diseases, including rheumatoid arthritis. Accordingly, the development of JAK2-specific inhibitors has tremendous clinical relevance. Critical to the function of JAK2 is its PTK domain. We report the 2.0 A crystal structure of the active conformation of the JAK2 PTK domain in complex with a high-affinity, pan-JAK inhibitor that appears to bind via an induced fit mechanism. This inhibitor, the tetracyclic pyridone 2-tert-butyl-9-fluoro-3,6-dihydro-7H-benz[h]-imidaz[4,5-f]isoquinoline-7-1, was buried deep within a constricted ATP-binding site, in which extensive interactions, including residues that are unique to JAK2 and the JAK family, are made with the inhibitor. We present a structural basis of high-affinity JAK-specific inhibition that will undoubtedly provide an invaluable tool for the further design of novel, potent, and specific therapeutics against the JAK family.
Rfam: annotating non-coding RNAs in complete genomes (2004)

Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.
Targeting insulin resistance in type 2 diabetes via immune modulation of cord blood-derived multipotent stem cells (CB-SCs) in stem cell educator therapy: phase I/II clinical trial (2013)

ClinicalTrials.gov number, NCT01415726.
Protection of macaques with a simian immunodeficiency virus envelope peptide vaccine based on conserved human immunodeficiency virus type 1 sequences. (1991)

This report describes the vaccination of rhesus macaques with peptides selected from regions of the simian immunodeficiency virus (SIV) envelope that are hydrophilic, immunoreactive, and highly homologous with corresponding conserved envelope sequences of the human immunodeficiency virus (HIV). The peptides, produced as beta-galactosidase fusion proteins, induced virus-neutralizing and peptide-specific antibodies. After challenge with virulent virus, controls became virus positive and developed gradually rising antibody titers to SIV over 63 weeks. Immunized macaques developed a postchallenge anamnestic response to SIVenv antigens within 3-6 weeks followed by a gradual, fluctuating decline in SIV antibody titers and partial or total suppression of detectable SIV. Virus suppression correlated with prechallenge neutralizing antibody titers. Although the average CD4+ cell count in the blood of immunized macaques remained constant, the control macaques exhibited a progressive decrease developing about week 55 after challenge. The conserved nature of the HIV and SIV peptides and the similar humoral immunoreactivity in the respective hosts suggest that homologous HIV peptides may be important components of a successful immunization strategy.
TrackMAC: An IEEE 802.11ad-compatible beam tracking-based MAC protocol for 5G millimeter-wave local area networks (2018)

This paper presents a novel framework for MAC design for millimeter-wave (mm-wave) mobile wireless networks. Specifically, we consider an infrastructure wireless network in which both the Access Point (AP) and the mobile stations (STAs) communicate in the 60GHz band. In order to overcome the high path loss that is characteristic of mm-wave frequencies, both the transmitter as well as the receivers employ beamforming and use highly directional beams for transmission and reception. In such a scenario, traditional Medium Access Control (MAC) protocols such as CSMA/CA, which rely on the omni-directional nature of transmissions, may no longer be viable for efficient medium access control. It is necessary for the AP to know the directions that the associated STAs are in so that it can steer its transmissions to an intended receiver in that receiver's direction. In light of this, we propose TrackMAC, a directional MAC protocol that (i) has the property that it continuously tracks the direction of every associated station which, in general, is mobile, and (ii) can be implemented squarely within the specifications of the IEEE 802.11ad standard for mm-wave Wireless Local Area Networks (WLAN). The efficacy of the proposed architecture is demonstrated using computer simulations.
Interleukin-2 enhances the depressed natural killer and cytomegalovirus-specific cytotoxic activities of lymphocytes from patients with the acquired immune deficiency syndrome. (1983)

The recently described acquired immune deficiency syndrome (AIDS) is characterized by the occurrence of severe opportunistic infections and an aggressive form of Kaposi's sarcoma. A variety of profound defects in cell-mediated immunity have been reported in association with the AIDS, including deficiencies in natural killer (NK) cell activity and cytomegalovirus (CMV)-specific cytotoxicity. In the present study, the in vitro effects of interleukin-2 (IL-2) and interferon beta (IFN Beta) on these abnormalities were examined to assess the potential use of these lymphokines in the immunotherapeutic treatment of this syndrome. The peripheral blood lymphocytes (PBL) from six male homosexuals with AIDS and an active CMV infection exhibited markedly depressed NK cell and CMV-specific cytotoxic lymphocyte responses compared with uninfected, heterosexual control subjects. Incubation of PBL with IFN Beta enhanced the NK cell activity and the CMV-specific cytotoxicity of only one of six and neither of two AIDS patients, respectively, while enhancing the NK cell activity of all six control subjects. In contrast, IL-2 dramatically enhanced both the NK cell and the CMV-specific cytotoxic lymphocyte activities of all of the patients. These results indicate that IL-2 can substantially potentiate the depressed cytotoxic effector functions of PBL from AIDS patients, while IFN Beta has little effect.
Purification and characterization of the extracellular alpha-amylase from Clostridium acetobutylicum ATCC 824 (1991)

The extracellular alpha-amylase (1,4-alpha-D-glucanglucanohydrolase; EC 3.2.1.1) from Clostridium acetobutylicum ATCC 824 was purified to homogeneity by anion-exchange chromatography (mono Q) and gel filtration (Superose 12). The enzyme had an isoelectric point of 4.7 and a molecular weight of 84,000, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It was a monomeric protein, the 19-amino-acid N terminus of which displayed 42% homology with the Bacillus subtilis saccharifying alpha-amylase. The amino acid composition of the enzyme showed a high number of acidic and hydrophobic residues and only one cysteine residue per mole. The activity of the alpha-amylase was not stimulated by calcium ions (or other metal ions) or inhibited by EDTA, although the enzyme contained seven calcium atoms per molecule. alpha-Amylase activity on soluble starch was optimal at pH 5.6 and 45 degrees C. The alpha-amylase was stable at an acidic pH but very sensitive to thermal inactivation. It hydrolyzed soluble starch, with a Km of 3.6 g . liter-1 and a Kcat of 122 mol of reducing sugars . s-1 . mol-1. The alpha-amylase showed greater activity with high-molecular-weight substrates than with low-molecular-weight maltooligosaccharides, hydrolyzed glycogen and pullulan slowly, but did not hydrolyze dextran or cyclodextrins. The major end products of maltohexaose degradation were glucose, maltose, and maltotriose; maltotetraose and maltopentaose were formed as intermediate products. Twenty seven percent of the glucoamylase activity generally detected in the culture supernatant of C. acetobutylicum can be attributed to the alpha-amylase.
A Compact Q-/K-Band Dual Frequency Feed Horn. (1983)

A millimeter-wave dual frequency circularly polarized feed for an offset reflector antenna is being developed for a portable satellite ground terminal. The two frequency bands are Q - and K -bands for transmit and receive, respectively. A compact feed design consisting of a single corrugated horn with two circular waveguide concentric openings at the horn throat is described. Good aperture efficiency and low sidelobes in both of the frequency bands are achieved.
Immunotherapy of a murine tumor with interleukin 2. Increased sensitivity after MHC class I gene transfection. (1987)

We have shown that two weakly immunogenic MCA sarcomas developed in our laboratory that are sensitive to high-dose IL-2 immunotherapy express class I MHC in vivo and in vitro. Two nonimmunogenic MCA sarcomas are relatively insensitive to IL-2 therapy and express minimal or no class I MHC molecules in vivo and in vitro. To study the role of MHC in the therapy of tumors with IL-2, a class I-deficient murine melanoma, B16BL6, was transfected with the Kb class I gene. Expression of class I MHC rendered B16BL6 advanced pulmonary macrometastases sensitive to IL-2 immunotherapy. 3-d micrometastases of CL8-2, a class I transfected clone of B16BL6, were significantly more sensitive to IL-2 therapy than a control nontransfected line. Expression of Iak, a class II MHC molecule, had no effect on IL-2 therapy of transfectant pulmonary micrometastases in F1 mice. By using lymphocyte subset depletion with mAbs directed against Lyt-2, therapy of class I transfectant macrometastases with high-dose IL-2 was shown to involve an Lyt-2 cell. In contrast, regression of micrometastases treated with low-dose IL-2 involved Lyt-2+ cells, but regression mediated by high doses of IL-2 did not. We hypothesize that both LAK and Lyt-2+ T cells effect IL-2-mediated elimination of micrometastases, but only Lyt-2+ T cells are involved in macrometastatic regression. Low doses of IL-2 stimulate Lyt-2+ cells to eliminate class I-expressing micrometastases, but high doses of IL-2 can recruit LAK cells to mediate regression of micrometastases independent of class I expression. Only high-dose IL-2, mediating its effect predominantly via Lyt-2+ cells, is capable of impacting on MHC class I-expressing macrometastases. Macrometastases devoid of class I MHC antigens appear to be resistant to IL-2 therapy.
Syringolin, a Novel Peptide Elicitor from Pseudomonas syringae pv. syringae that Induces Resistance to Pyricularia oryzae in Rice (1998)

Recognition by rice plants (Oryza sativa) of the nonhost pathogen Pseudomonas syringae pv. syringae leads to an active response ultimately resulting in local acquired resistance against the rice blast fungus Pyricularia oryzae. An observable aspect of this defense response is the increased abundance of a set of transcripts. The accumulation of one of these transcripts, Pir7b, was dependent on the function of the bacterial lemA gene, which encodes part of a two-component regulatory system. This suggested that the lemA regulatory system controlled the production of an elicitor of Pir7b transcript accumulation. This elicitor, which we name syringolin, was purified to homogeneity and its structure was elucidated. Syringolin is a novel and unusual secreted peptide consisting of a 12-membered ring formed by the two non-proteinogenic amino acids 5-methyl-4-amino-2-hexenoic acid and 3,4-dehydrolysine. The α-amino group of the latter is connected by a peptide bond to a valine that in turn is linked to a second valine via a urea moiety. Application of syringolin onto rice leaves elicited the accumulation of Pir7b as well as of other defense-related transcripts and induced resistance toward P. oryzae. Thus, syringolin is one of several determinants by which rice plants can perceive the nonhost pathogen P. syringae pv. syringae.
Liquid chromatographic profiling of monosaccharide concentrations in complex cell-culture media and fermentation broths (2010)

A solid phase extraction, liquid chromatography and fluorescence (SPE-RPLC-FL) based protocol for the determination of free monosaccharides in highly complex raw material powders and formulated fermentation feedstocks and broths has been developed. Monosaccharides within sample extracts were derivatised pre-column with anthranilic acid and the derivatives separated using reversed-phase LC with fluorescence detection. Using a 2.1 mm × 50 mm 1.8 µm Zorbax Eclipse XDB-C18 column, a flow rate of 0.4 mL min-1 and an acetonitrile gradient in a sodium acetate buffer (pH 4.3; 50 mmol L-1) the baseline resolution of glucosamine, mannosamine, galactosamine, galactose, mannose, glucose, ribose, xylose, fucose and sialic acid within 20 minutes was achieved. Pre-column derivatisation involved combining a 30 mg mL-1 solution of anthranilic acid in a 1 : 1 ratio with an aqueous standard prior to injection. Standard analytical performance criteria were used for evaluation purposes, with the method found to exhibit LOD's as low as 10 fmol, and be linear and precise (%RSD < 2.2% (n = 7). The method was applied to the analysis of a range of highly complex biopharmaceutical production samples, including yeastolate powders, chemically defined media and in-process fermentation broth samples. Sample preparation involved passing an aqueous sample through a C18 solid phase extraction cartridge to trap hydrophobic peptides and vitamins, with recovery of all test sugars exceeding 90%. Finally, standard statistical analysis was performed on samples taken from different lots in order to estimate lot-to-lot variability.
Mitogen-induced genes are subject to multiple pathways of regulation in the initial stages of T-cell activation. (1989)

The delivery of a mitogenic signal to T cells via any one of several cell surface molecules elicits a variety of intracellular responses, some or all of which regulate subsequent gene expression events. The expression of nine novel mitogen-induced genes in response to various T-cell-activating agents was examined to evaluate the diversity of pathways which regulate such genes. The relative contribution of distinct secondary signals, individually or together, to mitogen-stimulated gene induction and the capability of individual genes to respond to the sometimes divergent signals generated from different cell surface structures is addressed. The activation of T cells with mitogenic monoclonal antibodies directed against the CD2 or CD3 cell surface molecules, or with phytohemagglutinin, induced all nine genes. Thus, stimulation by fully mitogenic agents regardless of cell surface-binding specificity correlated with the expression of all of the genes studied. However, heterogeneous patterns of gene expression, encompassing five regulatory classes, were revealed by the use of phorbol 12-myristate 13-acetate, calcium ionophore, and anti-CD28 monoclonal antibody, agents which mediated only a subset of intracellular events and thus an incomplete mitogenic signal. Interleukin-2 and two novel lymphokines represented one regulatory class that appeared to require unique transcriptional activation signals relative to the other mitogen-induced genes. As demonstrated in the accompanying paper (P. F. Zipfel, S. G. Irving, K. Kelly, and U. Siebenlist, Mol. Cell. Biol. 9:1041-1048, 1989), the immediate transcriptional response of T cells to mitogenic stimulation is quite complex, involving numerous genes beyond those which have been previously described. Furthermore, the discrimination of several regulatory phenotypes among these nine genes suggests that a multiplicity of signaling pathways extends from the cell surface to the level of transcription.
Characterization of Insulin-Like Growth Factor Binding Proteins Produced in the Rat Central Nervous System* (1990)

Insulin-like growth factor binding proteins (IGFBP) are thought to modulate the biological actions of the insulin-like growth factors (IGF), including possible regulatory roles in the growth and differentiation of the central nervous system. Extracellular fluids usually contain a mixture of IGFBPs, three of which have been cloned, sequenced, and designated IGFBP-1, -2, and -3. We used Western ligand blotting, immunoprecipitation, and competitive binding analysis to characterize IGFBPs found in fetal and adult rat cerebrospinal fluid (CSF) and IGFBPs produced by cultures of neonatal rat choroid plexus, astrocytes, and C6 glial cells. Pooled rat CSF contains primarily IGFBP-2 (a narrow band at Mr = 29,000), lesser quantities of IGFBP-3 (a multicomponent broad band at Mr = 37,500-43,000), and trace amounts of low mol wt IGFBPs. Conditioned medium from cultures of choroid plexus cells contained a single binding protein corresponding to IGFBP-2, whereas C6 cells made predominately an IGFBP corresponding to IGFBP-3. Astrocytes secreted two IGFBPs corresponding to IGFBP-2 and -3, primarily IGFBP-3. Neonatal CSF contained substantially more binding activity corresponding to IGFBP-2 than did adult CSF. In all samples showing Western ligand binding profiles corresponding to IGFBP-2, identification was established by immunoprecipitation. Competitive binding analysis performed on choroid plexus IGFBP showed preferential high affinity binding for IGF-II compared with that for IGF-I. In conclusion, CSF contains a mixture of distinct IGFBPs, primarily IGFBP-2. The other IGFBPs found in CSF are capable of being synthesized locally within the central nervous system by glial cells and neurons, suggesting that they are not derived from plasma by transport across the blood-brain barrier.
Beam lead quartz chips for superconducting millimeter-wave circuits (2003)

The assembly of superconducting millimeter and submillimeter-wave circuits often requires RF ground connections. These are usually made by soldering, wire bonding, conductive adhesive or conductive wire gaskets. The difficulty of assembly increases with frequency as chip dimensions and tolerances shrink. The assembly issues, and also the throughput requirements of large radio astronomy projects such as ALMA (Atacama Large Millimeter Array), suggest the need of a beam lead technology for these circuits. Beam lead processes are already established for silicon and gallium arsenide wafers. However, niobium circuits on quartz substrates present unique difficulties. SIS junctions introduce additional thermal and chemical constraints to process development. For quartz, wet etches are isotropic and dry etches with high etch rates require large ion energies. Therefore, it is difficult to develop a conventional process in which gold pads on the substrate surface are formed into beam leads by a backside etch. Instead we have developed a topside process in which, after the mixer circuits are completed, dicing cuts are made at the finished chip dimensions but only partly through the wafer. The dicing cuts are then filled with a sacrificial material in a non-CMP process, and planarized. Gold plated pads are then defined, overhanging the planarized cuts. The sacrificial material is then removed from these cuts, leaving the gold beam leads. The wafer is then backside lapped into the cuts to the desired thickness, separating the individual chips. We discuss the new planarization scheme developed for this beam lead process and compare a variety of sacrificial materials.
Urinary incontinence-procedural and surgical treatments for women. (2008)

Women who fail to respond to pelvic floor physiotherapy for stress urinary incontinence have available to them a range of variably invasive surgical treatment options including bio-injectable agents, sling surgery, colposuspension, and prostheses. Women with urge urinary incontinence refractory to the newer anticholinergic agents can be treated with minimally invasive options such as bladder injections of botulinum toxin and sacral neuromodulation, as well as more invasive major urinary tract surgery.
Decoupling contention management from scheduling (2010)

Many parallel applications exhibit unpredictable communication between threads, leading to contention for shared objects. The choice of contention management strategy impacts strongly the performance and scalability of these applications: spinning provides maximum performance but wastes significant processor resources, while blocking-based approaches conserve processor resources but introduce high overheads on the critical path of computation. Under situations of high or changing load, the operating system complicates matters further with arbitrary scheduling decisions which often preempt lock holders, leading to long serialization delays until the preempted thread resumes execution. We observe that contention management is orthogonal to the problems of scheduling and load management and propose to decouple them so each may be solved independently and effectively. To this end, we propose a load control mechanism which manages the number of active threads in the system separately from any contention which may exist. By isolating contention management from damaging interactions with the OS scheduler, we combine the efficiency of spinning with the robustness of blocking. The proposed load control mechanism results in stable, high performance for both lightly and heavily loaded systems, requires no special privileges or modifications at the OS level, and can be implemented as a library which benefits existing code.
AS-level topology collection through looking glass servers (2013)

While accurate and complete modeling of the Internet topology at the Autonomous System (AS) level is critical for future protocol design, performance evaluation, simulation and analysis, still it remains a challenge to construct its accurate representation. In this paper, we collect BGP route announcements of ASes from Looking glass (LG) servers. By querying LG servers, we build an AS topology estimate of around 116 K AS links, from which we discover 11 K new AS links and 686 new ASes. We conclude that collecting BGP traces from LG servers can help enhance the current view of the AS topology from the BGP collector projects (e.g., RouteViews).